diff --git a/pkgdown.yml b/pkgdown.yml
index cb272913..cf62e539 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-30T02:59Z
+last_built: 2024-10-30T03:22Z
 urls:
   reference: https://jravilab.github.io/MolEvolvR/reference
   article: https://jravilab.github.io/MolEvolvR/articles
diff --git a/reference/plotSunburst.html b/reference/plotSunburst.html
index 712a0505..85d6df87 100644
--- a/reference/plotSunburst.html
+++ b/reference/plotSunburst.html
@@ -85,21 +85,21 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># sunburst plot</span></span></span>
 <span class="r-in"><span><span class="fu">plotSunburst</span><span class="op">(</span><span class="va">starwars_count</span><span class="op">)</span></span></span>
 <div id="htmlwidget-ac96cb3ee4656e2e9ec3" style="width:700px;height:432.632880098888px;" class="plotly html-widget"></div>
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Calamari.->.orange","Muun.->.gold","Nautolan.->.black","Neimodian.->.red","Pau'an.->.black","Quermian.->.yellow","Rodian.->.black","Skakoan.->.unknown","Sullustan.->.black","Tholothian.->.blue","Togruta.->.black","Toong.->.orange","Toydarian.->.yellow","Trandoshan.->.red","Twi'lek.->.hazel","Twi'lek.->.pink","Vulptereen.->.yellow","Wookiee.->.blue","Xexto.->.black","Yoda's species.->.brown","Zabrak.->.brown","Zabrak.->.yellow","NA.->.blue","NA.->.brown","NA.->.white","Aleena.->.unknown.->.Ratts Tyerel","Besalisk.->.yellow.->.Dexter Jettster","Cerean.->.yellow.->.Ki-Adi-Mundi","Chagrian.->.blue.->.Mas Amedda","Clawdite.->.yellow.->.Zam Wesell","Droid.->.black.->.BB8","Droid.->.red.->.IG-88","Droid.->.red.->.R2-D2","Droid.->.red.->.R5-D4","Droid.->.red, blue.->.R4-P17","Droid.->.yellow.->.C-3PO","Dug.->.orange.->.Sebulba","Ewok.->.brown.->.Wicket Systri Warrick","Geonosian.->.yellow.->.Poggle the Lesser","Gungan.->.orange.->.Jar Jar Binks","Gungan.->.orange.->.Roos 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1","column: species<br />value: Pau'an<br />n: 1","column: species<br />value: Quermian<br />n: 1","column: species<br />value: Rodian<br />n: 1","column: species<br />value: Skakoan<br />n: 1","column: species<br />value: Sullustan<br />n: 1","column: species<br />value: Tholothian<br />n: 1","column: species<br />value: Togruta<br />n: 1","column: species<br />value: Toong<br />n: 1","column: species<br />value: Toydarian<br />n: 1","column: species<br />value: Trandoshan<br />n: 1","column: species<br />value: Twi'lek<br />n: 2","column: species<br />value: Vulptereen<br />n: 1","column: species<br />value: Wookiee<br />n: 2","column: species<br />value: Xexto<br />n: 1","column: species<br />value: Yoda's species<br />n: 1","column: species<br />value: Zabrak<br />n: 2","column: species<br />value: NA<br />n: 4","column: eye_color<br />value: unknown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: red<br />n: 3","column: eye_color<br />value: red, blue<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: orange<br />n: 3","column: eye_color<br />value: blue<br />n: 12","column: eye_color<br />value: blue-gray<br />n: 1","column: eye_color<br />value: brown<br />n: 16","column: eye_color<br />value: dark<br />n: 1","column: eye_color<br />value: hazel<br />n: 2","column: eye_color<br />value: unknown<br />n: 1","column: eye_color<br />value: yellow<br />n: 2","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: green, yellow<br />n: 1","column: eye_color<br />value: black<br />n: 2","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: blue<br />n: 2","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: gold<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: red<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: unknown<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: red<br />n: 1","column: eye_color<br />value: hazel<br />n: 1","column: eye_color<br />value: pink<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 2","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: brown<br />n: 2","column: eye_color<br />value: white<br />n: 1","column: name<br />value: Ratts Tyerel<br />n: 1","column: name<br />value: Dexter Jettster<br />n: 1","column: name<br />value: Ki-Adi-Mundi<br />n: 1","column: name<br />value: Mas Amedda<br />n: 1","column: name<br />value: Zam Wesell<br />n: 1","column: name<br />value: BB8<br />n: 1","column: name<br />value: IG-88<br />n: 1","column: name<br />value: R2-D2<br />n: 1","column: name<br />value: R5-D4<br />n: 1","column: name<br />value: R4-P17<br />n: 1","column: name<br />value: C-3PO<br />n: 1","column: name<br />value: Sebulba<br />n: 1","column: name<br />value: Wicket Systri Warrick<br />n: 1","column: name<br />value: Poggle the Lesser<br />n: 1","column: name<br />value: Jar Jar Binks<br />n: 1","column: name<br />value: Roos Tarpals<br />n: 1","column: name<br />value: Rugor Nass<br />n: 1","column: name<br />value: Anakin Skywalker<br />n: 1","column: name<br />value: Beru Whitesun Lars<br />n: 1","column: name<br />value: Cliegg Lars<br />n: 1","column: name<br />value: Finis Valorum<br />n: 1","column: name<br />value: Jocasta Nu<br />n: 1","column: name<br />value: Lobot<br />n: 1","column: name<br />value: Luke Skywalker<br />n: 1","column: name<br />value: Mon Mothma<br />n: 1","column: name<br />value: Owen Lars<br />n: 1","column: name<br />value: Qui-Gon Jinn<br />n: 1","column: name<br />value: Ric Olié<br />n: 1","column: name<br />value: Wilhuff Tarkin<br />n: 1","column: name<br />value: Obi-Wan Kenobi<br />n: 1","column: name<br />value: Arvel Crynyd<br />n: 1","column: name<br />value: Bail Prestor Organa<br />n: 1","column: name<br />value: Biggs Darklighter<br />n: 1","column: name<br />value: Boba Fett<br />n: 1","column: name<br />value: Dooku<br />n: 1","column: name<br />value: Dormé<br />n: 1","column: name<br />value: Han Solo<br />n: 1","column: name<br />value: Jango Fett<br />n: 1","column: name<br />value: Lando Calrissian<br />n: 1","column: name<br />value: Leia Organa<br />n: 1","column: name<br />value: Mace Windu<br />n: 1","column: name<br />value: Padmé Amidala<br />n: 1","column: name<br />value: Poe Dameron<br />n: 1","column: name<br />value: Quarsh Panaka<br />n: 1","column: name<br />value: Raymus Antilles<br />n: 1","column: name<br />value: Shmi Skywalker<br />n: 1","column: name<br />value: Finn<br />n: 1","column: name<br />value: Rey<br />n: 1","column: name<br />value: Wedge Antilles<br />n: 1","column: name<br />value: Captain Phasma<br />n: 1","column: name<br />value: Darth Vader<br />n: 1","column: name<br />value: Palpatine<br />n: 1","column: name<br />value: Jabba Desilijic Tiure<br />n: 1","column: name<br />value: Saesee Tiin<br />n: 1","column: name<br />value: Grievous<br />n: 1","column: name<br />value: Lama Su<br />n: 1","column: name<br />value: Taun We<br />n: 1","column: name<br />value: Plo Koon<br />n: 1","column: name<br />value: Barriss Offee<br />n: 1","column: name<br />value: Luminara Unduli<br />n: 1","column: name<br />value: Ackbar<br />n: 1","column: name<br />value: San Hill<br />n: 1","column: name<br />value: Kit Fisto<br />n: 1","column: name<br />value: Nute Gunray<br />n: 1","column: name<br />value: Tion Medon<br />n: 1","column: name<br />value: Yarael Poof<br />n: 1","column: name<br />value: Greedo<br />n: 1","column: name<br />value: Wat Tambor<br />n: 1","column: name<br />value: Nien Nunb<br />n: 1","column: name<br />value: Adi Gallia<br />n: 1","column: name<br />value: Shaak Ti<br />n: 1","column: name<br />value: Ben Quadinaros<br />n: 1","column: name<br />value: Watto<br />n: 1","column: name<br />value: Bossk<br />n: 1","column: name<br />value: Ayla Secura<br />n: 1","column: name<br />value: Bib Fortuna<br />n: 1","column: name<br />value: Dud Bolt<br />n: 1","column: name<br />value: Chewbacca<br />n: 1","column: name<br />value: Tarfful<br />n: 1","column: name<br />value: Gasgano<br />n: 1","column: name<br />value: Yoda<br />n: 1","column: name<br />value: Eeth Koth<br />n: 1","column: name<br />value: Darth Maul<br />n: 1","column: name<br />value: Jek Tono Porkins<br />n: 1","column: name<br />value: Cordé<br />n: 1","column: name<br />value: Gregar Typho<br />n: 1","column: name<br />value: Sly Moore<br />n: 1"],"sort":false,"branchvalues":"total","type":"sunburst","marker":{"color":"rgba(31,119,180,1)","line":{"color":"rgba(255,255,255,1)"}},"frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script><span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># fill by group size</span></span></span>
 <span class="r-in"><span><span class="fu">plotSunburst</span><span class="op">(</span><span class="va">starwars_count</span>, fill_by_n <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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Organa","Mace Windu","Padmé Amidala","Poe Dameron","Quarsh Panaka","Raymus Antilles","Shmi Skywalker","Finn","Rey","Wedge Antilles","Captain Phasma","Darth Vader","Palpatine","Jabba Desilijic Tiure","Saesee Tiin","Grievous","Lama Su","Taun We","Plo Koon","Barriss Offee","Luminara Unduli","Ackbar","San Hill","Kit Fisto","Nute Gunray","Tion Medon","Yarael Poof","Greedo","Wat Tambor","Nien Nunb","Adi Gallia","Shaak Ti","Ben Quadinaros","Watto","Bossk","Ayla Secura","Bib Fortuna","Dud Bolt","Chewbacca","Tarfful","Gasgano","Yoda","Eeth Koth","Darth Maul","Jek Tono Porkins","Cordé","Gregar Typho","Sly Moore"],"values":[1,1,1,1,1,6,1,1,1,3,35,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,2,4,1,1,1,1,1,1,3,1,1,1,1,1,3,12,1,16,1,2,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"hovertext":["column: species<br />value: Aleena<br />n: 1","column: species<br />value: Besalisk<br />n: 1","column: species<br />value: Cerean<br />n: 1","column: species<br />value: Chagrian<br />n: 1","column: species<br />value: Clawdite<br />n: 1","column: species<br />value: Droid<br />n: 6","column: species<br />value: Dug<br />n: 1","column: species<br />value: Ewok<br />n: 1","column: species<br />value: Geonosian<br />n: 1","column: species<br />value: Gungan<br />n: 3","column: species<br />value: Human<br />n: 35","column: species<br />value: Hutt<br />n: 1","column: species<br />value: Iktotchi<br />n: 1","column: species<br />value: Kaleesh<br />n: 1","column: species<br />value: Kaminoan<br />n: 2","column: species<br />value: Kel Dor<br />n: 1","column: species<br />value: Mirialan<br />n: 2","column: species<br />value: Mon Calamari<br />n: 1","column: species<br />value: Muun<br />n: 1","column: species<br />value: Nautolan<br />n: 1","column: species<br />value: Neimodian<br />n: 1","column: species<br />value: Pau'an<br />n: 1","column: species<br />value: Quermian<br />n: 1","column: species<br />value: Rodian<br />n: 1","column: species<br />value: Skakoan<br />n: 1","column: species<br />value: Sullustan<br />n: 1","column: species<br />value: Tholothian<br />n: 1","column: species<br />value: Togruta<br />n: 1","column: species<br />value: Toong<br />n: 1","column: species<br />value: Toydarian<br />n: 1","column: species<br />value: Trandoshan<br />n: 1","column: species<br />value: Twi'lek<br />n: 2","column: species<br />value: Vulptereen<br />n: 1","column: species<br />value: Wookiee<br />n: 2","column: species<br />value: Xexto<br />n: 1","column: species<br />value: Yoda's species<br />n: 1","column: species<br />value: Zabrak<br />n: 2","column: species<br />value: NA<br />n: 4","column: eye_color<br />value: unknown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: red<br />n: 3","column: eye_color<br />value: red, blue<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: orange<br />n: 3","column: eye_color<br />value: blue<br />n: 12","column: eye_color<br />value: blue-gray<br />n: 1","column: eye_color<br />value: brown<br />n: 16","column: eye_color<br />value: dark<br />n: 1","column: eye_color<br />value: hazel<br />n: 2","column: eye_color<br />value: unknown<br />n: 1","column: eye_color<br />value: yellow<br />n: 2","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: green, yellow<br />n: 1","column: eye_color<br />value: black<br />n: 2","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: blue<br />n: 2","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: gold<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: red<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: unknown<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: orange<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: red<br />n: 1","column: eye_color<br />value: hazel<br />n: 1","column: eye_color<br />value: pink<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 2","column: eye_color<br />value: black<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: brown<br />n: 2","column: eye_color<br />value: white<br />n: 1","column: name<br />value: Ratts Tyerel<br />n: 1","column: name<br />value: Dexter Jettster<br />n: 1","column: name<br />value: Ki-Adi-Mundi<br />n: 1","column: name<br />value: Mas Amedda<br />n: 1","column: name<br />value: Zam Wesell<br />n: 1","column: name<br />value: BB8<br />n: 1","column: name<br />value: IG-88<br />n: 1","column: name<br />value: R2-D2<br />n: 1","column: name<br />value: R5-D4<br />n: 1","column: name<br />value: R4-P17<br />n: 1","column: name<br />value: C-3PO<br />n: 1","column: name<br />value: Sebulba<br />n: 1","column: name<br />value: Wicket Systri Warrick<br />n: 1","column: name<br />value: Poggle the Lesser<br />n: 1","column: name<br />value: Jar Jar Binks<br />n: 1","column: name<br />value: Roos Tarpals<br />n: 1","column: name<br />value: Rugor Nass<br />n: 1","column: name<br />value: Anakin Skywalker<br />n: 1","column: name<br />value: Beru Whitesun Lars<br />n: 1","column: name<br />value: Cliegg Lars<br />n: 1","column: name<br />value: Finis Valorum<br />n: 1","column: name<br />value: Jocasta Nu<br />n: 1","column: name<br />value: Lobot<br />n: 1","column: name<br />value: Luke Skywalker<br />n: 1","column: name<br />value: Mon Mothma<br />n: 1","column: name<br />value: Owen Lars<br />n: 1","column: name<br />value: Qui-Gon Jinn<br />n: 1","column: name<br />value: Ric Olié<br />n: 1","column: name<br />value: Wilhuff Tarkin<br />n: 1","column: name<br />value: Obi-Wan Kenobi<br />n: 1","column: name<br />value: Arvel Crynyd<br />n: 1","column: name<br />value: Bail Prestor Organa<br />n: 1","column: name<br />value: Biggs Darklighter<br />n: 1","column: name<br />value: Boba Fett<br />n: 1","column: name<br />value: Dooku<br />n: 1","column: name<br />value: Dormé<br />n: 1","column: name<br />value: Han Solo<br />n: 1","column: name<br />value: Jango Fett<br />n: 1","column: name<br />value: Lando Calrissian<br />n: 1","column: name<br />value: Leia Organa<br />n: 1","column: name<br />value: Mace Windu<br />n: 1","column: name<br />value: Padmé Amidala<br />n: 1","column: name<br />value: Poe Dameron<br />n: 1","column: name<br />value: Quarsh Panaka<br />n: 1","column: name<br />value: Raymus Antilles<br />n: 1","column: name<br />value: Shmi Skywalker<br />n: 1","column: name<br />value: Finn<br />n: 1","column: name<br />value: Rey<br />n: 1","column: name<br />value: Wedge Antilles<br />n: 1","column: name<br />value: Captain Phasma<br />n: 1","column: name<br />value: Darth Vader<br />n: 1","column: name<br />value: Palpatine<br />n: 1","column: name<br />value: Jabba Desilijic Tiure<br />n: 1","column: name<br />value: Saesee Tiin<br />n: 1","column: name<br />value: Grievous<br />n: 1","column: name<br />value: Lama Su<br />n: 1","column: name<br />value: Taun We<br />n: 1","column: name<br />value: Plo Koon<br />n: 1","column: name<br />value: Barriss Offee<br />n: 1","column: name<br />value: Luminara Unduli<br />n: 1","column: name<br />value: Ackbar<br />n: 1","column: name<br />value: San Hill<br />n: 1","column: name<br />value: Kit Fisto<br />n: 1","column: name<br />value: Nute Gunray<br />n: 1","column: name<br />value: Tion Medon<br />n: 1","column: name<br />value: Yarael Poof<br />n: 1","column: name<br />value: Greedo<br />n: 1","column: name<br />value: Wat Tambor<br />n: 1","column: name<br />value: Nien Nunb<br />n: 1","column: name<br />value: Adi Gallia<br />n: 1","column: name<br />value: Shaak Ti<br />n: 1","column: name<br />value: Ben Quadinaros<br />n: 1","column: name<br />value: Watto<br />n: 1","column: name<br />value: Bossk<br />n: 1","column: name<br />value: Ayla Secura<br />n: 1","column: name<br />value: Bib Fortuna<br />n: 1","column: name<br />value: Dud Bolt<br />n: 1","column: name<br />value: Chewbacca<br />n: 1","column: name<br />value: Tarfful<br />n: 1","column: name<br />value: Gasgano<br />n: 1","column: name<br />value: Yoda<br />n: 1","column: name<br />value: Eeth Koth<br />n: 1","column: name<br />value: Darth Maul<br />n: 1","column: name<br />value: Jek Tono Porkins<br />n: 1","column: name<br />value: Cordé<br />n: 1","column: name<br />value: Gregar Typho<br />n: 1","column: name<br />value: Sly Moore<br />n: 1"],"sort":false,"marker":{"color":"rgba(31,119,180,1)","colorbar":{"bgcolor":""},"line":{"color":"rgba(255,255,255,1)"}},"branchvalues":"total","type":"sunburst","frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script><span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># treemap plot, ordered by group size</span></span></span>
 <span class="r-in"><span><span class="fu">plotTreemap</span><span class="op">(</span><span class="va">starwars_count</span>, sort_by_n <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <div id="htmlwidget-36aa3d2a04d42bbc2145" style="width:700px;height:432.632880098888px;" class="plotly html-widget"></div>
-<script type="application/json" data-for="htmlwidget-36aa3d2a04d42bbc2145">{"x":{"visdat":{"17c379a8763b":["function () ","plotlyVisDat"]},"cur_data":"17c379a8763b","attrs":{"17c379a8763b":{"ids":["Aleena","Besalisk","Cerean","Chagrian","Clawdite","Droid","Dug","Ewok","Geonosian","Gungan","Human","Hutt","Iktotchi","Kaleesh","Kaminoan","Kel Dor","Mirialan","Mon Calamari","Muun","Nautolan","Neimodian","Pau'an","Quermian","Rodian","Skakoan","Sullustan","Tholothian","Togruta","Toong","Toydarian","Trandoshan","Twi'lek","Vulptereen","Wookiee","Xexto","Yoda's species","Zabrak","NA","Aleena.->.unknown","Besalisk.->.yellow","Cerean.->.yellow","Chagrian.->.blue","Clawdite.->.yellow","Droid.->.black","Droid.->.red","Droid.->.red, blue","Droid.->.yellow","Dug.->.orange","Ewok.->.brown","Geonosian.->.yellow","Gungan.->.orange","Human.->.blue","Human.->.blue-gray","Human.->.brown","Human.->.dark","Human.->.hazel","Human.->.unknown","Human.->.yellow","Hutt.->.orange","Iktotchi.->.orange","Kaleesh.->.green, yellow","Kaminoan.->.black","Kel Dor.->.black","Mirialan.->.blue","Mon Calamari.->.orange","Muun.->.gold","Nautolan.->.black","Neimodian.->.red","Pau'an.->.black","Quermian.->.yellow","Rodian.->.black","Skakoan.->.unknown","Sullustan.->.black","Tholothian.->.blue","Togruta.->.black","Toong.->.orange","Toydarian.->.yellow","Trandoshan.->.red","Twi'lek.->.hazel","Twi'lek.->.pink","Vulptereen.->.yellow","Wookiee.->.blue","Xexto.->.black","Yoda's species.->.brown","Zabrak.->.brown","Zabrak.->.yellow","NA.->.blue","NA.->.brown","NA.->.white","Aleena.->.unknown.->.Ratts Tyerel","Besalisk.->.yellow.->.Dexter Jettster","Cerean.->.yellow.->.Ki-Adi-Mundi","Chagrian.->.blue.->.Mas Amedda","Clawdite.->.yellow.->.Zam Wesell","Droid.->.black.->.BB8","Droid.->.red.->.IG-88","Droid.->.red.->.R2-D2","Droid.->.red.->.R5-D4","Droid.->.red, blue.->.R4-P17","Droid.->.yellow.->.C-3PO","Dug.->.orange.->.Sebulba","Ewok.->.brown.->.Wicket Systri Warrick","Geonosian.->.yellow.->.Poggle the Lesser","Gungan.->.orange.->.Jar Jar Binks","Gungan.->.orange.->.Roos Tarpals","Gungan.->.orange.->.Rugor Nass","Human.->.blue.->.Anakin Skywalker","Human.->.blue.->.Beru Whitesun Lars","Human.->.blue.->.Cliegg Lars","Human.->.blue.->.Finis Valorum","Human.->.blue.->.Jocasta Nu","Human.->.blue.->.Lobot","Human.->.blue.->.Luke Skywalker","Human.->.blue.->.Mon Mothma","Human.->.blue.->.Owen Lars","Human.->.blue.->.Qui-Gon Jinn","Human.->.blue.->.Ric Olié","Human.->.blue.->.Wilhuff Tarkin","Human.->.blue-gray.->.Obi-Wan Kenobi","Human.->.brown.->.Arvel Crynyd","Human.->.brown.->.Bail Prestor Organa","Human.->.brown.->.Biggs Darklighter","Human.->.brown.->.Boba Fett","Human.->.brown.->.Dooku","Human.->.brown.->.Dormé","Human.->.brown.->.Han Solo","Human.->.brown.->.Jango Fett","Human.->.brown.->.Lando Calrissian","Human.->.brown.->.Leia Organa","Human.->.brown.->.Mace Windu","Human.->.brown.->.Padmé Amidala","Human.->.brown.->.Poe Dameron","Human.->.brown.->.Quarsh Panaka","Human.->.brown.->.Raymus Antilles","Human.->.brown.->.Shmi Skywalker","Human.->.dark.->.Finn","Human.->.hazel.->.Rey","Human.->.hazel.->.Wedge Antilles","Human.->.unknown.->.Captain Phasma","Human.->.yellow.->.Darth Vader","Human.->.yellow.->.Palpatine","Hutt.->.orange.->.Jabba Desilijic Tiure","Iktotchi.->.orange.->.Saesee Tiin","Kaleesh.->.green, yellow.->.Grievous","Kaminoan.->.black.->.Lama Su","Kaminoan.->.black.->.Taun We","Kel Dor.->.black.->.Plo Koon","Mirialan.->.blue.->.Barriss Offee","Mirialan.->.blue.->.Luminara Unduli","Mon Calamari.->.orange.->.Ackbar","Muun.->.gold.->.San Hill","Nautolan.->.black.->.Kit Fisto","Neimodian.->.red.->.Nute Gunray","Pau'an.->.black.->.Tion Medon","Quermian.->.yellow.->.Yarael Poof","Rodian.->.black.->.Greedo","Skakoan.->.unknown.->.Wat Tambor","Sullustan.->.black.->.Nien Nunb","Tholothian.->.blue.->.Adi Gallia","Togruta.->.black.->.Shaak Ti","Toong.->.orange.->.Ben Quadinaros","Toydarian.->.yellow.->.Watto","Trandoshan.->.red.->.Bossk","Twi'lek.->.hazel.->.Ayla Secura","Twi'lek.->.pink.->.Bib Fortuna","Vulptereen.->.yellow.->.Dud Bolt","Wookiee.->.blue.->.Chewbacca","Wookiee.->.blue.->.Tarfful","Xexto.->.black.->.Gasgano","Yoda's species.->.brown.->.Yoda","Zabrak.->.brown.->.Eeth Koth","Zabrak.->.yellow.->.Darth Maul","NA.->.blue.->.Jek Tono Porkins","NA.->.brown.->.Cordé","NA.->.brown.->.Gregar Typho","NA.->.white.->.Sly 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black<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: brown<br />n: 1","column: eye_color<br />value: yellow<br />n: 1","column: eye_color<br />value: blue<br />n: 1","column: eye_color<br />value: brown<br />n: 2","column: eye_color<br />value: white<br />n: 1","column: name<br />value: Ratts Tyerel<br />n: 1","column: name<br />value: Dexter Jettster<br />n: 1","column: name<br />value: Ki-Adi-Mundi<br />n: 1","column: name<br />value: Mas Amedda<br />n: 1","column: name<br />value: Zam Wesell<br />n: 1","column: name<br />value: BB8<br />n: 1","column: name<br />value: IG-88<br />n: 1","column: name<br />value: R2-D2<br />n: 1","column: name<br />value: R5-D4<br />n: 1","column: name<br />value: R4-P17<br />n: 1","column: name<br />value: C-3PO<br />n: 1","column: name<br />value: Sebulba<br />n: 1","column: name<br />value: Wicket Systri Warrick<br />n: 1","column: name<br />value: Poggle the Lesser<br />n: 1","column: name<br />value: Jar Jar Binks<br />n: 1","column: name<br />value: Roos Tarpals<br />n: 1","column: name<br />value: Rugor Nass<br />n: 1","column: name<br />value: Anakin Skywalker<br />n: 1","column: name<br />value: Beru Whitesun Lars<br />n: 1","column: name<br />value: Cliegg Lars<br />n: 1","column: name<br />value: Finis Valorum<br />n: 1","column: name<br />value: Jocasta Nu<br />n: 1","column: name<br />value: Lobot<br />n: 1","column: name<br />value: Luke Skywalker<br />n: 1","column: name<br />value: Mon Mothma<br />n: 1","column: name<br />value: Owen Lars<br />n: 1","column: name<br />value: Qui-Gon Jinn<br />n: 1","column: name<br />value: Ric Olié<br />n: 1","column: name<br />value: Wilhuff Tarkin<br />n: 1","column: name<br />value: Obi-Wan Kenobi<br />n: 1","column: name<br />value: Arvel Crynyd<br />n: 1","column: name<br />value: Bail Prestor Organa<br />n: 1","column: name<br />value: Biggs Darklighter<br />n: 1","column: name<br />value: Boba Fett<br />n: 1","column: name<br />value: Dooku<br />n: 1","column: name<br />value: Dormé<br />n: 1","column: name<br />value: Han Solo<br />n: 1","column: name<br />value: Jango Fett<br />n: 1","column: name<br />value: Lando Calrissian<br />n: 1","column: name<br />value: Leia Organa<br />n: 1","column: name<br />value: Mace Windu<br />n: 1","column: name<br />value: Padmé Amidala<br />n: 1","column: name<br />value: Poe Dameron<br />n: 1","column: name<br />value: Quarsh Panaka<br />n: 1","column: name<br />value: Raymus Antilles<br />n: 1","column: name<br />value: Shmi Skywalker<br />n: 1","column: name<br />value: Finn<br />n: 1","column: name<br />value: Rey<br />n: 1","column: name<br />value: Wedge Antilles<br />n: 1","column: name<br />value: Captain Phasma<br />n: 1","column: name<br />value: Darth Vader<br />n: 1","column: name<br />value: Palpatine<br />n: 1","column: name<br />value: Jabba Desilijic Tiure<br />n: 1","column: name<br />value: Saesee Tiin<br />n: 1","column: name<br />value: Grievous<br />n: 1","column: name<br />value: Lama Su<br />n: 1","column: name<br />value: Taun We<br />n: 1","column: name<br />value: Plo Koon<br />n: 1","column: name<br />value: Barriss Offee<br />n: 1","column: name<br />value: Luminara Unduli<br />n: 1","column: name<br />value: Ackbar<br />n: 1","column: name<br />value: San Hill<br />n: 1","column: name<br />value: Kit Fisto<br />n: 1","column: name<br />value: Nute Gunray<br />n: 1","column: name<br />value: Tion Medon<br />n: 1","column: name<br />value: Yarael Poof<br />n: 1","column: name<br />value: Greedo<br />n: 1","column: name<br />value: Wat Tambor<br />n: 1","column: name<br />value: Nien Nunb<br />n: 1","column: name<br />value: Adi Gallia<br />n: 1","column: name<br />value: Shaak Ti<br />n: 1","column: name<br />value: Ben Quadinaros<br />n: 1","column: name<br />value: Watto<br />n: 1","column: name<br />value: Bossk<br />n: 1","column: name<br />value: Ayla Secura<br />n: 1","column: name<br />value: Bib Fortuna<br />n: 1","column: name<br />value: Dud Bolt<br />n: 1","column: name<br />value: Chewbacca<br />n: 1","column: name<br />value: Tarfful<br />n: 1","column: name<br />value: Gasgano<br />n: 1","column: name<br />value: Yoda<br />n: 1","column: name<br />value: Eeth Koth<br />n: 1","column: name<br />value: Darth Maul<br />n: 1","column: name<br />value: Jek Tono Porkins<br />n: 1","column: name<br />value: Cordé<br />n: 1","column: name<br />value: Gregar Typho<br />n: 1","column: name<br />value: Sly Moore<br />n: 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class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># display al charchaters by homeworld</span></span></span>
 <span class="r-in"><span><span class="va">starwars</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/count.html" class="external-link">count</a></span><span class="op">(</span><span class="va">homeworld</span>, <span class="va">name</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu">plotTreemap</span><span class="op">(</span>sort_by_n <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <div id="htmlwidget-febe03efa1a2d8d52a86" style="width:700px;height:432.632880098888px;" class="plotly html-widget"></div>
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 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/search.json b/search.json
index 7c5bbb74..af62daf1 100644
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-[{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement janani.ravi@cuanschutz.edu. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to MolEvolvR","title":"Contributing to MolEvolvR","text":"outlines propose change MolEvolvR. detailed discussion contributing tidyverse packages, please see development contributing guide code review principles.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to MolEvolvR","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to MolEvolvR","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed). See guide create great issue advice.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to MolEvolvR","text":"Fork package clone onto computer. haven’t done , recommend using usethis. Install load usethis package : Clone fork MolEvolvR package using: Install BiocManager Bioconductor: Install development dependencies ensure package passes R CMD check using devtools: R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using: Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number.","code":"install.packages(\"usethis\")  library(\"usethis\") usethis::create_from_github(\"JRaviLab/MolEvolvR\", fork = TRUE) if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\") BiocManager::install(version = \"3.19\") install.packages(\"devtools\")  library(\"devtools\")  devtools::install_dev_deps()  devtools::check() usethis::pr_init(\"brief-description-of-change\")"},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to MolEvolvR","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. Lint Code: Ensure code adheres style guidelines using lintr: use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":"install.packages(\"lintr\")  library(\"lintr\")  lintr::lint(\"path/to/your/file.R\")"},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to MolEvolvR","text":"Please note MolEvolvR project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"BSD 3-clause License","title":"BSD 3-clause License","text":"Copyright (c) 2024 MolEvolvR authors rights reserved. Redistribution use source binary forms, without modification, permitted provided following conditions met: Redistributions source code must retain copyright notice, list conditions following disclaimer. Redistributions binary form must reproduce copyright notice, list conditions following disclaimer documentation /materials provided distribution. Neither name copyright holder names contributors may used endorse promote products derived software without specific prior written permission. SOFTWARE PROVIDED COPYRIGHT HOLDERS CONTRIBUTORS “” EXPRESS IMPLIED WARRANTIES, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE DISCLAIMED. EVENT SHALL COPYRIGHT HOLDER CONTRIBUTORS LIABLE DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, CONSEQUENTIAL DAMAGES (INCLUDING, LIMITED , PROCUREMENT SUBSTITUTE GOODS SERVICES; LOSS USE, DATA, PROFITS; BUSINESS INTERRUPTION) HOWEVER CAUSED THEORY LIABILITY, WHETHER CONTRACT, STRICT LIABILITY, TORT (INCLUDING NEGLIGENCE OTHERWISE) ARISING WAY USE SOFTWARE, EVEN ADVISED POSSIBILITY DAMAGE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Janani Ravi. Author, maintainer. David Mayer. Author. Evan Brenner. Author. Faisal Alquaddoomi. Author. Samuel Chen. Contributor. Lo Sosinski. Contributor. Joseph Burke. Contributor. Jacob Krol. Contributor.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ravi J, Mayer D, Brenner E, Alquaddoomi F (2024). MolEvolvR: Molecular Evolution Phylogeny. R package version 0.99.9, https://jravilab.github.io/MolEvolvR/, https://github.com/jravilab/molevolvr.","code":"@Manual{,   title = {MolEvolvR: Molecular Evolution and Phylogeny},   author = {Janani Ravi and David Mayer and Evan Brenner and Faisal Alquaddoomi},   year = {2024},   note = {R package version 0.99.9, https://jravilab.github.io/MolEvolvR/},   url = {https://github.com/jravilab/molevolvr}, }"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"molevolvr-","dir":"","previous_headings":"","what":"Molecular Evolution and Phylogeny","title":"Molecular Evolution and Phylogeny","text":"MolEvolvR R-package provides framework characterizing proteins using molecular evolution phylogeny. Check pkgdown page : jravilab.github.io/MolEvolvR","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Molecular Evolution and Phylogeny","text":"can install development version MolEvolvR GitHub :","code":"# Install Bioconductor if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\") BiocManager::install(version = \"3.19\")  # Install Development Version of MolEvolvR BiocManager::install(\"JRaviLab/MolEvolvR\")"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"loading-the-package","dir":"","previous_headings":"Installation","what":"Loading the package","title":"Molecular Evolution and Phylogeny","text":"","code":"library(MolEvolvR)"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Molecular Evolution and Phylogeny","text":"basic example shows analyze favorite protein:","code":"library(MolEvolvR) ## basic example code ## ⏳ Stay tuned!"},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"related-molevolvr-codebases","dir":"","previous_headings":"Companion repos & projects","what":"Related MolEvolvR codebases","title":"Molecular Evolution and Phylogeny","text":"MolEvolvR web-app 1.0 | 🔒Repo | Live web-app | Preprint | Case studies MolEvolvR web-app 2.0 | 🔒Repo","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"specific-use-cases","dir":"","previous_headings":"Companion repos & projects","what":"Specific use cases","title":"Molecular Evolution and Phylogeny","text":"PSP evolution across tree life | 🔒Repo | Live web-app | PubMed Bacterial phage defense system, avcDI | Repo | PubMed DciA evolution across bacteria | Repo | PubMed Internalins Listeria | Repo | PubMed","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"current-contributors","dir":"","previous_headings":"","what":"Current contributors","title":"Molecular Evolution and Phylogeny","text":"David Mayer | R-package, back-end Faisal Alquaddoomi | Front-end 1.0, back-end Evan Brenner | MolEvolvR functionality Vince Rubinetti | Front-end 2.0 Dave Bunten | Data management, engineering Janani Ravi | PI","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"contribution-guidelines","dir":"","previous_headings":"Current contributors","what":"Contribution guidelines","title":"Molecular Evolution and Phylogeny","text":"welcome contributions community! ensure smooth collaborative process, please follow guidelines. Outreachy interns, please check pointers get started. 📜 License","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"code-of-conduct","dir":"","previous_headings":"Current contributors","what":"Code of Conduct","title":"Molecular Evolution and Phylogeny","text":"Please note MolEvolvR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/outreachy_guidelines.html","id":null,"dir":"","previous_headings":"","what":"Getting started","title":"Getting started","text":"Welcome aboard, Outreachy intern! 🙌 JRaviLab Onboarding Visit MolEvolvR package repository; please start README doc repository. Read companion MolEvolvR web-app preprint . Follow instructions repo README install MolEvolvR, starting bioconductor installation instructions. Make sure can build package R CMD build run tests devtools. Check open issues, select task labeled Outreachy, ask assigned . Create branch specific task submit PR (“pull request”), respond feedback reviewers.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/outreachy_guidelines.html","id":"resources","dir":"","previous_headings":"","what":"Resources","title":"Getting started","text":"💻Code Learn R Git/GitHub basics 🗣️Scientific Communication 👥Lab Culture & working JRaviLab | Expectations Contact 📧 Janani Ravi | Email","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"Function map GCA_ID TaxID, TaxID Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"","code":"GCA2Lineage(   prot_data,   assembly_path = \"/data/research/jravilab/common_data/assembly_summary_genbank.txt\",   lineagelookup_path = \"/data/research/jravilab/common_data/lineage_lookup.tsv\",   acc_col = \"AccNum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"prot_data Dataframe containing column GCA_ID assembly_path String path assembly_summary path file can generated using \"downloadAssemblySummary()\" function lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using \"createLineageLookup()\" function acc_col Character. name column prot_data containing accession numbers. Default \"AccNum\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"dataframe containing merged information GCA_IDs, TaxIDs, corresponding lineage phylum level. dataframe include information input prot_data lineage data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"Currently configured kingdom phylum","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"","code":"if (FALSE) { # \\dontrun{ result <- GCA2Lineage(prot_data = my_prot_data,                        assembly_path = \"path/to/assembly_summary.txt\",                        lineagelookup_path = \"path/to/lineage_lookup.tsv\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"IPG2Lineage — IPG2Lineage","title":"IPG2Lineage — IPG2Lineage","text":"Takes resulting file efetch run ipg database Takes resulting file efetch run ipg database append lineage, taxid columns","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"IPG2Lineage — IPG2Lineage","text":"","code":"IPG2Lineage(   accessions,   ipg_file,   refseq_assembly_path,   genbank_assembly_path,   lineagelookup_path )  IPG2Lineage(   accessions,   ipg_file,   refseq_assembly_path,   genbank_assembly_path,   lineagelookup_path )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"IPG2Lineage — IPG2Lineage","text":"accessions Character vector protein accessions ipg_file Path file containing results efetch run ipg database. protein accession 'accessions' contained file refseq_assembly_path String. Path RefSeq assembly summary file. genbank_assembly_path String. Path GenBank assembly summary file. lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using \"createLineageLookup()\" function assembly_path String path assembly_summary path file can generated using downloadAssemblySummary function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"IPG2Lineage — IPG2Lineage","text":"data.table lineage information provided protein accessions. data table containing protein accessions along corresponding TaxIDs lineage information.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"IPG2Lineage — IPG2Lineage","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"IPG2Lineage — IPG2Lineage","text":"","code":"if (FALSE) { # \\dontrun{ IPG2Lineage() } # }  if (FALSE) { # \\dontrun{ lins <- IPG2Lineage(   accessions = c(\"P12345\", \"Q67890\"),   ipg_file = \"path/to/ipg_results.txt\",   refseq_assembly_path = \"path/to/refseq_assembly_summary.txt\",   genbank_assembly_path = \"path/to/genbank_assembly_summary.txt\",   lineagelookup_path = \"path/to/lineage_lookup.tsv\" ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"MolEvolvR Summary — MolEvolvR_summary","title":"MolEvolvR Summary — MolEvolvR_summary","text":"collection summary functions MolEvolvR package. Function summarize retrieve counts Domains & Domains+Lineage Function retrieve counts many lineages DomArch appears Creates data frame totalcount column function designed sum counts column either Genomic Context Domain Architecture creates totalcount column sums.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MolEvolvR Summary — MolEvolvR_summary","text":"","code":"summarizeByLineage(prot = \"prot\", column = \"DomArch\", by = \"Lineage\", query)  summarizeDomArch_ByLineage(x)  summarizeDomArch(x)  summarizeGenContext_ByDomArchLineage(x)  summarizeGenContext_ByLineage(x)  summarizeGenContext(x)  totalGenContextOrDomArchCounts(   prot,   column = \"DomArch\",   lineage_col = \"Lineage\",   cutoff = 90,   RowsCutoff = FALSE,   digits = 2 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MolEvolvR Summary — MolEvolvR_summary","text":"prot data frame must contain columns: count column Character. column summarize, default \"DomArch\". string representing grouping column (e.g., Lineage). Default \"Lineage\". query string specifying query pattern filtering target column. Use \"\" skip filtering include rows. x dataframe tibble containing data. must columns named GenContext, DomArch, Lineage. lineage_col Character. name lineage column, default \"Lineage\". cutoff Numeric. Cutoff total count. Counts cutoff value shown. Default 0. RowsCutoff Logical. TRUE, filters based cumulative percentage cutoff. Default FALSE. digits Numeric. Number decimal places percentage columns. Default 2.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MolEvolvR Summary — MolEvolvR_summary","text":"tibble summarizing counts occurrences elements column, grouped column. result includes number occurrences (count) arranged descending order count. tibble summarizing counts unique domain architectures (DomArch) per lineage (Lineage). resulting table contains three columns: DomArch, Lineage, count, indicates frequency domain architecture lineage. results arranged descending order count. tibble summarizing unique DomArch, along following columns: totalcount: total occurrences DomArch across lineages. totallin: total number unique lineages DomArch appears. results arranged descending order totallin totalcount. tibble summarizing unique combination GenContext, DomArch, Lineage, along following columns: GenContext: genomic context entry. DomArch: domain architecture entry. Lineage: lineage associated entry. count: total number occurrences combination GenContext, DomArch, Lineage. results arranged descending order count. Describe return, detail tibble summarizing unique combination GenContext Lineage, along following columns: GenContext: genomic context entry. Lineage: lineage associated entry. count: total number occurrences combination GenContext Lineage. results arranged descending order count. data frame following columns: {{ column }}: Unique values specified column. totalcount: total count occurrences unique value specified column. IndividualCountPercent: percentage totalcount relative overall count. CumulativePercent: cumulative percentage total counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"MolEvolvR Summary — MolEvolvR_summary","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MolEvolvR Summary — MolEvolvR_summary","text":"","code":"if (FALSE) { # \\dontrun{ library(tidyverse) tibble(DomArch = c(\"a+b\", \"a+b\", \"b+c\", \"a+b\"), Lineage = c(\"l1\", \"l1\", \"l1\", \"l2\")) |>     summarizeByLineage(query = \"all\") } # }  if (FALSE) { # \\dontrun{ summarizeDomArch_ByLineage() } # } if (FALSE) { # \\dontrun{ summarizeDomArch() } # } if (FALSE) { # \\dontrun{ summarizeGenContext_ByDomArchLineage } # } if (FALSE) { # \\dontrun{ summarizeGenContext_ByLineage() } # } if (FALSE) { # \\dontrun{ summarizeGenContext() } # } if (FALSE) { # \\dontrun{ totalGenContextOrDomArchCounts(pspa - gc_lin_counts, 0, \"GC\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"acc2FA — acc2FA","title":"acc2FA — acc2FA","text":"converts protein accession numbers fasta format. Resulting fasta file written outpath. converts protein accession numbers fasta format. Resulting fasta file written outpath. acc2FA converts protein accession numbers fasta format. Resulting fasta file written outpath.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"acc2FA — acc2FA","text":"","code":"acc2FA(accessions, outpath, plan = \"sequential\")  acc2FA(accessions, outpath, plan = \"sequential\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"acc2FA — acc2FA","text":"accessions Character vector containing protein accession numbers generate fasta sequences . Function may work vectors length > 10,000 outpath str. Location fasta file written . plan Character. plan use processing. Default \"sequential\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"acc2FA — acc2FA","text":"logical value indicating whether retrieval conversion successful. Returns TRUE successful FALSE otherwise. Fasta file written specified outpath.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"acc2FA — acc2FA","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"acc2FA — acc2FA","text":"","code":"if (FALSE) { # \\dontrun{ acc2FA(accessions = c(\"ACU53894.1\", \"APJ14606.1\", \"ABK37082.1\"), outpath = \"my_proteins.fasta\") Entrez:accessions <- rep(\"ANY95992.1\", 201) |> acc2FA(outpath = \"entrez.fa\") EBI:accessions <- c(\"P12345\", \"Q9UHC1\", \"O15530\", \"Q14624\", \"P0DTD1\") |> acc2FA(outpath = \"ebi.fa\") } # } if (FALSE) { # \\dontrun{ acc2FA(accessions = c(\"ACU53894.1\", \"APJ14606.1\", \"ABK37082.1\"), outpath = \"my_proteins.fasta\") Entrez:accessions <- rep(\"ANY95992.1\", 201) |> acc2FA(outpath = \"entrez.fa\") EBI:accessions <- c(\"P12345\", \"Q9UHC1\", \"O15530\", \"Q14624\", \"P0DTD1\") |> acc2FA(outpath = \"ebi.fa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"acc2Lineage — acc2Lineage","title":"acc2Lineage — acc2Lineage","text":"function combines 'efetchIPG()' 'IPG2Lineage()' map set protein accessions assembly (GCA_ID), tax ID, lineage. Function map protein accession numbers lineage function combines 'efetchIPG()' 'IPG2Lineage()' map set protein accessions assembly (GCA_ID), tax ID, lineage.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"acc2Lineage — acc2Lineage","text":"","code":"acc2Lineage(   accessions,   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )  acc2Lineage(   accessions,   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"acc2Lineage — acc2Lineage","text":"accessions Character vector protein accessions assembly_path String path assembly_summary path file can generated using \"downloadAssemblySummary()\" function lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using ipgout_path Path write results efetch run accessions ipg database. NULL, file written. Defaults NULL plan Character. Specifies execution plan parallel processing. Default \"multicore\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"acc2Lineage — acc2Lineage","text":"data.table contains lineage information, mapping protein accessions tax IDs lineages. dataframe containing lineage information mapped given protein accessions. dataframe includes relevant columns TaxID, GCA_ID, Protein, Protein Name, Species, Lineage.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"acc2Lineage — acc2Lineage","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"acc2Lineage — acc2Lineage","text":"","code":"if (FALSE) { # \\dontrun{ acc2Lineage() } # } if (FALSE) { # \\dontrun{ lineage_data <- acc2Lineage(   accessions = c(\"P12345\", \"Q67890\"),   assembly_path = \"path/to/assembly_summary.txt\",   lineagelookup_path = \"path/to/lineage_lookup.tsv\",   ipgout_path = \"path/to/output.txt\" ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":null,"dir":"Reference","previous_headings":"","what":"addLeaves2Alignment — addLeaves2Alignment","title":"addLeaves2Alignment — addLeaves2Alignment","text":"Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures. Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addLeaves2Alignment — addLeaves2Alignment","text":"","code":"addLeaves2Alignment(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   reduced = FALSE )  addLeaves2Alignment(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   reduced = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addLeaves2Alignment — addLeaves2Alignment","text":"aln_file Character. Path file. Input tab-delimited file + alignment file accnum & alignment. Default 'pspa_snf7.aln' lin_file Character. Path file. Protein file accession + number lineage mapping. Default 'pspa.txt' reduced Boolean. TRUE, reduced data frame generated one sequence per lineage. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addLeaves2Alignment — addLeaves2Alignment","text":"data frame containing enriched alignment data lineage information. data frame containing combined alignment lineage information.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"addLeaves2Alignment — addLeaves2Alignment","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"addLeaves2Alignment — addLeaves2Alignment","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"addLeaves2Alignment — addLeaves2Alignment","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addLeaves2Alignment — addLeaves2Alignment","text":"","code":"if (FALSE) { # \\dontrun{ addLeaves2Alignment(\"pspa_snf7.aln\", \"pspa.txt\") } # } if (FALSE) { # \\dontrun{ addLeaves2Alignment(\"pspa_snf7.aln\", \"pspa.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"addLineage — addLineage","title":"addLineage — addLineage","text":"addLineage addLineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addLineage — addLineage","text":"","code":"addLineage(   df,   acc_col = \"AccNum\",   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )  addLineage(   df,   acc_col = \"AccNum\",   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addLineage — addLineage","text":"df Dataframe containing accession numbers. dataframe column specified acc_col contains accession numbers. acc_col Character. name column df containing accession numbers. Default \"AccNum\". assembly_path String. path assembly summary file generated using downloadAssemblySummary() function. lineagelookup_path String. path lineage lookup file (taxid lineage mapping) generated using create_lineage_lookup() function. ipgout_path String. Optional path save intermediate output files. Default NULL. plan Character. Specifies execution plan parallel processing. Default \"multicore\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addLineage — addLineage","text":"data.frame combines original df lineage information. dataframe combines original dataframe df lineage information retrieved based provided accession numbers.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addLineage — addLineage","text":"","code":"if (FALSE) { # \\dontrun{ addLineage() } # } if (FALSE) { # \\dontrun{ enriched_df <- addLineage(df = my_data,                            acc_col = \"AccNum\",                            assembly_path = \"path/to/assembly_summary.txt\",                            lineagelookup_path = \"path/to/lineage_lookup.tsv\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":null,"dir":"Reference","previous_headings":"","what":"addName — addName","title":"addName — addName","text":"function adds new 'Name' column comprised components Kingdom, Phylum, Genus, species, well accession function adds new 'Name' column comprised components Kingdom, Phylum, Genus, species, well accession","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addName — addName","text":"","code":"addName(   data,   accnum_col = \"AccNum\",   spec_col = \"Species\",   lin_col = \"Lineage\",   lin_sep = \">\",   out_col = \"Name\" )  addName(   data,   accnum_col = \"AccNum\",   spec_col = \"Species\",   lin_col = \"Lineage\",   lin_sep = \">\",   out_col = \"Name\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addName — addName","text":"data Data add name column accnum_col Column containing accession numbers spec_col Column containing species lin_col Column containing lineage lin_sep Character separating lineage levels out_col Column contains new 'Name' derived Species, Lineage, AccNum info","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addName — addName","text":"Original data 'Name' column Original data 'Name' column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"addName — addName","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addName — addName","text":"","code":"# Example usage of the addName function data <- data.frame(   AccNum = c(\"ACC123\", \"ACC456\"),   Species = c(\"Homo sapiens\", \"Mus musculus\"),   Lineage = c(\"Eukaryota>Chordata\", \"Eukaryota>Chordata\") ) enriched_data <- addName(data) enriched_data #>   AccNum      Species            Lineage                     Name #> 1 ACC123 Homo sapiens Eukaryota>Chordata  EChorda_Hsapiens_ACC123 #> 2 ACC456 Mus musculus Eukaryota>Chordata EChorda_Mmusculus_ACC456 if (FALSE) { # \\dontrun{ addName(data_frame) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":null,"dir":"Reference","previous_headings":"","what":"addTaxID — addTaxID","title":"addTaxID — addTaxID","text":"addTaxID","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addTaxID — addTaxID","text":"","code":"addTaxID(data, acc_col = \"AccNum\", version = T)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addTaxID — addTaxID","text":"data data frame data table containing protein accession numbers. acc_col string specifying column name data contains accession numbers. Defaults \"AccNum\". version logical indicating whether remove last two characters accession numbers TaxID retrieval. Defaults TRUE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addTaxID — addTaxID","text":"data table includes original data along new column containing corresponding TaxIDs.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addTaxID — addTaxID","text":"","code":"if (FALSE) { # \\dontrun{ # Create a sample data table with accession numbers sample_data <- data.table(AccNum = c(\"ABC123.1\", \"XYZ456.1\", \"LMN789.2\")) enriched_data <- addTaxID(sample_data, acc_col = \"AccNum\", version = TRUE) enriched_data } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":null,"dir":"Reference","previous_headings":"","what":"alignFasta — alignFasta","title":"alignFasta — alignFasta","text":"Perform Multiple Sequence Alignment FASTA file. Perform Multiple Sequence Alignment FASTA file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"alignFasta — alignFasta","text":"","code":"alignFasta(fasta_file, tool = \"Muscle\", outpath = NULL)  alignFasta(fasta_file, tool = \"Muscle\", outpath = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"alignFasta — alignFasta","text":"fasta_file Path FASTA file aligned tool Type alignment tool use. One three options: \"Muscle\", \"ClustalO\", \"ClustalW\" outpath Path write resulting alignment FASTA file. NULL, file written","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"alignFasta — alignFasta","text":"aligned fasta sequence MsaAAMultipleAlignment object aligned fasta sequence MsaAAMultipleAlignment object","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"alignFasta — alignFasta","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"alignFasta — alignFasta","text":"","code":"if (FALSE) { # \\dontrun{ aligned_sequences <- alignFasta(\"my_sequences.fasta\", tool = \"Muscle\", outpath = \"aligned_output.fasta\") } # } if (FALSE) { # \\dontrun{ # Example usage aligned_sequences <- alignFasta(\"path/to/sequences.fasta\", tool = \"ClustalO\", outpath = \"path/to/aligned_sequences.fasta\") aligned_sequences } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":null,"dir":"Reference","previous_headings":"","what":"assignJobQueue — assignJobQueue","title":"assignJobQueue — assignJobQueue","text":"Decision function assign job queue","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"assignJobQueue — assignJobQueue","text":"","code":"assignJobQueue(t_sec_estimate, t_cutoff = 21600)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"assignJobQueue — assignJobQueue","text":"t_sec_estimate estimated number seconds job process (calculateEstimatedWallTimeFromOpts    ()) t_long threshold value defines lower bound assigning job \"long queue\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"assignJobQueue — assignJobQueue","text":"string \"short\" \"long\" example: calculateEstimatedWallTimeFromOpts\t(c(\"homology_search\", \"domain_architecture\"), 3) |> assignJobQueue()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"Given MolEvolvR advanced options number inputs, calculate total estimated walltime job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"","code":"calculateEstimatedWallTimeFromOpts(   advanced_opts,   n_inputs = 1L,   n_hits = NULL,   verbose = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"advanced_opts character vector MolEvolvR advanced options (see mapOption2Process options) n_inputs total number input proteins","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"total estimated number seconds job process (walltime) example: calculateEstimatedWallTimeFromOpts\t(c(\"homology_search\", \"domain_architecture\"), n_inputs = 3, n_hits = 50L)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateProcessRuntime — calculateProcessRuntime","title":"calculateProcessRuntime — calculateProcessRuntime","text":"Scrape MolEvolvR logs calculate median processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateProcessRuntime — calculateProcessRuntime","text":"","code":"calculateProcessRuntime(dir_job_results)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateProcessRuntime — calculateProcessRuntime","text":"dir_job_results chr path MolEvolvR job_results directory","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateProcessRuntime — calculateProcessRuntime","text":"list names: processes; values: median runtime (seconds) see molevol_scripts/R/metrics.R info functions called examples:  dir_job_results <- \"/data/scratch/janani/molevolvr_out\" list_proc_medians <- calculateProcessRuntime(dir_job_results) outside container environment common_root <- \"/data/molevolvr_transfer/molevolvr_dev\" dir_job_results <- \"/data/molevolvr_transfer/molevolvr_dev/job_results\" list_proc_medians <- calculateProcessRuntime(dir_job_results)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean Cluster File — cleanClusterFile","title":"Clean Cluster File — cleanClusterFile","text":"Reads cleans cluster file function reads space-separated cluster file converts cleaned data frame.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean Cluster File — cleanClusterFile","text":"","code":"cleanClusterFile(path, writepath = NULL, query)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean Cluster File — cleanClusterFile","text":"path character path cluster file cleaned writepath character designating tsv file cleaned cluster file written . value NULL file written. Default NULL query character identifying query file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean Cluster File — cleanClusterFile","text":"cleaned cluster data frame returned tsv file written \"writepath\" parameter used.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean Cluster File — cleanClusterFile","text":"","code":"if (FALSE) { # \\dontrun{ cleanClusterFile(\"data/pspa.op_ins_cls\", writepath = NULL, query = \"pspa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Clust — cleanClusters","title":"Cleanup Clust — cleanClusters","text":"Cleanup cluster file Cleans cluster file removing rows contain query cluster. function removes irrelevant rows contain query protein within ClustName column. return value cleaned data frame.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Clust — cleanClusters","text":"","code":"cleanClusters(   prot,   domains_rename,   domains_keep,   condenseRepeatedDomains = TRUE,   removeTails = FALSE,   removeEmptyRows = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Clust — cleanClusters","text":"prot data frame must contain columns Query ClustName. domains_rename data frame containing domain names replaced column 'old' corresponding replacement values column 'new'. domains_keep data frame containing domain names retained. condenseRepeatedDomains Boolean. TRUE, repeated domains 'ClustName' condensed. Default TRUE. removeTails Boolean. TRUE, 'ClustName' filtered based domains keep/remove. Default FALSE. removeEmptyRows Boolean. TRUE, rows empty/unnecessary values 'ClustName' removed. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Clust — cleanClusters","text":"Cleaned data frame","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Clust — cleanClusters","text":"","code":"if (FALSE) { # \\dontrun{ cleanClusters(prot, TRUE, FALSE, domains_keep, domains_rename) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup DomArch — cleanDomainArchitecture","title":"Cleanup DomArch — cleanDomainArchitecture","text":"Cleanup Domain Architectures Cleans DomArch column replacing/removing certain domains function cleans DomArch column one data frame renaming certain domains according second data frame. Certain domains can removed according additional data frame. original data frame returned clean DomArchs column old domains DomArchs.old column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup DomArch — cleanDomainArchitecture","text":"","code":"cleanDomainArchitecture(   prot,   old = \"DomArch.orig\",   new = \"DomArch\",   domains_keep,   domains_rename,   condenseRepeatedDomains = TRUE,   removeTails = FALSE,   removeEmptyRows = F,   domains_ignore = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup DomArch — cleanDomainArchitecture","text":"prot data frame containing 'DomArch' column old name original column containing domain architecture. Defaults \"DomArch.orig\". new name cleaned column created. Defaults \"DomArch\". domains_keep data frame containing domain names retained. domains_rename data frame containing domain names replaced column 'old' corresponding replacement values column 'new'. condenseRepeatedDomains Boolean. TRUE, repeated domains 'DomArch' condensed. Default TRUE. removeTails Boolean. TRUE, 'ClustName' filtered based domains keep/remove. Default FALSE. removeEmptyRows Boolean. TRUE, rows empty/unnecessary values 'DomArch' removed. Default FALSE. domains_ignore data frame containing domain names removed column called 'domains'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup DomArch — cleanDomainArchitecture","text":"original data frame returned clean DomArchs column old domains DomArchs.old column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup DomArch — cleanDomainArchitecture","text":"","code":"if (FALSE) { # \\dontrun{ cleanDomainArchitecture(prot, TRUE, FALSE,  omains_keep, domains_rename, domains_ignore = NULL) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup FASTA Header — cleanFAHeaders","title":"Cleanup FASTA Header — cleanFAHeaders","text":"Parse accesion numbers fasta add suffix ith occurence handle duplicates","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup FASTA Header — cleanFAHeaders","text":"","code":"cleanFAHeaders(fasta)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup FASTA Header — cleanFAHeaders","text":"fasta XStringSet object representing sequences FASTA file. sequence names (headers) adjusted uniqueness sanitized.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup FASTA Header — cleanFAHeaders","text":"XStringSet fasta adjusted names (headers)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup FASTA Header — cleanFAHeaders","text":"","code":"if (FALSE) { # \\dontrun{ AAStringSet(c(\"xxx\" = \"ATCG\", \"xxx\" = \"GGGC\")) |>     cleanFAHeaders() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup GeneDesc — cleanGeneDescription","title":"Cleanup GeneDesc — cleanGeneDescription","text":"Cleanup GeneDesc","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup GeneDesc — cleanGeneDescription","text":"","code":"cleanGeneDescription(prot, column)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup GeneDesc — cleanGeneDescription","text":"prot data frame containing gene descriptions. column name column gene descriptions pulled cleanup.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup GeneDesc — cleanGeneDescription","text":"Return trailing period occurs GeneDesc column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup GeneDesc — cleanGeneDescription","text":"","code":"if (FALSE) { # \\dontrun{ cleanGeneDescription() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Genomic Contexts — cleanGenomicContext","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"Cleans GenContext column data frame removing certain characters rows. function removes empty rows based 'GenContext' column. cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"","code":"cleanGenomicContext(   prot,   domains_rename = data.frame(old = character(0), new = character(0), stringsAsFactors =     F),   condenseRepeatedDomains = TRUE,   remove_asterisk = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"prot data frame contains columns 'GenContext.orig' domains_rename data frame containing domain names replaced column 'old' replacement column 'new'. Defaults empty data frame new old column non domains renamed condenseRepeatedDomains Boolean. TRUE, repeated domains 'GenContext' condensed. Default TRUE. remove_asterisk Boolean. TRUE, asterisks 'ClustName' removed. Default TRUE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"","code":"if (FALSE) { # \\dontrun{ cleanGenomicContext(prot, domains_rename, T, F) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Lineage — cleanLineage","title":"Cleanup Lineage — cleanLineage","text":"Cleanup Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Lineage — cleanLineage","text":"","code":"cleanLineage(prot, lins_rename)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Lineage — cleanLineage","text":"prot data frame containing 'Lineage' column needs cleaned . lins_rename data frame two columns: 'old' containing terms replaced 'new' containing corresponding replacement terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Lineage — cleanLineage","text":"original data frame 'Lineage' column updated based provided replacements.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Lineage — cleanLineage","text":"","code":"if (FALSE) { # \\dontrun{ cleanLineage() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Species — cleanSpecies","title":"Cleanup Species — cleanSpecies","text":"Cleanup Species Cleans species column data frame removing certain characters rows. function removes unneccessary characters 'Species' column. cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Species — cleanSpecies","text":"","code":"cleanSpecies(prot, removeEmptyRows = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Species — cleanSpecies","text":"prot data frame contains columns 'Species'. removeEmptyRows Boolean. TRUE, rows empty/unnecessary values 'Species' removed. Default false.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Species — cleanSpecies","text":"original data frame Species cleaned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Species — cleanSpecies","text":"","code":"if (FALSE) { # \\dontrun{ cleanSpecies(prot, TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean String — cleanString","title":"Clean String — cleanString","text":"Keep alphanumerics, \"\", \"+\", \".\" strings substitute spaces \"\". Used MolEvolvR codebase cleanup domain architecture values","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean String — cleanString","text":"","code":"cleanString(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean String — cleanString","text":"string","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean String — cleanString","text":"string string alphanumerics, \"_\", \"+\", \".\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean String — cleanString","text":"","code":"if (FALSE) { # \\dontrun{ cleanString() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":null,"dir":"Reference","previous_headings":"","what":"Download the combined assembly summaries of genbank and refseq — combineFiles","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"Download combined assembly summaries genbank refseq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"","code":"combineFiles(   inpath = c(\"../molevol_data/project_data/phage_defense/\"),   pattern = \"*full_analysis.tsv\",   delim = \"\\t\",   skip = 0,   col_names = T )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"inpath Character. master directory path files reside. search recursive (.e., look subdirectories well). pattern Character. search pattern identify files combined. Default \"*full_analysis.tsv\". delim Character. delimiter used input files. Default tab (\"\"). skip Integer. number lines skip beginning file. Default 0. col_names Logical character vector. TRUE, first row file treated column names. Alternatively, character vector can provided specify custom column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"data frame containing combined contents matched files. row include new column \"ByFile\" indicating source file data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"","code":"if (FALSE) { # \\dontrun{ combined_data <- combineFiles(inpath = \"../molevol_data/project_data/phage_defense/\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Combining full_analysis files — combineFullAnalysis","title":"Combining full_analysis files — combineFullAnalysis","text":"Combining full_analysis files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combining full_analysis files — combineFullAnalysis","text":"","code":"combineFullAnalysis(inpath, ret = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combining full_analysis files — combineFullAnalysis","text":"inpath Character. path directory containing .full_analysis.tsv files combined. ret Logical. TRUE, function return combined data frame. Default FALSE, meaning write file return data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combining full_analysis files — combineFullAnalysis","text":"ret TRUE, data frame containing combined data input files. ret FALSE, function writes combined data TSV file named cln_combined.tsv specified directory returns NULL.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combining full_analysis files — combineFullAnalysis","text":"","code":"if (FALSE) { # \\dontrun{ combined_data <- combineFullAnalysis(\"path/to/full_analysis/files\", ret = TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":null,"dir":"Reference","previous_headings":"","what":"Combining clean ipr files — combineIPR","title":"Combining clean ipr files — combineIPR","text":"Combining clean ipr files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combining clean ipr files — combineIPR","text":"","code":"combineIPR(inpath, ret = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combining clean ipr files — combineIPR","text":"inpath Character. path directory containing .iprscan_cln.tsv files combined. ret Logical. TRUE, function return combined data frame. Default FALSE, meaning write file return data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combining clean ipr files — combineIPR","text":"ret TRUE, data frame containing combined data input files. ret FALSE, function writes combined data TSV file named ipr_combined.tsv specified directory returns NULL.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combining clean ipr files — combineIPR","text":"","code":"if (FALSE) { # \\dontrun{ combineIPR <- combine_ipr(\"path/to/ipr/files\", ret = TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":null,"dir":"Reference","previous_headings":"","what":"condenseRepeatedDomains — condenseRepeatedDomains","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"Condense repeated domains Condenses repeated domains specified column. function identifies repeated domains condenses (s). ?? Certain domains can removed according additional data frame. original data frame returned corresponding cleaned column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"","code":"condenseRepeatedDomains(prot, by_column = \"DomArch\", excluded_prots = c())"},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"prot data frame containing 'DomArch', 'GenContext', 'ClustName' columns. by_column Column repeats condensed domain+domain -> domain(s). excluded_prots Vector strings condenseRepeatedDomains reduce (s). Defaults c()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"data frame condensed repeated domains specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"","code":"if (FALSE) { # \\dontrun{ condenseRepeatedDomains(prot, \"DomArch\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":null,"dir":"Reference","previous_headings":"","what":"Changing case to 'Title Case' — convert2TitleCase","title":"Changing case to 'Title Case' — convert2TitleCase","text":"Translate string Title Case w/ delimitter. Translate string Title Case w/ delimitter. Changing case 'Title Case'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Changing case to 'Title Case' — convert2TitleCase","text":"","code":"convert2TitleCase(text, delimitter)  to_titlecase(text, delimitter)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Changing case to 'Title Case' — convert2TitleCase","text":"x Character vector. y Delimitter. Default space (\" \").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Changing case to 'Title Case' — convert2TitleCase","text":"Character vector input strings converted title case. character vector title case.","code":""},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Changing case to 'Title Case' — convert2TitleCase","text":"Andrie, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Changing case to 'Title Case' — convert2TitleCase","text":"","code":"# Convert a single string to title case convert2TitleCase(\"hello world\") # Returns \"Hello World\" #> [1] \"Hello World\"  convert2TitleCase(\"hello world\") #> [1] \"Hello World\" convert2TitleCase(\"this is a test\", \"_\") #> [1] \"This is a test\""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"convertAlignment2FA — convertAlignment2FA","title":"convertAlignment2FA — convertAlignment2FA","text":"Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertAlignment2FA — convertAlignment2FA","text":"","code":"convertAlignment2FA(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   fa_outpath = \"\",   reduced = FALSE )  convertAlignment2FA(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   fa_outpath = \"\",   reduced = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertAlignment2FA — convertAlignment2FA","text":"aln_file Character. Path file. Input tab-delimited file + alignment file accnum & alignment. Default 'pspa_snf7.aln' lin_file Character. Path file. Protein file accession + number lineage mapping. Default 'pspa.txt' fa_outpath Character. Path written fasta file. Default 'NULL' reduced Boolean. TRUE, fasta file contain one sequence per lineage. Default 'FALSE'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertAlignment2FA — convertAlignment2FA","text":"character string representing FASTA formatted sequences. fa_outpath provided, FASTA also saved specified file. Character string containing Fasta formatted sequences. fa_outpath specified, function also writes sequences Fasta file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"convertAlignment2FA — convertAlignment2FA","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"convertAlignment2FA — convertAlignment2FA","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"convertAlignment2FA — convertAlignment2FA","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convertAlignment2FA — convertAlignment2FA","text":"","code":"if (FALSE) { # \\dontrun{ addLeaves2Alignment(\"pspa_snf7.aln\", \"pspa.txt\") } # }  if (FALSE) { # \\dontrun{ convertAlignment2FA(\"pspa_snf7.aln\", \"pspa.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":null,"dir":"Reference","previous_headings":"","what":"convertAlignment2Trees — convertAlignment2Trees","title":"convertAlignment2Trees — convertAlignment2Trees","text":"Generate Trees fasta files \"data/alns\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertAlignment2Trees — convertAlignment2Trees","text":"","code":"convertAlignment2Trees(aln_path = here(\"data/alns/\"))"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertAlignment2Trees — convertAlignment2Trees","text":"aln_path Path directory containing alignment FASTA files (.fa) trees generated. Default \"data/alns/\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertAlignment2Trees — convertAlignment2Trees","text":"return value. function generates tree files (.tre) alignment file specified directory.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convertAlignment2Trees — convertAlignment2Trees","text":"","code":"if (FALSE) { # \\dontrun{ generate_trees(here(\"data/alns/\")) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":null,"dir":"Reference","previous_headings":"","what":"convertFA2Tree — convertFA2Tree","title":"convertFA2Tree — convertFA2Tree","text":"convertFA2Tree","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertFA2Tree — convertFA2Tree","text":"","code":"convertFA2Tree(   fa_path = here(\"data/alns/pspa_snf7.fa\"),   tre_path = here(\"data/alns/pspa_snf7.tre\"),   fasttree_path = here(\"src/FastTree\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertFA2Tree — convertFA2Tree","text":"fa_path Path input FASTA alignment file (.fa). Default path \"data/alns/pspa_snf7.fa\". tre_path Path output file generated tree (.tre) saved. Default path \"data/alns/pspa_snf7.tre\". fasttree_path Path FastTree executable, used generate phylogenetic tree. Default \"src/FastTree\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertFA2Tree — convertFA2Tree","text":"return value. function generates tree file (.tre) input FASTA file.","code":""},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"Using table returned createIPRScanDomainTable, construct domain fasta single accession number original fasta (.e., original fasta argument createIPRScanDomainTable())","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"","code":"convertIPRScanDomainTable2FA(df_iprscan_domains)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"df_iprscan_domains tbl_df return value createIPRScanDomainTable","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"AAStringSet domain fasta containing domains single protein original fasta passed argument createIPRScanDomainTable()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"","code":"if (FALSE) { # \\dontrun{ path_molevol_scripts <- file.path(Sys.getenv(\"DEV\", unset = \"/data/molevolvr_transfer/molevolvr_dev\"), \"molevol_scripts\") setwd(path_molevol_scripts) source(\"R/fa2domain.R\") fasta <- Biostrings::readAAStringSet(\"./tests/example_protein.fa\") df_iprscan <- readIPRScanTSV(\"./tests/example_iprscan_valid.tsv\") accnum <- df_iprscan$AccNum[1] df_iprscan_domains <- createIPRScanDomainTable(accnum, fasta, df_iprscan) fasta_domains <- df_iprscan_domains |> convertIPRScanDomainTable2FA() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":null,"dir":"Reference","previous_headings":"","what":"countByColumn — countByColumn","title":"countByColumn — countByColumn","text":"Function obtain element counts (DA, GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"countByColumn — countByColumn","text":"","code":"countByColumn(prot = prot, column = \"DomArch\", min.freq = 1)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"countByColumn — countByColumn","text":"prot data frame containing dataset analyze, typically multiple columns including one specified column parameter. column character string specifying name column analyze. default \"DomArch\". min.freq integer specifying minimum frequency element must included output. Default 1.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"countByColumn — countByColumn","text":"tibble two columns: column unique elements specified column (e.g., \"DomArch\"). freq frequency element, .e., number times element appears specified column. tibble filtered include elements frequency greater equal min.freq include elements NA values starting hyphen (\"-\").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"countByColumn — countByColumn","text":"","code":"if (FALSE) { # \\dontrun{ countByColumn(prot = my_data, column = \"DomArch\", min.freq = 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Domain Network — createBinaryDomainNetwork","title":"Domain Network — createBinaryDomainNetwork","text":"function creates domain network 'DomArch' column. Domains part 'domains_of_interest' different node color domains. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Domain Network — createBinaryDomainNetwork","text":"","code":"createBinaryDomainNetwork(   prot,   column = \"DomArch\",   domains_of_interest,   cutoff = 70,   layout = \"nice\",   query_color = adjustcolor(\"yellow\", alpha.f = 0.5),   partner_color = adjustcolor(\"skyblue\", alpha.f = 0.5),   border_color = adjustcolor(\"grey\", alpha.f = 0.8),   IsDirected = T )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Domain Network — createBinaryDomainNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. domains_of_interest Character vector specifying domains interest. cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" query_color Color nodes domains domains_of_interest vector colored partner_color Color nodes part domains_of_interest vector colored border_color Color borders nodes. IsDirected network directed? Set false eliminate arrows","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Domain Network — createBinaryDomainNetwork","text":"network visualization domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Domain Network — createBinaryDomainNetwork","text":"","code":"if (FALSE) { # \\dontrun{ createBinaryDomainNetwork(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Domain Network — createDomainNetwork","title":"Domain Network — createDomainNetwork","text":"function creates domain network 'DomArch' column. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Domain Network — createDomainNetwork","text":"","code":"createDomainNetwork(   prot,   column = \"DomArch\",   domains_of_interest,   cutoff = 70,   layout = \"nice\",   query_color = adjustcolor(\"green\", alpha.f = 0.5) )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Domain Network — createDomainNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. domains_of_interest Character vector specifying domains interest. cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" query_color Character. Color represent queried domain network.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Domain Network — createDomainNetwork","text":"network visualization domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Domain Network — createDomainNetwork","text":"","code":"if (FALSE) { # \\dontrun{ createDomainNetwork(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":null,"dir":"Reference","previous_headings":"","what":"createFA2Tree — createFA2Tree","title":"createFA2Tree — createFA2Tree","text":"Generating phylogenetic tree alignment file '.fa'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createFA2Tree — createFA2Tree","text":"","code":"createFA2Tree(   fa_file = \"data/alns/pspa_snf7.fa\",   out_file = \"data/alns/pspa_snf7.tre\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createFA2Tree — createFA2Tree","text":"fa_file Character. Path alignment FASTA file (.fa) phylogenetic tree generated. Default 'pspa_snf7.fa'. out_file Path output file generated tree (.tre) saved. Default \"data/alns/pspa_snf7.tre\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createFA2Tree — createFA2Tree","text":"return value. function generates phylogenetic tree file (.tre) based different approaches like Neighbor Joining, UPGMA, Maximum Likelihood.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createFA2Tree — createFA2Tree","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"createFA2Tree — createFA2Tree","text":"Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"createFA2Tree — createFA2Tree","text":"Janani Ravi, MolEcologist","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createFA2Tree — createFA2Tree","text":"","code":"if (FALSE) { # \\dontrun{ generate_aln2tree(\"pspa_snf7.fa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Genomic Context Directed Network — createGenomicContextNetwork","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"function creates Genomic Context network 'GenContext' column. network Genomic Context returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"","code":"createGenomicContextNetwork(   prot,   domains_of_interest,   column = \"GenContext\",   cutoff = 40,   layout = \"grid\",   directed = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"prot data frame contains column 'GenContext'. domains_of_interest Character vector domains interest. column Name column containing Genomic Context nodes edges generated. cutoff Integer. use GenContexts occur cutoff percentage total count layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" \"nice\" directed network directed?","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"plot genomic context network.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"","code":"if (FALSE) { # \\dontrun{ gc_directed_network(pspa, column = \"GenContext\", cutoff = 55) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":null,"dir":"Reference","previous_headings":"","what":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"given accession number, get domain sequences using interproscan output table & original FASTA file","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"","code":"createIPRScanDomainTable(   accnum,   fasta,   df_iprscan,   analysis = c(\"Pfam\", \"Gene3D\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"accnum chr single accession number original fasta (fasta param) used search sequence's domains (df_iprscan param) fasta AAStringSet original fasta file fed interproscan df_iprscan tbl_df output TSV interproscan, read tibble readIPRScanTSV() analysis chr domain databases extract sequences ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"tbl_df table domain sequence new identifier column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"","code":"if (FALSE) { # \\dontrun{ path_molevol_scripts <- file.path(Sys.getenv(\"DEV\", unset = \"/data/molevolvr_transfer/molevolvr_dev\"), \"molevol_scripts\") setwd(path_molevol_scripts) source(\"R/fa2domain.R\") fasta <- Biostrings::readAAStringSet(\"./tests/example_protein.fa\") df_iprscan <- readIPRScanTSV(\"./tests/example_iprscan_valid.tsv\") accnum <- df_iprscan$AccNum[1] df_iprscan_domains <- createIPRScanDomainTable(accnum, fasta, df_iprscan) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":null,"dir":"Reference","previous_headings":"","what":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"'base_url' parameter set environment variable 'BASE_URL' available, defaults \"http://jravilab.org/molevolvr/\" .","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"","code":"createJobResultsURL(   pin_id,   base_url = Sys.getenv(\"BASE_URL\", unset = \"http://jravilab.org/molevolvr/\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"pin_id unique identifier job base_url base URL MolEvolvR web app","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"URL user can check status job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":null,"dir":"Reference","previous_headings":"","what":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"Produces mail message can sent user job accepted. Used sendJobStatusEmail() method.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"","code":"createJobStatusEmailMessage(   job_dir,   pin_id,   job_results_url,   event_type,   context )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"job_dir directory job's arguments stored, job_args.yml pin_id unique identifier job job_results_url URL user can check status job event_type either 'start' 'end', returns corresponding email given type context list additional values, e.g. job runtime info, can used template emails","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"result sendmailR::sendmail() call","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":null,"dir":"Reference","previous_headings":"","what":"createLineageLookup — createLineageLookup","title":"createLineageLookup — createLineageLookup","text":"Create look table goes TaxID, Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createLineageLookup — createLineageLookup","text":"","code":"createLineageLookup(   lineage_file = here(\"data/rankedlineage.dmp\"),   outfile,   taxonomic_rank = \"phylum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createLineageLookup — createLineageLookup","text":"lineage_file Path rankedlineage.dmp file containing taxid's corresponding taxonomic rank. rankedlineage.dmp can downloaded https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/ outfile File resulting lineage lookup table written taxonomic_rank upperbound taxonomic rank lineage includes. lineaege include superkingdom>...>taxonomic_rank. Choices include: \"supperkingdom\", \"phylum\",   \"class\",\"order\", \"family\", \"genus\", \"species\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createLineageLookup — createLineageLookup","text":"tibble containing tax IDs respective lineages specified taxonomic rank, saved tab-separated file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"createLineageLookup — createLineageLookup","text":"Samuel Chen","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createLineageLookup — createLineageLookup","text":"","code":"if (FALSE) { # \\dontrun{ createLineageLookup(lineage_file = \"data/rankedlineage.dmp\",                       outfile = \"data/lineage_lookup.tsv\",                       taxonomic_rank = \"family\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to generate MSA using kalign — createMSA_Kalign","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"Function generate MSA using kalign","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"","code":"createMSA_Kalign(fa_file = \"\", outfile = \"\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"fa_file Character. path input FASTA file containing protein sequences. outfile Character. path output file alignment saved.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"list containing alignment object output file path.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"","code":"if (FALSE) { # \\dontrun{ createMSA_Kalign(fa_file = \"path/to/sequences.fasta\",                   outfile = \"path/to/alignment.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Sequence Alignment — createMSA_PDF","title":"Multiple Sequence Alignment — createMSA_PDF","text":"Generates multiple sequence alignment fasta file createMSA_PDF function reads fasta file generates multiple sequence alignment pdf","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Sequence Alignment — createMSA_PDF","text":"","code":"createMSA_PDF(   fasta_path,   out_path = NULL,   lowerbound = NULL,   upperbound = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Sequence Alignment — createMSA_PDF","text":"fasta_path Character. path location fasta file read. out_path Character. path location output pdf write. Default NULL. value NULL, pdf written directory fasta file. lowerbound Numeric. column determines starting location MSA. Default NULL. value NULL, entire multiple sequence alignment printed. upperbound Numeric. column determines ending location MSA. Default NULL. value NULL, entire multiple sequence alignment printed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Sequence Alignment — createMSA_PDF","text":"PDF file containing multiple sequence alignment.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multiple Sequence Alignment — createMSA_PDF","text":"","code":"if (FALSE) { # \\dontrun{ createMSA_PDF(fasta_path = \"path/to/your/file.fasta\",          out_path = \"path/to/output/alignment.pdf\",          lowerbound = 10,          upperbound = 200) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":null,"dir":"Reference","previous_headings":"","what":"createRepresentativeAccNum — createRepresentativeAccNum","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"Function generate vector one Accession number per distinct observation 'reduced' column Function generate vector one Accession number per distinct observation 'reduced' column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"","code":"createRepresentativeAccNum(   prot_data,   reduced = \"Lineage\",   accnum_col = \"AccNum\" )  createRepresentativeAccNum(   prot_data,   reduced = \"Lineage\",   accnum_col = \"AccNum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"prot_data Data frame containing Accession Numbers reduced Column prot_data distinct observations generated . One accession number assigned observations accnum_col Column prot_data contains Accession Numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"character vector containing one Accession number per distinct observation specified reduced column. character vector containing representative accession numbers, one distinct observation specified 'reduced' column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"","code":"if (FALSE) { # \\dontrun{ createRepresentativeAccNum(prot) } # } if (FALSE) { # \\dontrun{ # Example usage with a data frame called `protein_data` createRepresentativeAccNum <- RepresentativeAccNums(prot_data = protein_data,                                                     reduced = \"Lineage\",                                                     accnum_col = \"AccNum\") representative_accessions } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"function creates domain network 'DomArch' column. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"","code":"createUndirectedGenomicContextNetwork(   prot,   column = \"GenContext\",   domains_of_interest,   cutoff_type = \"Lineage\",   cutoff = 1,   layout = \"grid\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. domains_of_interest Character vector specifying domains interest. cutoff_type Character. Used determine data filtered. Either \"Total Count\" filter total amount times domain architecture occurs cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"plot domain architecture network.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"","code":"if (FALSE) { # \\dontrun{ createUndirectedGenomicContextNetwork(pspa, column = \"DomArch\",  domains_of_interest = c(\"Domain1\", \"Domain2\"),  cutoff_type = \"Total Count\", cutoff = 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":null,"dir":"Reference","previous_headings":"","what":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"Wordclouds predominant domains (DAs) DAs (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"","code":"createWordCloud2Element(   query_data = \"prot\",   colname = \"DomArch\",   cutoff = 70,   UsingRowsCutoff = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default \"prot\". colname Character. name column query_data generate word cloud . Default \"DomArch\". cutoff Numeric. cutoff value filtering elements based frequency. Default 70. UsingRowsCutoff Logical. Whether use row-based cutoff instead frequency cutoff. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"word cloud plot showing frequency elements selected column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"","code":"if (FALSE) { # \\dontrun{ createWordCloudElement(prot, \"da2doms\", 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":null,"dir":"Reference","previous_headings":"","what":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"Wordclouds predominant domains (DAs) DAs (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"","code":"createWordCloudElement(   query_data = \"prot\",   colname = \"DomArch\",   cutoff = 70,   UsingRowsCutoff = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default \"prot\". colname Character. name column query_data generate word cloud . Default \"DomArch\". cutoff Numeric. cutoff value filtering elements based frequency. Default 70. UsingRowsCutoff Logical. Whether use row-based cutoff instead frequency cutoff. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"word cloud plot showing frequency elements selected column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"","code":"if (FALSE) { # \\dontrun{ createWordCloudElement(prot, \"da2doms\", 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":null,"dir":"Reference","previous_headings":"","what":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"Download combined assembly summaries genbank refseq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"","code":"downloadAssemblySummary(   outpath,   keep = c(\"assembly_accession\", \"taxid\", \"species_taxid\", \"organism_name\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"outpath String path assembly summary file written keep Character vector containing columns retained downloaded","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"tab-separated file containing assembly summary. function notreturn value writes output directly specified file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"","code":"if (FALSE) { # \\dontrun{ downloadAssemblySummary(outpath = \"assembly_summary.tsv\",      keep = c(\"assembly_accession\", \"taxid\", \"organism_name\")) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":null,"dir":"Reference","previous_headings":"","what":"efetchIPG — efetchIPG","title":"efetchIPG — efetchIPG","text":"Perform efetch ipg database write results out_path Perform efetch ipg database write results out_path","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"efetchIPG — efetchIPG","text":"","code":"efetchIPG(accessions, out_path, plan = \"multicore\")  efetchIPG(accessions, out_path, plan = \"multicore\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"efetchIPG — efetchIPG","text":"accessions Character vector containing accession numbers query ipg database out_path Path write efetch results plan Character. Specifies execution plan parallel processing. Default \"multicore\". accnums Character vector containing accession numbers query ipg database","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"efetchIPG — efetchIPG","text":"return value. function writes fetched results out_path. function return value writes efetch results directly specified out_path.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"efetchIPG — efetchIPG","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"efetchIPG — efetchIPG","text":"","code":"if (FALSE) { # \\dontrun{ efetchIPG() } # } if (FALSE) { # \\dontrun{ efetchIPG(   accessions = c(\"P12345\", \"Q67890\", \"A12345\"),   out_path = \"path/to/efetch_results.xml\" ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":null,"dir":"Reference","previous_headings":"","what":"elements2Words — elements2Words","title":"elements2Words — elements2Words","text":"Break string ELEMENTS WORDS domain architecture (DA) genomic context (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"elements2Words — elements2Words","text":"","code":"elements2Words(prot, column = \"DomArch\", conversion_type = \"da2doms\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"elements2Words — elements2Words","text":"prot dataframe containing dataset analyze. specified column contains string elements processed. column character string specifying name column analyze. Default \"DomArch\". conversion_type character string specifying type conversion. Two options available: da2doms Convert domain architectures individual domains replacing + symbols spaces. gc2da Convert genomic context domain architectures replacing directional symbols (<-, ->, |) spaces.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"elements2Words — elements2Words","text":"single string elements delimited spaces. function performs necessary substitutions based conversion_type cleans extraneous characters like newlines, tabs, multiple spaces.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"elements2Words — elements2Words","text":"","code":"if (FALSE) { # \\dontrun{ tibble::tibble(DomArch = c(\"aaa+bbb\",  \"a+b\", \"b+c\", \"b-c\")) |> elements2Words() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":null,"dir":"Reference","previous_headings":"","what":"make accnums unique — ensureUniqAccNum","title":"make accnums unique — ensureUniqAccNum","text":"Append index occurence suffix accession number (character vector) making unique","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"make accnums unique — ensureUniqAccNum","text":"","code":"ensureUniqAccNum(accnums)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"make accnums unique — ensureUniqAccNum","text":"accnums chr vector accession numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"make accnums unique — ensureUniqAccNum","text":"chr vector adjusted, unique accession numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"make accnums unique — ensureUniqAccNum","text":"","code":"if (FALSE) { # \\dontrun{ c(\"xxx\", \"xxx\", \"xxx\", \"yyy\", \"yyy\") |>     ensureUniqAccNum() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":null,"dir":"Reference","previous_headings":"","what":"extractAccNum — extractAccNum","title":"extractAccNum — extractAccNum","text":"extractAccNum","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"extractAccNum — extractAccNum","text":"","code":"extractAccNum(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"extractAccNum — extractAccNum","text":"string string extract accession number. string may contain accession information delimited | spaces.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"extractAccNum — extractAccNum","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"extractAccNum — extractAccNum","text":"","code":"if (FALSE) { # \\dontrun{ extractAccNum() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":null,"dir":"Reference","previous_headings":"","what":"filterByDomains — filterByDomains","title":"filterByDomains — filterByDomains","text":"filterByDomains filters data frame identifying exact domain matches either keeping removing rows identified domain","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filterByDomains — filterByDomains","text":"","code":"filterByDomains(   prot,   column = \"DomArch\",   doms_keep = c(),   doms_remove = c(),   ignore.case = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filterByDomains — filterByDomains","text":"prot Dataframe filter column Column search domains (DomArch column) doms_keep Vector domains must identified within column order observation kept doms_remove Vector domains , found within observation, removed ignore.case matching non case sensitive","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"filterByDomains — filterByDomains","text":"Filtered data frame","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"filterByDomains — filterByDomains","text":"need make domains 'regex safe', handled function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"filterByDomains — filterByDomains","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"filterByDomains — filterByDomains","text":"","code":"if (FALSE) { # \\dontrun{ filterByDomains() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":null,"dir":"Reference","previous_headings":"","what":"filterByFrequency — filterByFrequency","title":"filterByFrequency — filterByFrequency","text":"Function filter based frequencies","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filterByFrequency — filterByFrequency","text":"","code":"filterByFrequency(x, min.freq)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filterByFrequency — filterByFrequency","text":"x tibble (tbl_df) containing least two columns: one elements (e.g., words) one frequency (e.g., freq). min.freq numeric value specifying minimum frequency threshold. elements frequencies greater equal value retained.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"filterByFrequency — filterByFrequency","text":"tibble structure x, filtered include rows frequency greater equal min.freq.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"filterByFrequency — filterByFrequency","text":"","code":"if (FALSE) { # \\dontrun{ filterByFrequency() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":null,"dir":"Reference","previous_headings":"","what":"findParalogs — findParalogs","title":"findParalogs — findParalogs","text":"Creates data frame paralogs.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"findParalogs — findParalogs","text":"","code":"findParalogs(prot)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"findParalogs — findParalogs","text":"prot data frame filtered Query, containing columns Species Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"findParalogs — findParalogs","text":"returns dataframe containing paralogs counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"findParalogs — findParalogs","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"findParalogs — findParalogs","text":"","code":"if (FALSE) { # \\dontrun{ findParalogs(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":null,"dir":"Reference","previous_headings":"","what":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"Format job arguments html-formatted key/value pairs, including email","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"","code":"formatJobArgumentsHTML(job_args)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"job_args list job arguments, e.g. read job_args.yml file","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"list HTML-formatted key/value pairs","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"","code":"if (FALSE) { # \\dontrun{ formatJobArgumentsHTML(\"/data/scratch/janani/molevolvr_out/Ba5sV1_full\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"generateAllAlignments2FA — generateAllAlignments2FA","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"Adding Leaves alignment file w/ accessions Adding Leaves alignment files w/ accessions & DAs? Adding Leaves alignment file w/ accessions Adding Leaves alignment files w/ accessions & DAs?","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"","code":"generateAllAlignments2FA(   aln_path = here(\"data/rawdata_aln/\"),   fa_outpath = here(\"data/alns/\"),   lin_file = here(\"data/rawdata_tsv/all_semiclean.txt\"),   reduced = F )  generateAllAlignments2FA(   aln_path = here(\"data/rawdata_aln/\"),   fa_outpath = here(\"data/alns/\"),   lin_file = here(\"data/rawdata_tsv/all_semiclean.txt\"),   reduced = F )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"aln_path Character. Path alignment files. Default '(\"data/rawdata_aln/\")' fa_outpath Character. Path file. Master protein file AccNum & lineages. Default '(\"data/rawdata_tsv/all_semiclean.txt\")' lin_file Character. Path written fasta file. Default '(\"data/alns/\")'. reduced Boolean. TRUE, fasta file contain one sequence per lineage. Default 'FALSE'.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"NULL. function saves output FASTA files specified directory. NULL. function saves output FASTA files specified directory.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"alignment files need two columns separated spaces: AccNum 2. alignment. protein homolog file AccNum, Species, Lineages. alignment files need two columns separated spaces: AccNum 2. alignment. protein homolog file AccNum, Species, Lineages.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"","code":"if (FALSE) { # \\dontrun{ generateAllAlignments2FA() } # } if (FALSE) { # \\dontrun{ generateAllAlignments2FA() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":null,"dir":"Reference","previous_headings":"","what":"getAccNumFromFA — getAccNumFromFA","title":"getAccNumFromFA — getAccNumFromFA","text":"getAccNumFromFA getAccNumFromFA","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getAccNumFromFA — getAccNumFromFA","text":"","code":"getAccNumFromFA(fasta_file)  getAccNumFromFA(fasta_file)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getAccNumFromFA — getAccNumFromFA","text":"fasta_file Character. Path FASTA file accession numbers extracted.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getAccNumFromFA — getAccNumFromFA","text":"character vector containing extracted accession numbers. character vector containing extracted accession numbers.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getAccNumFromFA — getAccNumFromFA","text":"","code":"if (FALSE) { # \\dontrun{ getAccNumFromFA(\"my_sequences.fasta\") } # } if (FALSE) { # \\dontrun{ # Example usage accnums <- getAccNumFromFA(\"path/to/sequences.fasta\") accnums } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":null,"dir":"Reference","previous_headings":"","what":"getDomainsFromFA — getDomainsFromFA","title":"getDomainsFromFA — getDomainsFromFA","text":"getDomainsFromFA","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getDomainsFromFA — getDomainsFromFA","text":"","code":"getDomainsFromFA(   fasta,   df_iprscan,   analysis = c(\"Pfam\", \"Gene3D\"),   verbose = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getDomainsFromFA — getDomainsFromFA","text":"fasta AAStringSet protein (AA) fasta df_iprscan tbl_df interproscan results original fasta analysis chr domain databases extract sequences ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getDomainsFromFA — getDomainsFromFA","text":"fasta_domains AAStringSet fasta domains","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getDomainsFromFA — getDomainsFromFA","text":"","code":"if (FALSE) { # \\dontrun{ path_molevol_scripts <- file.path(Sys.getenv(\"DEV\", unset = \"/data/molevolvr_transfer/molevolvr_dev\"), \"molevol_scripts\") setwd(path_molevol_scripts) source(\"R/fa2domain.R\") fasta <- Biostrings::readAAStringSet(\"./tests/example_protein.fa\") df_iprscan <- readIPRScanTSV(\"./tests/example_iprscan_valid.tsv\") getDomainsFromFA(fasta, df_iprscan) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColNames.html","id":null,"dir":"Reference","previous_headings":"","what":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","title":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","text":"Constructor function interproscan column names (based upon global variable written molevol_scripts/R/colnames_molevol.R)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColNames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","text":"","code":"getIPRScanColNames()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColNames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","text":"chr interproscan column names used throughout molevolvr","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColTypes.html","id":null,"dir":"Reference","previous_headings":"","what":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","title":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","text":"construct column types reading interproscan output TSVs (based upon global variable written molevol_scripts/R/colnames_molevol.R)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColTypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","text":"","code":"getIPRScanColTypes()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColTypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","text":"collector named vector type expecatations interproscan columns","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":null,"dir":"Reference","previous_headings":"","what":"getProcessRuntimeWeights — getProcessRuntimeWeights","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"Quickly get runtime weights MolEvolvR backend processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"","code":"getProcessRuntimeWeights(medians_yml_path = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"dir_job_results chr path MolEvolvR job_results directory","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"list names: processes; values: median runtime (seconds) example: writeProcessRuntime2YML()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":null,"dir":"Reference","previous_headings":"","what":"getTopAccByLinDomArch — getTopAccByLinDomArch","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"Group lineage + DA take top 20","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"","code":"getTopAccByLinDomArch(   infile_full,   DA_col = \"DomArch.Pfam\",   lin_col = \"Lineage_short\",   n = 20,   query )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"infile_full data frame containing full dataset lineage domain architecture information. DA_col string representing name domain architecture column. Default \"DomArch.Pfam\". lin_col string representing name lineage column. Default \"Lineage_short\". n integer specifying number top accession numbers return. Default 20. query string filtering specific query name. \"\", data matching query processed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"vector top N accession numbers (AccNum) based counts grouped lineage domain architecture.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"","code":"if (FALSE) { # \\dontrun{ top_accessions <- getTopAccByLinDomArch(infile_full = my_data, DA_col = \"DomArch.Pfam\", lin_col = \"Lineage_short\", n = 20, query = \"specific_query_name\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":null,"dir":"Reference","previous_headings":"","what":"mapAcc2Name — mapAcc2Name","title":"mapAcc2Name — mapAcc2Name","text":"Default renameFA() replacement function. Maps accession number name Default rename_fasta() replacement function. Maps accession number name","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mapAcc2Name — mapAcc2Name","text":"","code":"mapAcc2Name(line, acc2name, acc_col = \"AccNum\", name_col = \"Name\")  mapAcc2Name(line, acc2name, acc_col = \"AccNum\", name_col = \"Name\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mapAcc2Name — mapAcc2Name","text":"line line fasta file starting '>' acc2name Data Table containing column accession numbers name column acc_col Name column containing Accession numbers name_col Name column containing names accession numbers mapped ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mapAcc2Name — mapAcc2Name","text":"character string representing updated FASTA line, accession number replaced corresponding name. Character string. modified line Fasta file header name instead accession number.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"mapAcc2Name — mapAcc2Name","text":"","code":"if (FALSE) { # \\dontrun{ mapAcc2Name(\">P12345 some description\", acc2name, \"AccNum\", \"Name\") } # } if (FALSE) { # \\dontrun{ acc2name_table <- data.table(AccNum = c(\"ACC001\", \"ACC002\"), Name = c(\"Species A\", \"Species B\")) line <- \">ACC001 some additional info\" mapped_line <- mapAcc2Name(line, acc2name_table) mapped_line  # Expected output: \">Species A\" } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":null,"dir":"Reference","previous_headings":"","what":"mapAdvOption2Process — mapAdvOption2Process","title":"mapAdvOption2Process — mapAdvOption2Process","text":"Use MolEvolvR advanced options get associated processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mapAdvOption2Process — mapAdvOption2Process","text":"","code":"mapAdvOption2Process(advanced_opts)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mapAdvOption2Process — mapAdvOption2Process","text":"advanced_opts character vector MolEvolvR advanced options","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mapAdvOption2Process — mapAdvOption2Process","text":"character vector process names execute given advanced options example: advanced_opts <- c(\"homology_search\", \"domain_architecture\") procs <- mapAdvOption2Process(advanced_opts)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapOption2Process.html","id":null,"dir":"Reference","previous_headings":"","what":"mapOption2Process — mapOption2Process","title":"mapOption2Process — mapOption2Process","text":"Construct list names (MolEvolvR advanced options) point processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapOption2Process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mapOption2Process — mapOption2Process","text":"","code":"mapOption2Process()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapOption2Process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mapOption2Process — mapOption2Process","text":"list names (MolEvolvR advanced options) point processes example: list_opts2procs <- mapOption2Process","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotEstimatedWallTimes.html","id":null,"dir":"Reference","previous_headings":"","what":"plotEstimatedWallTimes — plotEstimatedWallTimes","title":"plotEstimatedWallTimes — plotEstimatedWallTimes","text":"Plot estimated runtimes different advanced options number inputs function just fun; , messy code","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotEstimatedWallTimes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotEstimatedWallTimes — plotEstimatedWallTimes","text":"","code":"plotEstimatedWallTimes()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotEstimatedWallTimes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotEstimatedWallTimes — plotEstimatedWallTimes","text":"line plot object example: p <- plotEstimatedWallTimes() ggplot2::ggsave(filename = \"/data/molevolvr_transfer/molevolvr_ dev/molevol_scripts/docs/estimate_walltimes.png\", plot = p)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":null,"dir":"Reference","previous_headings":"","what":"plotIPR2Viz — plotIPR2Viz","title":"plotIPR2Viz — plotIPR2Viz","text":"plotIPR2Viz","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotIPR2Viz — plotIPR2Viz","text":"","code":"plotIPR2Viz(   infile_ipr = NULL,   infile_full = NULL,   accessions = c(),   analysis = c(\"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"),   group_by = \"Analysis\",   topn = 20,   name = \"Name\",   text_size = 15,   query = \"All\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotIPR2Viz — plotIPR2Viz","text":"infile_ipr path input IPR file (TSV format) containing domain information. infile_full path full input file (TSV format) containing lineage accession information. accessions character vector accession numbers filter analysis. Default empty vector. analysis character vector specifying types analysis include (e.g., \"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"). Default vector analyses. group_by string specifying group visualization. Default \"Analysis\". Options include \"Analysis\" \"Query\". topn integer specifying number top accessions visualize. Default 20. name string representing name use y-axis labels. Default \"Name\". text_size integer specifying text size plot. Default 15. query string filtering specific query name. \"\", data matching query processed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotIPR2Viz — plotIPR2Viz","text":"ggplot object representing domain architecture visualization.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotIPR2Viz — plotIPR2Viz","text":"","code":"if (FALSE) { # \\dontrun{ plot <- plotIPR2Viz(infile_ipr = \"path/to/ipr_file.tsv\",                     infile_full = \"path/to/full_file.tsv\",                     accessions = c(\"ACC123\", \"ACC456\"),                     analysis = c(\"Pfam\", \"TMHMM\"),                     group_by = \"Analysis\",                     topn = 20,                     name = \"Gene Name\",                     text_size = 15,                     query = \"All\") plot } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":null,"dir":"Reference","previous_headings":"","what":"plotIPR2VizWeb — plotIPR2VizWeb","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"plotIPR2VizWeb","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"","code":"plotIPR2VizWeb(   infile_ipr,   accessions,   analysis = c(\"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"),   group_by = \"Analysis\",   name = \"Name\",   text_size = 15,   legend_name = \"ShortName\",   cols = 5,   rows = 10 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"infile_ipr path input IPR file (TSV format) containing domain information. accessions character vector accession numbers filter analysis. analysis character vector specifying types analysis include (e.g., \"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"). Default vector analyses. group_by string specifying group visualization. Default \"Analysis\". Options include \"Analysis\" \"Query\". name string representing name use y-axis labels. Default \"Name\". text_size integer specifying text size plot. Default 15. legend_name string representing column use legend labels. Default \"ShortName\". cols integer specifying number columns facet wrap. Default 5. rows integer specifying number rows legend. Default 10.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"ggplot object representing domain architecture visualization web display.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"","code":"if (FALSE) { # \\dontrun{ plot <- plotIPR2VizWeb(infile_ipr = \"path/to/ipr_file.tsv\",                        accessions = c(\"ACC123\", \"ACC456\"),                        analysis = c(\"Pfam\", \"TMHMM\"),                        group_by = \"Analysis\",                        name = \"Gene Name\",                        text_size = 15,                        legend_name = \"ShortName\",                        cols = 5,                        rows = 10) plot } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"Lineage plot Domains, Domain Architectures Genomic Contexts. Heatmap.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"","code":"plotLineageDA(   query_data = \"prot\",   colname = \"DomArch\",   cutoff = 90,   RowsCutoff = FALSE,   color = \"default\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default prot (variable w/ protein data). colname Column name query_data: \"DomArch.norep\", \"GenContext.norep\", \"DomArch.PFAM.norep\" \"DomArch.LADB.norep\". Default \"DomArch.norep\". cutoff Numeric. Cutoff word frequency. Default 90. RowsCutoff Boolean. TRUE, applies row cutoff remove data rows based certain condition. Default FALSE. color Color heatmap. One six options: \"default\", \"magma\", \"inferno\", \"plasma\", \"viridis\", \"cividis\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"LineageDA plot object.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageDA(toast_rack_data, 10, \"DomArch.norep\", \"da2doms\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"Lineage Domain Repeats Plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"","code":"plotLineageDomainRepeats(query_data, colname)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"query_data Data frame containing protein homolog data, including relevant domain architectures lineages. colname Character. name column query_data contains domain architectures structural information.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"ggplot object representing heatmap (tile plot) domain repeat counts across different lineages, color intensity representing occurrence domains.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageDomainRepeats() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"plotLineageHeatmap — plotLineageHeatmap","title":"plotLineageHeatmap — plotLineageHeatmap","text":"Generate lineage plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotLineageHeatmap — plotLineageHeatmap","text":"","code":"plotLineageHeatmap(prot, domains_of_interest, level = 3, label.size = 8)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotLineageHeatmap — plotLineageHeatmap","text":"prot Data frame containing DomArch Lineage Columns domains_of_interest Vector domains check presence lineages level max depth Lineage. ie) = Kingdom, 2 = Phylum, 3 = class ... label.size Size text labels","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotLineageHeatmap — plotLineageHeatmap","text":"ggplot object representing heatmap (tile plot) domain repeat counts across different lineages, color intensity representing occurrence domains.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"plotLineageHeatmap — plotLineageHeatmap","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotLineageHeatmap — plotLineageHeatmap","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageHeatmap(psp_data,     c(         \"PspA\", \"Snf7\", \"Classical-AAA\", \"PspF\", \"PspB\", \"PspC\", \"ClgR\", \"PspM\",         \"Thioredoxin\", \"PspN_N\", \"DUF3046\", \"LiaI-LiaF-TM\", \"Toast_rack\", \"REC\",         \"HISKIN\", \"HAAS\", \"SHOCT-bihelical\", \"SHOCT-like\", \"Tfu_1009\", \"PspAA\",         \"Spermine_synth\", \"TM-Flotillin\", \"Band-7\", \"Betapropeller\",         \"MacB_PCD\", \"FTSW_RODA_SPOVE\", \"Cest_Tir\", \"SIGMA-HTH\", \"GNTR-HTH\",         \"DUF2089-HTH\", \"PadR-HTH\", \"RHH\", \"ZnR\"     ),     level = 2 ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Plot for top neighbors — plotLineageNeighbors","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"Lineage plot top neighbors obtained DAs Genomic Contexts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"","code":"plotLineageNeighbors(   query_data = \"prot\",   query = \"pspa\",   colname = \"GenContext.norep\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default pspa_data. query Name query protein/domain. Default \"pspa\". colname Column name query_data. Default \"GenContext.norep\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"ggplot object representing heatmap (tile plot) lineage versus top neighboring domain architectures, color intensity representing frequency occurrences.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageNeighbors(pspa_data, pspa, \"GenContext.norep\", \"da2doms\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"Lineage plot queries. Heatmap.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"","code":"plotLineageQuery(   query_data = all,   queries,   colname = \"ClustName\",   cutoff,   color = \"default\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default prot (variable w/ protein data). queries Character Vector containing queries used categories. colname Character. column used filtering based queries. Default \"ClustName\". cutoff Numeric. cutoff value filtering rows based total count. Rows values cutoff excluded. color Character. Defines color palette used heatmap. Default red gradient.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"ggplot object representing heatmap (tile plot) showing relationship queries lineages, intensity color representing count matching records.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"Janani Ravi, Samuel Chen","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageQuery(prot, c(\"PspA\", \"PspB\", \"PspC\", \"PspM\", \"PspN\"), 95) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Sunburst — plotLineageSunburst","title":"Lineage Sunburst — plotLineageSunburst","text":"Lineage Sunburst","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Sunburst — plotLineageSunburst","text":"","code":"plotLineageSunburst(   prot,   lineage_column = \"Lineage\",   type = \"sunburst\",   levels = 2,   colors = NULL,   legendOrder = NULL,   showLegend = TRUE,   maxLevels = 5 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Sunburst — plotLineageSunburst","text":"prot Data frame containing lineage column sunburst plot generated lineage_column String. Name lineage column within data frame. Defaults \"Lineage\" type String, either \"sunburst\" \"sund2b\". type \"sunburst\", sunburst plot lineage levels Integer. Number levels sunburst . colors vector colors sunburst plot. NULL, default colors used. legendOrder String vector. order legend. legendOrder NULL, showLegend Boolean. TRUE, legend enabled component first renders. maxLevels Integer, maximum number levels display sunburst; 5 default, NULL disable legend descending order top level hierarchy. rendered. type sund2b, sund2b plot rendered.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Sunburst — plotLineageSunburst","text":"sunburst sund2b plot based input lineage data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Sunburst — plotLineageSunburst","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageSunburst(prot, lineage_column = \"Lineage\", type = \"sunburst\", levels = 3) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Stacked Lineage Plot — plotStackedLineage","title":"Stacked Lineage Plot — plotStackedLineage","text":"Stacked Lineage Plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stacked Lineage Plot — plotStackedLineage","text":"","code":"plotStackedLineage(   prot,   column = \"DomArch\",   cutoff,   Lineage_col = \"Lineage\",   xlabel = \"Domain Architecture\",   reduce_lineage = TRUE,   label.size = 8,   legend.position = c(0.7, 0.4),   legend.text.size = 10,   legend.cols = 2,   legend.size = 0.7,   coord_flip = TRUE,   legend = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stacked Lineage Plot — plotStackedLineage","text":"prot Data frame containing protein data including domain architecture lineage information. column Character. name column prot representing domain architectures (default \"DomArch\"). cutoff Numeric. threshold value filtering domain architectures protein counts. Lineage_col Character. name column representing lineage data (default \"Lineage\"). xlabel Character. Label x-axis (default \"Domain Architecture\"). reduce_lineage Logical. Whether shorten lineage names (default TRUE). label.size Numeric. size axis text labels (default 8). legend.position Numeric vector. Coordinates placing legend (default c(0.7, 0.4)). legend.text.size Numeric. Size text legend (default 10). legend.cols Numeric. Number columns legend (default 2). legend.size Numeric. Size legend keys (default 0.7). coord_flip Logical. Whether flip coordinates plot (default TRUE). legend Logical. Whether display legend (default TRUE).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stacked Lineage Plot — plotStackedLineage","text":"ggplot object representing stacked bar plot showing distribution protein domain architectures across lineages.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stacked Lineage Plot — plotStackedLineage","text":"","code":"if (FALSE) { # \\dontrun{ plotStackedLineage() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an interactive plotly from count data — plotSunburst","title":"Create an interactive plotly from count data — plotSunburst","text":"functions help quickly create interactive hierarchical plots categorical data. expect summary data created dplyr::count() produce either sunburst plot (plotSunburst()) treemap plot (plotTreemap())","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an interactive plotly from count data — plotSunburst","text":"","code":"plotSunburst(count_data, fill_by_n = FALSE, sort_by_n = FALSE, maxdepth = 2)  plotTreemap(count_data, fill_by_n = FALSE, sort_by_n = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an interactive plotly from count data — plotSunburst","text":"count_data data frame containing data. fill_by_n Logical indicating fill color based counts. sort_by_n Logical indicating data sorted counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an interactive plotly from count data — plotSunburst","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union starwars_count <- count(starwars, species, eye_color, name)  # sunburst plot plotSunburst(starwars_count)  {\"x\":{\"visdat\":{\"17c354a6b442\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"17c354a6b442\",\"attrs\":{\"17c354a6b442\":{\"ids\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.white\",\"Aleena.->.unknown.->.Ratts Tyerel\",\"Besalisk.->.yellow.->.Dexter Jettster\",\"Cerean.->.yellow.->.Ki-Adi-Mundi\",\"Chagrian.->.blue.->.Mas Amedda\",\"Clawdite.->.yellow.->.Zam Wesell\",\"Droid.->.black.->.BB8\",\"Droid.->.red.->.IG-88\",\"Droid.->.red.->.R2-D2\",\"Droid.->.red.->.R5-D4\",\"Droid.->.red, blue.->.R4-P17\",\"Droid.->.yellow.->.C-3PO\",\"Dug.->.orange.->.Sebulba\",\"Ewok.->.brown.->.Wicket Systri Warrick\",\"Geonosian.->.yellow.->.Poggle the Lesser\",\"Gungan.->.orange.->.Jar Jar Binks\",\"Gungan.->.orange.->.Roos Tarpals\",\"Gungan.->.orange.->.Rugor Nass\",\"Human.->.blue.->.Anakin Skywalker\",\"Human.->.blue.->.Beru Whitesun Lars\",\"Human.->.blue.->.Cliegg Lars\",\"Human.->.blue.->.Finis Valorum\",\"Human.->.blue.->.Jocasta Nu\",\"Human.->.blue.->.Lobot\",\"Human.->.blue.->.Luke Skywalker\",\"Human.->.blue.->.Mon Mothma\",\"Human.->.blue.->.Owen Lars\",\"Human.->.blue.->.Qui-Gon Jinn\",\"Human.->.blue.->.Ric Olié\",\"Human.->.blue.->.Wilhuff Tarkin\",\"Human.->.blue-gray.->.Obi-Wan Kenobi\",\"Human.->.brown.->.Arvel Crynyd\",\"Human.->.brown.->.Bail Prestor Organa\",\"Human.->.brown.->.Biggs Darklighter\",\"Human.->.brown.->.Boba Fett\",\"Human.->.brown.->.Dooku\",\"Human.->.brown.->.Dormé\",\"Human.->.brown.->.Han Solo\",\"Human.->.brown.->.Jango Fett\",\"Human.->.brown.->.Lando Calrissian\",\"Human.->.brown.->.Leia Organa\",\"Human.->.brown.->.Mace Windu\",\"Human.->.brown.->.Padmé Amidala\",\"Human.->.brown.->.Poe Dameron\",\"Human.->.brown.->.Quarsh Panaka\",\"Human.->.brown.->.Raymus Antilles\",\"Human.->.brown.->.Shmi Skywalker\",\"Human.->.dark.->.Finn\",\"Human.->.hazel.->.Rey\",\"Human.->.hazel.->.Wedge Antilles\",\"Human.->.unknown.->.Captain Phasma\",\"Human.->.yellow.->.Darth Vader\",\"Human.->.yellow.->.Palpatine\",\"Hutt.->.orange.->.Jabba Desilijic Tiure\",\"Iktotchi.->.orange.->.Saesee Tiin\",\"Kaleesh.->.green, yellow.->.Grievous\",\"Kaminoan.->.black.->.Lama Su\",\"Kaminoan.->.black.->.Taun We\",\"Kel Dor.->.black.->.Plo Koon\",\"Mirialan.->.blue.->.Barriss Offee\",\"Mirialan.->.blue.->.Luminara Unduli\",\"Mon Calamari.->.orange.->.Ackbar\",\"Muun.->.gold.->.San Hill\",\"Nautolan.->.black.->.Kit Fisto\",\"Neimodian.->.red.->.Nute Gunray\",\"Pau'an.->.black.->.Tion Medon\",\"Quermian.->.yellow.->.Yarael Poof\",\"Rodian.->.black.->.Greedo\",\"Skakoan.->.unknown.->.Wat Tambor\",\"Sullustan.->.black.->.Nien Nunb\",\"Tholothian.->.blue.->.Adi Gallia\",\"Togruta.->.black.->.Shaak 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Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.brown\",\"NA.->.white\"],\"labels\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon 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/>value: white<br />n: 1\",\"column: name<br />value: Ratts Tyerel<br />n: 1\",\"column: name<br />value: Dexter Jettster<br />n: 1\",\"column: name<br />value: Ki-Adi-Mundi<br />n: 1\",\"column: name<br />value: Mas Amedda<br />n: 1\",\"column: name<br />value: Zam Wesell<br />n: 1\",\"column: name<br />value: BB8<br />n: 1\",\"column: name<br />value: IG-88<br />n: 1\",\"column: name<br />value: R2-D2<br />n: 1\",\"column: name<br />value: R5-D4<br />n: 1\",\"column: name<br />value: R4-P17<br />n: 1\",\"column: name<br />value: C-3PO<br />n: 1\",\"column: name<br />value: Sebulba<br />n: 1\",\"column: name<br />value: Wicket Systri Warrick<br />n: 1\",\"column: name<br />value: Poggle the Lesser<br />n: 1\",\"column: name<br />value: Jar Jar Binks<br />n: 1\",\"column: name<br />value: Roos Tarpals<br />n: 1\",\"column: name<br />value: Rugor Nass<br />n: 1\",\"column: name<br />value: Anakin Skywalker<br />n: 1\",\"column: name<br />value: Beru Whitesun Lars<br />n: 1\",\"column: name<br />value: Cliegg Lars<br />n: 1\",\"column: name<br />value: Finis Valorum<br />n: 1\",\"column: name<br />value: Jocasta Nu<br />n: 1\",\"column: name<br />value: Lobot<br />n: 1\",\"column: name<br />value: Luke Skywalker<br />n: 1\",\"column: name<br />value: Mon Mothma<br />n: 1\",\"column: name<br />value: Owen Lars<br />n: 1\",\"column: name<br />value: Qui-Gon Jinn<br />n: 1\",\"column: name<br />value: Ric Olié<br />n: 1\",\"column: name<br />value: Wilhuff Tarkin<br />n: 1\",\"column: name<br />value: Obi-Wan Kenobi<br />n: 1\",\"column: name<br />value: Arvel Crynyd<br />n: 1\",\"column: name<br />value: Bail Prestor Organa<br />n: 1\",\"column: name<br />value: Biggs Darklighter<br />n: 1\",\"column: name<br />value: Boba Fett<br />n: 1\",\"column: name<br />value: Dooku<br />n: 1\",\"column: name<br />value: Dormé<br />n: 1\",\"column: name<br />value: Han Solo<br />n: 1\",\"column: name<br />value: Jango Fett<br />n: 1\",\"column: name<br />value: Lando Calrissian<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: Tarfful<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\"],\"sort\":false,\"branchvalues\":\"total\",\"type\":\"sunburst\",\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]} # fill by group size plotSunburst(starwars_count, fill_by_n = TRUE)  {\"x\":{\"visdat\":{\"17c3788e5bf2\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"17c3788e5bf2\",\"attrs\":{\"17c3788e5bf2\":{\"ids\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.white\",\"Aleena.->.unknown.->.Ratts Tyerel\",\"Besalisk.->.yellow.->.Dexter Jettster\",\"Cerean.->.yellow.->.Ki-Adi-Mundi\",\"Chagrian.->.blue.->.Mas Amedda\",\"Clawdite.->.yellow.->.Zam Wesell\",\"Droid.->.black.->.BB8\",\"Droid.->.red.->.IG-88\",\"Droid.->.red.->.R2-D2\",\"Droid.->.red.->.R5-D4\",\"Droid.->.red, blue.->.R4-P17\",\"Droid.->.yellow.->.C-3PO\",\"Dug.->.orange.->.Sebulba\",\"Ewok.->.brown.->.Wicket Systri Warrick\",\"Geonosian.->.yellow.->.Poggle the Lesser\",\"Gungan.->.orange.->.Jar Jar Binks\",\"Gungan.->.orange.->.Roos Tarpals\",\"Gungan.->.orange.->.Rugor Nass\",\"Human.->.blue.->.Anakin Skywalker\",\"Human.->.blue.->.Beru Whitesun Lars\",\"Human.->.blue.->.Cliegg Lars\",\"Human.->.blue.->.Finis Valorum\",\"Human.->.blue.->.Jocasta Nu\",\"Human.->.blue.->.Lobot\",\"Human.->.blue.->.Luke Skywalker\",\"Human.->.blue.->.Mon Mothma\",\"Human.->.blue.->.Owen Lars\",\"Human.->.blue.->.Qui-Gon Jinn\",\"Human.->.blue.->.Ric Olié\",\"Human.->.blue.->.Wilhuff Tarkin\",\"Human.->.blue-gray.->.Obi-Wan Kenobi\",\"Human.->.brown.->.Arvel Crynyd\",\"Human.->.brown.->.Bail Prestor Organa\",\"Human.->.brown.->.Biggs Darklighter\",\"Human.->.brown.->.Boba Fett\",\"Human.->.brown.->.Dooku\",\"Human.->.brown.->.Dormé\",\"Human.->.brown.->.Han Solo\",\"Human.->.brown.->.Jango Fett\",\"Human.->.brown.->.Lando Calrissian\",\"Human.->.brown.->.Leia Organa\",\"Human.->.brown.->.Mace Windu\",\"Human.->.brown.->.Padmé Amidala\",\"Human.->.brown.->.Poe Dameron\",\"Human.->.brown.->.Quarsh Panaka\",\"Human.->.brown.->.Raymus Antilles\",\"Human.->.brown.->.Shmi Skywalker\",\"Human.->.dark.->.Finn\",\"Human.->.hazel.->.Rey\",\"Human.->.hazel.->.Wedge Antilles\",\"Human.->.unknown.->.Captain Phasma\",\"Human.->.yellow.->.Darth Vader\",\"Human.->.yellow.->.Palpatine\",\"Hutt.->.orange.->.Jabba Desilijic Tiure\",\"Iktotchi.->.orange.->.Saesee Tiin\",\"Kaleesh.->.green, yellow.->.Grievous\",\"Kaminoan.->.black.->.Lama Su\",\"Kaminoan.->.black.->.Taun We\",\"Kel Dor.->.black.->.Plo Koon\",\"Mirialan.->.blue.->.Barriss Offee\",\"Mirialan.->.blue.->.Luminara Unduli\",\"Mon Calamari.->.orange.->.Ackbar\",\"Muun.->.gold.->.San Hill\",\"Nautolan.->.black.->.Kit Fisto\",\"Neimodian.->.red.->.Nute Gunray\",\"Pau'an.->.black.->.Tion Medon\",\"Quermian.->.yellow.->.Yarael Poof\",\"Rodian.->.black.->.Greedo\",\"Skakoan.->.unknown.->.Wat Tambor\",\"Sullustan.->.black.->.Nien Nunb\",\"Tholothian.->.blue.->.Adi Gallia\",\"Togruta.->.black.->.Shaak Ti\",\"Toong.->.orange.->.Ben Quadinaros\",\"Toydarian.->.yellow.->.Watto\",\"Trandoshan.->.red.->.Bossk\",\"Twi'lek.->.hazel.->.Ayla Secura\",\"Twi'lek.->.pink.->.Bib Fortuna\",\"Vulptereen.->.yellow.->.Dud Bolt\",\"Wookiee.->.blue.->.Chewbacca\",\"Wookiee.->.blue.->.Tarfful\",\"Xexto.->.black.->.Gasgano\",\"Yoda's species.->.brown.->.Yoda\",\"Zabrak.->.brown.->.Eeth Koth\",\"Zabrak.->.yellow.->.Darth Maul\",\"NA.->.blue.->.Jek Tono Porkins\",\"NA.->.brown.->.Cordé\",\"NA.->.brown.->.Gregar Typho\",\"NA.->.white.->.Sly Moore\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Droid\",\"Droid\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"Zabrak\",\"NA\",\"NA\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.brown\",\"NA.->.white\"],\"labels\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",null,\"unknown\",\"yellow\",\"yellow\",\"blue\",\"yellow\",\"black\",\"red\",\"red, blue\",\"yellow\",\"orange\",\"brown\",\"yellow\",\"orange\",\"blue\",\"blue-gray\",\"brown\",\"dark\",\"hazel\",\"unknown\",\"yellow\",\"orange\",\"orange\",\"green, yellow\",\"black\",\"black\",\"blue\",\"orange\",\"gold\",\"black\",\"red\",\"black\",\"yellow\",\"black\",\"unknown\",\"black\",\"blue\",\"black\",\"orange\",\"yellow\",\"red\",\"hazel\",\"pink\",\"yellow\",\"blue\",\"black\",\"brown\",\"brown\",\"yellow\",\"blue\",\"brown\",\"white\",\"Ratts Tyerel\",\"Dexter Jettster\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Zam Wesell\",\"BB8\",\"IG-88\",\"R2-D2\",\"R5-D4\",\"R4-P17\",\"C-3PO\",\"Sebulba\",\"Wicket Systri Warrick\",\"Poggle the Lesser\",\"Jar Jar Binks\",\"Roos Tarpals\",\"Rugor Nass\",\"Anakin Skywalker\",\"Beru Whitesun Lars\",\"Cliegg Lars\",\"Finis Valorum\",\"Jocasta Nu\",\"Lobot\",\"Luke Skywalker\",\"Mon Mothma\",\"Owen Lars\",\"Qui-Gon Jinn\",\"Ric Olié\",\"Wilhuff Tarkin\",\"Obi-Wan Kenobi\",\"Arvel Crynyd\",\"Bail Prestor Organa\",\"Biggs Darklighter\",\"Boba Fett\",\"Dooku\",\"Dormé\",\"Han Solo\",\"Jango Fett\",\"Lando Calrissian\",\"Leia Organa\",\"Mace Windu\",\"Padmé Amidala\",\"Poe Dameron\",\"Quarsh Panaka\",\"Raymus Antilles\",\"Shmi Skywalker\",\"Finn\",\"Rey\",\"Wedge Antilles\",\"Captain Phasma\",\"Darth Vader\",\"Palpatine\",\"Jabba Desilijic Tiure\",\"Saesee Tiin\",\"Grievous\",\"Lama Su\",\"Taun We\",\"Plo Koon\",\"Barriss Offee\",\"Luminara Unduli\",\"Ackbar\",\"San Hill\",\"Kit Fisto\",\"Nute Gunray\",\"Tion Medon\",\"Yarael Poof\",\"Greedo\",\"Wat Tambor\",\"Nien Nunb\",\"Adi Gallia\",\"Shaak Ti\",\"Ben Quadinaros\",\"Watto\",\"Bossk\",\"Ayla Secura\",\"Bib Fortuna\",\"Dud Bolt\",\"Chewbacca\",\"Tarfful\",\"Gasgano\",\"Yoda\",\"Eeth Koth\",\"Darth Maul\",\"Jek Tono Porkins\",\"Cordé\",\"Gregar Typho\",\"Sly Moore\"],\"values\":[1,1,1,1,1,6,1,1,1,3,35,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,2,4,1,1,1,1,1,1,3,1,1,1,1,1,3,12,1,16,1,2,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],\"hovertext\":[\"column: species<br />value: Aleena<br />n: 1\",\"column: species<br />value: Besalisk<br />n: 1\",\"column: species<br />value: Cerean<br />n: 1\",\"column: species<br />value: Chagrian<br />n: 1\",\"column: species<br />value: Clawdite<br />n: 1\",\"column: species<br />value: Droid<br />n: 6\",\"column: species<br />value: Dug<br />n: 1\",\"column: species<br />value: Ewok<br />n: 1\",\"column: species<br />value: Geonosian<br />n: 1\",\"column: species<br 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Ti\",\"Toong.->.orange.->.Ben Quadinaros\",\"Toydarian.->.yellow.->.Watto\",\"Trandoshan.->.red.->.Bossk\",\"Twi'lek.->.hazel.->.Ayla Secura\",\"Twi'lek.->.pink.->.Bib Fortuna\",\"Vulptereen.->.yellow.->.Dud Bolt\",\"Wookiee.->.blue.->.Chewbacca\",\"Wookiee.->.blue.->.Tarfful\",\"Xexto.->.black.->.Gasgano\",\"Yoda's species.->.brown.->.Yoda\",\"Zabrak.->.brown.->.Eeth Koth\",\"Zabrak.->.yellow.->.Darth Maul\",\"NA.->.blue.->.Jek Tono Porkins\",\"NA.->.brown.->.Cordé\",\"NA.->.brown.->.Gregar Typho\",\"NA.->.white.->.Sly Moore\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Droid\",\"Droid\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"Zabrak\",\"NA\",\"NA\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.brown\",\"NA.->.white\"],\"labels\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",null,\"unknown\",\"yellow\",\"yellow\",\"blue\",\"yellow\",\"black\",\"red\",\"red, blue\",\"yellow\",\"orange\",\"brown\",\"yellow\",\"orange\",\"blue\",\"blue-gray\",\"brown\",\"dark\",\"hazel\",\"unknown\",\"yellow\",\"orange\",\"orange\",\"green, yellow\",\"black\",\"black\",\"blue\",\"orange\",\"gold\",\"black\",\"red\",\"black\",\"yellow\",\"black\",\"unknown\",\"black\",\"blue\",\"black\",\"orange\",\"yellow\",\"red\",\"hazel\",\"pink\",\"yellow\",\"blue\",\"black\",\"brown\",\"brown\",\"yellow\",\"blue\",\"brown\",\"white\",\"Ratts Tyerel\",\"Dexter Jettster\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Zam Wesell\",\"BB8\",\"IG-88\",\"R2-D2\",\"R5-D4\",\"R4-P17\",\"C-3PO\",\"Sebulba\",\"Wicket Systri Warrick\",\"Poggle the Lesser\",\"Jar Jar Binks\",\"Roos Tarpals\",\"Rugor Nass\",\"Anakin Skywalker\",\"Beru Whitesun Lars\",\"Cliegg Lars\",\"Finis Valorum\",\"Jocasta Nu\",\"Lobot\",\"Luke Skywalker\",\"Mon Mothma\",\"Owen Lars\",\"Qui-Gon Jinn\",\"Ric Olié\",\"Wilhuff Tarkin\",\"Obi-Wan Kenobi\",\"Arvel Crynyd\",\"Bail Prestor Organa\",\"Biggs Darklighter\",\"Boba Fett\",\"Dooku\",\"Dormé\",\"Han Solo\",\"Jango Fett\",\"Lando Calrissian\",\"Leia Organa\",\"Mace Windu\",\"Padmé Amidala\",\"Poe Dameron\",\"Quarsh Panaka\",\"Raymus Antilles\",\"Shmi Skywalker\",\"Finn\",\"Rey\",\"Wedge Antilles\",\"Captain Phasma\",\"Darth Vader\",\"Palpatine\",\"Jabba Desilijic Tiure\",\"Saesee Tiin\",\"Grievous\",\"Lama Su\",\"Taun We\",\"Plo Koon\",\"Barriss Offee\",\"Luminara Unduli\",\"Ackbar\",\"San Hill\",\"Kit Fisto\",\"Nute Gunray\",\"Tion Medon\",\"Yarael Poof\",\"Greedo\",\"Wat Tambor\",\"Nien Nunb\",\"Adi Gallia\",\"Shaak Ti\",\"Ben Quadinaros\",\"Watto\",\"Bossk\",\"Ayla Secura\",\"Bib Fortuna\",\"Dud Bolt\",\"Chewbacca\",\"Tarfful\",\"Gasgano\",\"Yoda\",\"Eeth Koth\",\"Darth Maul\",\"Jek Tono Porkins\",\"Cordé\",\"Gregar Typho\",\"Sly Moore\"],\"values\":[1,1,1,1,1,6,1,1,1,3,35,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,2,4,1,1,1,1,1,1,3,1,1,1,1,1,3,12,1,16,1,2,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],\"hovertext\":[\"column: species<br />value: Aleena<br />n: 1\",\"column: species<br />value: Besalisk<br />n: 1\",\"column: species<br />value: Cerean<br />n: 1\",\"column: species<br />value: Chagrian<br />n: 1\",\"column: species<br />value: Clawdite<br />n: 1\",\"column: species<br />value: Droid<br />n: 6\",\"column: species<br />value: Dug<br />n: 1\",\"column: species<br />value: Ewok<br />n: 1\",\"column: species<br />value: Geonosian<br />n: 1\",\"column: species<br />value: Gungan<br />n: 3\",\"column: species<br />value: Human<br />n: 35\",\"column: species<br />value: Hutt<br />n: 1\",\"column: species<br />value: Iktotchi<br />n: 1\",\"column: species<br />value: Kaleesh<br />n: 1\",\"column: species<br />value: Kaminoan<br />n: 2\",\"column: species<br />value: Kel Dor<br />n: 1\",\"column: species<br />value: Mirialan<br />n: 2\",\"column: species<br />value: Mon Calamari<br />n: 1\",\"column: species<br />value: Muun<br />n: 1\",\"column: species<br />value: Nautolan<br />n: 1\",\"column: species<br />value: Neimodian<br />n: 1\",\"column: species<br />value: Pau'an<br />n: 1\",\"column: species<br />value: Quermian<br />n: 1\",\"column: species<br />value: Rodian<br />n: 1\",\"column: species<br />value: Skakoan<br />n: 1\",\"column: species<br />value: Sullustan<br />n: 1\",\"column: species<br />value: Tholothian<br />n: 1\",\"column: species<br />value: Togruta<br />n: 1\",\"column: species<br />value: Toong<br />n: 1\",\"column: species<br />value: Toydarian<br />n: 1\",\"column: species<br />value: Trandoshan<br />n: 1\",\"column: species<br />value: Twi'lek<br />n: 2\",\"column: species<br />value: Vulptereen<br />n: 1\",\"column: species<br />value: Wookiee<br />n: 2\",\"column: species<br />value: Xexto<br />n: 1\",\"column: species<br />value: Yoda's species<br />n: 1\",\"column: species<br />value: Zabrak<br />n: 2\",\"column: species<br />value: NA<br />n: 4\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 3\",\"column: eye_color<br />value: red, blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 3\",\"column: eye_color<br />value: blue<br />n: 12\",\"column: eye_color<br />value: blue-gray<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 16\",\"column: eye_color<br />value: dark<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 2\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: green, yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: gold<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 1\",\"column: eye_color<br />value: pink<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 2\",\"column: eye_color<br />value: white<br />n: 1\",\"column: name<br />value: Ratts Tyerel<br />n: 1\",\"column: name<br />value: Dexter Jettster<br />n: 1\",\"column: name<br />value: Ki-Adi-Mundi<br />n: 1\",\"column: name<br />value: Mas Amedda<br />n: 1\",\"column: name<br />value: Zam Wesell<br />n: 1\",\"column: name<br />value: BB8<br />n: 1\",\"column: name<br />value: IG-88<br />n: 1\",\"column: name<br />value: R2-D2<br />n: 1\",\"column: name<br />value: R5-D4<br />n: 1\",\"column: name<br />value: R4-P17<br />n: 1\",\"column: name<br />value: C-3PO<br />n: 1\",\"column: name<br />value: Sebulba<br />n: 1\",\"column: name<br />value: Wicket Systri Warrick<br />n: 1\",\"column: name<br />value: Poggle the Lesser<br />n: 1\",\"column: name<br />value: Jar Jar Binks<br />n: 1\",\"column: name<br />value: Roos Tarpals<br />n: 1\",\"column: name<br />value: Rugor Nass<br />n: 1\",\"column: name<br />value: Anakin Skywalker<br />n: 1\",\"column: name<br />value: Beru Whitesun Lars<br />n: 1\",\"column: name<br />value: Cliegg Lars<br />n: 1\",\"column: name<br />value: Finis Valorum<br />n: 1\",\"column: name<br />value: Jocasta Nu<br />n: 1\",\"column: name<br />value: Lobot<br />n: 1\",\"column: name<br />value: Luke Skywalker<br />n: 1\",\"column: name<br />value: Mon Mothma<br />n: 1\",\"column: name<br />value: Owen Lars<br />n: 1\",\"column: name<br />value: Qui-Gon Jinn<br />n: 1\",\"column: name<br />value: Ric Olié<br />n: 1\",\"column: name<br />value: Wilhuff Tarkin<br />n: 1\",\"column: name<br />value: Obi-Wan Kenobi<br />n: 1\",\"column: name<br />value: Arvel Crynyd<br />n: 1\",\"column: name<br />value: Bail Prestor Organa<br />n: 1\",\"column: name<br />value: Biggs Darklighter<br />n: 1\",\"column: name<br />value: Boba Fett<br />n: 1\",\"column: name<br />value: Dooku<br />n: 1\",\"column: name<br />value: Dormé<br />n: 1\",\"column: name<br />value: Han Solo<br />n: 1\",\"column: name<br />value: Jango Fett<br />n: 1\",\"column: name<br />value: Lando Calrissian<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: Tarfful<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\"],\"sort\":false,\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"colorbar\":{\"bgcolor\":\"\"},\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"branchvalues\":\"total\",\"type\":\"sunburst\",\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]} # treemap plot, ordered by group size plotTreemap(starwars_count, sort_by_n = TRUE)  {\"x\":{\"visdat\":{\"17c379a8763b\":[\"function () 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Calrissian<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: Tarfful<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\"],\"sort\":true,\"branchvalues\":\"total\",\"hoverinfo\":[\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\"],\"type\":\"treemap\",\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]} # display al charchaters by homeworld starwars %>%     count(homeworld, name) %>%     plotTreemap(sort_by_n = TRUE)  {\"x\":{\"visdat\":{\"17c31a44ea90\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"17c31a44ea90\",\"attrs\":{\"17c31a44ea90\":{\"ids\":[\"Alderaan\",\"Aleen Minor\",\"Bespin\",\"Bestine IV\",\"Cato Neimoidia\",\"Cerea\",\"Champala\",\"Chandrila\",\"Concord Dawn\",\"Corellia\",\"Coruscant\",\"Dathomir\",\"Dorin\",\"Endor\",\"Eriadu\",\"Geonosis\",\"Glee Anselm\",\"Haruun Kal\",\"Iktotch\",\"Iridonia\",\"Kalee\",\"Kamino\",\"Kashyyyk\",\"Malastare\",\"Mirial\",\"Mon Cala\",\"Muunilinst\",\"Naboo\",\"Nal Hutta\",\"Ojom\",\"Quermia\",\"Rodia\",\"Ryloth\",\"Serenno\",\"Shili\",\"Skako\",\"Socorro\",\"Stewjon\",\"Sullust\",\"Tatooine\",\"Toydaria\",\"Trandosha\",\"Troiken\",\"Tund\",\"Umbara\",\"Utapau\",\"Vulpter\",\"Zolan\",\"NA\",\"Alderaan.->.Bail Prestor Organa\",\"Alderaan.->.Leia Organa\",\"Alderaan.->.Raymus Antilles\",\"Aleen Minor.->.Ratts Tyerel\",\"Bespin.->.Lobot\",\"Bestine IV.->.Jek Tono Porkins\",\"Cato Neimoidia.->.Nute Gunray\",\"Cerea.->.Ki-Adi-Mundi\",\"Champala.->.Mas Amedda\",\"Chandrila.->.Mon Mothma\",\"Concord Dawn.->.Jango Fett\",\"Corellia.->.Han Solo\",\"Corellia.->.Wedge Antilles\",\"Coruscant.->.Adi Gallia\",\"Coruscant.->.Finis Valorum\",\"Coruscant.->.Jocasta Nu\",\"Dathomir.->.Darth Maul\",\"Dorin.->.Plo Koon\",\"Endor.->.Wicket Systri Warrick\",\"Eriadu.->.Wilhuff Tarkin\",\"Geonosis.->.Poggle the Lesser\",\"Glee Anselm.->.Kit Fisto\",\"Haruun Kal.->.Mace Windu\",\"Iktotch.->.Saesee Tiin\",\"Iridonia.->.Eeth Koth\",\"Kalee.->.Grievous\",\"Kamino.->.Boba Fett\",\"Kamino.->.Lama Su\",\"Kamino.->.Taun We\",\"Kashyyyk.->.Chewbacca\",\"Kashyyyk.->.Tarfful\",\"Malastare.->.Sebulba\",\"Mirial.->.Barriss Offee\",\"Mirial.->.Luminara Unduli\",\"Mon Cala.->.Ackbar\",\"Muunilinst.->.San Hill\",\"Naboo.->.Cordé\",\"Naboo.->.Dormé\",\"Naboo.->.Gregar Typho\",\"Naboo.->.Jar Jar Binks\",\"Naboo.->.Padmé Amidala\",\"Naboo.->.Palpatine\",\"Naboo.->.Quarsh Panaka\",\"Naboo.->.R2-D2\",\"Naboo.->.Ric Olié\",\"Naboo.->.Roos Tarpals\",\"Naboo.->.Rugor Nass\",\"Nal Hutta.->.Jabba Desilijic Tiure\",\"Ojom.->.Dexter Jettster\",\"Quermia.->.Yarael Poof\",\"Rodia.->.Greedo\",\"Ryloth.->.Ayla Secura\",\"Ryloth.->.Bib Fortuna\",\"Serenno.->.Dooku\",\"Shili.->.Shaak Ti\",\"Skako.->.Wat Tambor\",\"Socorro.->.Lando Calrissian\",\"Stewjon.->.Obi-Wan Kenobi\",\"Sullust.->.Nien Nunb\",\"Tatooine.->.Anakin Skywalker\",\"Tatooine.->.Beru Whitesun Lars\",\"Tatooine.->.Biggs Darklighter\",\"Tatooine.->.C-3PO\",\"Tatooine.->.Cliegg Lars\",\"Tatooine.->.Darth Vader\",\"Tatooine.->.Luke Skywalker\",\"Tatooine.->.Owen Lars\",\"Tatooine.->.R5-D4\",\"Tatooine.->.Shmi Skywalker\",\"Toydaria.->.Watto\",\"Trandosha.->.Bossk\",\"Troiken.->.Gasgano\",\"Tund.->.Ben Quadinaros\",\"Umbara.->.Sly Moore\",\"Utapau.->.Tion Medon\",\"Vulpter.->.Dud Bolt\",\"Zolan.->.Zam Wesell\",\"NA.->.Arvel Crynyd\",\"NA.->.BB8\",\"NA.->.Captain Phasma\",\"NA.->.Finn\",\"NA.->.IG-88\",\"NA.->.Poe Dameron\",\"NA.->.Qui-Gon Jinn\",\"NA.->.R4-P17\",\"NA.->.Rey\",\"NA.->.Yoda\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Alderaan\",\"Alderaan\",\"Alderaan\",\"Aleen Minor\",\"Bespin\",\"Bestine IV\",\"Cato Neimoidia\",\"Cerea\",\"Champala\",\"Chandrila\",\"Concord Dawn\",\"Corellia\",\"Corellia\",\"Coruscant\",\"Coruscant\",\"Coruscant\",\"Dathomir\",\"Dorin\",\"Endor\",\"Eriadu\",\"Geonosis\",\"Glee Anselm\",\"Haruun Kal\",\"Iktotch\",\"Iridonia\",\"Kalee\",\"Kamino\",\"Kamino\",\"Kamino\",\"Kashyyyk\",\"Kashyyyk\",\"Malastare\",\"Mirial\",\"Mirial\",\"Mon Cala\",\"Muunilinst\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Nal Hutta\",\"Ojom\",\"Quermia\",\"Rodia\",\"Ryloth\",\"Ryloth\",\"Serenno\",\"Shili\",\"Skako\",\"Socorro\",\"Stewjon\",\"Sullust\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Toydaria\",\"Trandosha\",\"Troiken\",\"Tund\",\"Umbara\",\"Utapau\",\"Vulpter\",\"Zolan\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\"],\"labels\":[\"Alderaan\",\"Aleen Minor\",\"Bespin\",\"Bestine IV\",\"Cato Neimoidia\",\"Cerea\",\"Champala\",\"Chandrila\",\"Concord Dawn\",\"Corellia\",\"Coruscant\",\"Dathomir\",\"Dorin\",\"Endor\",\"Eriadu\",\"Geonosis\",\"Glee Anselm\",\"Haruun Kal\",\"Iktotch\",\"Iridonia\",\"Kalee\",\"Kamino\",\"Kashyyyk\",\"Malastare\",\"Mirial\",\"Mon Cala\",\"Muunilinst\",\"Naboo\",\"Nal Hutta\",\"Ojom\",\"Quermia\",\"Rodia\",\"Ryloth\",\"Serenno\",\"Shili\",\"Skako\",\"Socorro\",\"Stewjon\",\"Sullust\",\"Tatooine\",\"Toydaria\",\"Trandosha\",\"Troiken\",\"Tund\",\"Umbara\",\"Utapau\",\"Vulpter\",\"Zolan\",null,\"Bail Prestor Organa\",\"Leia Organa\",\"Raymus Antilles\",\"Ratts Tyerel\",\"Lobot\",\"Jek Tono Porkins\",\"Nute Gunray\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Mon Mothma\",\"Jango Fett\",\"Han Solo\",\"Wedge Antilles\",\"Adi Gallia\",\"Finis Valorum\",\"Jocasta Nu\",\"Darth Maul\",\"Plo Koon\",\"Wicket Systri Warrick\",\"Wilhuff Tarkin\",\"Poggle the Lesser\",\"Kit Fisto\",\"Mace Windu\",\"Saesee Tiin\",\"Eeth Koth\",\"Grievous\",\"Boba Fett\",\"Lama Su\",\"Taun We\",\"Chewbacca\",\"Tarfful\",\"Sebulba\",\"Barriss Offee\",\"Luminara Unduli\",\"Ackbar\",\"San Hill\",\"Cordé\",\"Dormé\",\"Gregar Typho\",\"Jar Jar Binks\",\"Padmé Amidala\",\"Palpatine\",\"Quarsh Panaka\",\"R2-D2\",\"Ric Olié\",\"Roos Tarpals\",\"Rugor Nass\",\"Jabba Desilijic Tiure\",\"Dexter Jettster\",\"Yarael Poof\",\"Greedo\",\"Ayla Secura\",\"Bib Fortuna\",\"Dooku\",\"Shaak Ti\",\"Wat Tambor\",\"Lando Calrissian\",\"Obi-Wan Kenobi\",\"Nien Nunb\",\"Anakin Skywalker\",\"Beru Whitesun Lars\",\"Biggs Darklighter\",\"C-3PO\",\"Cliegg Lars\",\"Darth Vader\",\"Luke Skywalker\",\"Owen Lars\",\"R5-D4\",\"Shmi Skywalker\",\"Watto\",\"Bossk\",\"Gasgano\",\"Ben Quadinaros\",\"Sly Moore\",\"Tion Medon\",\"Dud Bolt\",\"Zam Wesell\",\"Arvel Crynyd\",\"BB8\",\"Captain Phasma\",\"Finn\",\"IG-88\",\"Poe Dameron\",\"Qui-Gon Jinn\",\"R4-P17\",\"Rey\",\"Yoda\"],\"values\":[3,1,1,1,1,1,1,1,1,2,3,1,1,1,1,1,1,1,1,1,1,3,2,1,2,1,1,11,1,1,1,1,2,1,1,1,1,1,1,10,1,1,1,1,1,1,1,1,10,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],\"hovertext\":[\"column: homeworld<br />value: Alderaan<br />n: 3\",\"column: homeworld<br />value: Aleen Minor<br />n: 1\",\"column: homeworld<br />value: Bespin<br />n: 1\",\"column: homeworld<br />value: Bestine IV<br />n: 1\",\"column: homeworld<br />value: Cato Neimoidia<br />n: 1\",\"column: homeworld<br />value: Cerea<br />n: 1\",\"column: homeworld<br />value: Champala<br />n: 1\",\"column: homeworld<br />value: Chandrila<br />n: 1\",\"column: homeworld<br />value: Concord Dawn<br />n: 1\",\"column: homeworld<br />value: Corellia<br />n: 2\",\"column: homeworld<br />value: Coruscant<br />n: 3\",\"column: homeworld<br />value: Dathomir<br />n: 1\",\"column: homeworld<br />value: Dorin<br />n: 1\",\"column: homeworld<br />value: Endor<br />n: 1\",\"column: homeworld<br />value: Eriadu<br />n: 1\",\"column: homeworld<br />value: Geonosis<br />n: 1\",\"column: homeworld<br />value: Glee Anselm<br />n: 1\",\"column: homeworld<br />value: Haruun Kal<br />n: 1\",\"column: homeworld<br />value: Iktotch<br />n: 1\",\"column: homeworld<br />value: Iridonia<br />n: 1\",\"column: homeworld<br />value: Kalee<br />n: 1\",\"column: homeworld<br />value: Kamino<br />n: 3\",\"column: homeworld<br />value: Kashyyyk<br />n: 2\",\"column: homeworld<br />value: Malastare<br />n: 1\",\"column: homeworld<br />value: Mirial<br />n: 2\",\"column: homeworld<br />value: Mon Cala<br />n: 1\",\"column: homeworld<br />value: Muunilinst<br />n: 1\",\"column: homeworld<br />value: Naboo<br />n: 11\",\"column: homeworld<br />value: Nal Hutta<br />n: 1\",\"column: homeworld<br />value: Ojom<br />n: 1\",\"column: homeworld<br />value: Quermia<br />n: 1\",\"column: homeworld<br />value: Rodia<br />n: 1\",\"column: homeworld<br />value: Ryloth<br />n: 2\",\"column: homeworld<br />value: Serenno<br />n: 1\",\"column: homeworld<br />value: Shili<br />n: 1\",\"column: homeworld<br />value: Skako<br />n: 1\",\"column: homeworld<br />value: Socorro<br />n: 1\",\"column: homeworld<br />value: Stewjon<br />n: 1\",\"column: homeworld<br />value: Sullust<br />n: 1\",\"column: homeworld<br />value: Tatooine<br />n: 10\",\"column: homeworld<br />value: Toydaria<br />n: 1\",\"column: homeworld<br />value: Trandosha<br />n: 1\",\"column: homeworld<br />value: Troiken<br />n: 1\",\"column: homeworld<br />value: Tund<br />n: 1\",\"column: homeworld<br />value: Umbara<br />n: 1\",\"column: homeworld<br />value: Utapau<br />n: 1\",\"column: homeworld<br />value: Vulpter<br />n: 1\",\"column: homeworld<br />value: Zolan<br />n: 1\",\"column: homeworld<br />value: NA<br />n: 10\",\"column: name<br />value: Bail Prestor Organa<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Ratts Tyerel<br />n: 1\",\"column: name<br />value: Lobot<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Ki-Adi-Mundi<br />n: 1\",\"column: name<br />value: Mas Amedda<br />n: 1\",\"column: name<br />value: Mon Mothma<br />n: 1\",\"column: name<br />value: Jango Fett<br />n: 1\",\"column: name<br />value: Han Solo<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Finis Valorum<br />n: 1\",\"column: name<br />value: Jocasta Nu<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Wicket Systri Warrick<br />n: 1\",\"column: name<br />value: Wilhuff Tarkin<br />n: 1\",\"column: name<br />value: Poggle the Lesser<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Boba Fett<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: 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Plot — plotUpSet","title":"UpSet Plot — plotUpSet","text":"UpSet plot Domain Architectures vs Domains Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UpSet Plot — plotUpSet","text":"","code":"plotUpSet(   query_data = \"toast_rack.sub\",   colname = \"DomArch\",   cutoff = 90,   RowsCutoff = FALSE,   text.scale = 1.5,   point.size = 2.2,   line.size = 0.8 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UpSet Plot — plotUpSet","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default toast_rack.sub colname Column name query_data: \"DomArch.norep\", \"GenContext.norep\", \"DomArch.PFAM.norep\" \"DomArch.LADB.norep\". Default \"DomArch.norep\". cutoff Numeric. Cutoff word frequency. Default 90. RowsCutoff Boolean. TRUE, applies row cutoff remove data rows based certain condition. Default FALSE. text.scale Allows scaling axis title, tick lables, numbers intersection size bars. text.scale can either take universal scale form integer, vector specific scales format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers bars) point.size Numeric. Sets size points UpSet plot. Default 2.2. line.size Numeric. Sets line width UpSet plot. Default 0.8.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UpSet Plot — plotUpSet","text":"UpSet plot object. plot visualizes intersections sets based provided colname query_data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"UpSet Plot — plotUpSet","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"UpSet Plot — plotUpSet","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"UpSet Plot — plotUpSet","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UpSet Plot — plotUpSet","text":"","code":"if (FALSE) { # \\dontrun{ plotUpSet(pspa.sub, 10, \"da2doms\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":null,"dir":"Reference","previous_headings":"","what":"prepareColumnParams — prepareColumnParams","title":"prepareColumnParams — prepareColumnParams","text":"prepareColumnParams","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prepareColumnParams — prepareColumnParams","text":"","code":"prepareColumnParams(count_data, fill_by_n, sort_by_n)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prepareColumnParams — prepareColumnParams","text":"count_data data frame containing data. fill_by_n Logical indicating fill color based counts. sort_by_n Logical indicating data sorted counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"prepareColumnParams — prepareColumnParams","text":"data frame parameters treemap visualization.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prepareColumnParams — prepareColumnParams","text":"","code":"if (FALSE) { # \\dontrun{ count_data <- data.frame(Category = c(\"A\", \"B\", \"C\"),                           n = c(10, 20, 15)) params <- prepareColumnParams(count_data, fill_by_n = TRUE, sort_by_n = FALSE) params } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":null,"dir":"Reference","previous_headings":"","what":"prepareSingleColumnParams — prepareSingleColumnParams","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"prepareSingleColumnParams","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"","code":"prepareSingleColumnParams(df, col_num, root)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"df data frame containing data processed. col_num integer representing column number process. root string representing root node treemap.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"data frame containing parameters specified column treemap visualization.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"","code":"if (FALSE) { # \\dontrun{ df <- data.frame(Category = c(\"A\", \"A\", \"B\", \"B\", \"C\"),                  n = c(10, 20, 30, 40, 50)) params <- prepareSingleColumnParams(df, col_num = 1, root = \"Root\") params } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":null,"dir":"Reference","previous_headings":"","what":"proteinAcc2TaxID — proteinAcc2TaxID","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"proteinAcc2TaxID","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"","code":"proteinAcc2TaxID(accnums, suffix, out_path, return_dt = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"accnums character vector protein accession numbers mapped TaxIDs. suffix string suffix used name output file generated script. out_path string specifying directory output file saved. return_dt logical indicating whether return result data table. Defaults FALSE. TRUE, output file read data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"return_dt TRUE, data table containing mapping protein accession numbers TaxIDs. FALSE, function returns NULL.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"","code":"if (FALSE) { # \\dontrun{ # Example accession numbers accessions <- c(\"ABC123\", \"XYZ456\", \"LMN789\") tax_data <- proteinAcc2TaxID(accessions, suffix = \"example\", out_path = \"/path/to/output\", return_dt = TRUE) tax_data } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":null,"dir":"Reference","previous_headings":"","what":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"Perform elink go protein database taxonomy database write resulting file taxid lineage out_path","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"","code":"proteinAcc2TaxID_old(accessions, out_path, plan = \"multicore\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"accessions character vector containing accession numbers query protein database. out_path string specifying path results query written. set NULL, temporary directory used. plan character string specifies execution plan parallel processing. default \"multicore\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"function return value. writes results specified output path.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"","code":"if (FALSE) { # \\dontrun{ accessions <- c(\"ABC123\", \"XYZ456\", \"LMN789\") proteinAcc2TaxID_old(accessions, out_path = \"/path/to/output\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":null,"dir":"Reference","previous_headings":"","what":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"Read interproscan output TSV standardized column names types","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"","code":"readIPRScanTSV(filepath)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"filepath chr path interproscan output TSV","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"tbl_df interproscan output table","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove Asterisk — removeAsterisks","title":"Remove Asterisk — removeAsterisks","text":"Remove asterisks column data Used removing * GenContext columns","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove Asterisk — removeAsterisks","text":"","code":"removeAsterisks(query_data, colname = \"GenContext\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove Asterisk — removeAsterisks","text":"query_data data frame containing data processed. colname name column asterisks removed. Defaults \"GenContext\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove Asterisk — removeAsterisks","text":"original data frame asterisks removed specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove Asterisk — removeAsterisks","text":"","code":"if (FALSE) { # \\dontrun{ removeAsterisks() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove Empty — removeEmptyRows","title":"Remove Empty — removeEmptyRows","text":"Remove empty rows column Removes empty rows specified column. function ... original data frame returned corresponding cleaned column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove Empty — removeEmptyRows","text":"","code":"removeEmptyRows(prot, by_column = \"DomArch\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove Empty — removeEmptyRows","text":"prot data frame containing 'DomArch', 'Species', 'GenContext', 'ClustName' columns. by_column Column empty rows removed domain+domain -> domain(s). Default column 'DomArch'. Can also take following input, 'Species', 'GenContext', 'ClustName'.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove Empty — removeEmptyRows","text":"tibble rows removed specified column contains \"-\", \"NA\", empty string.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove Empty — removeEmptyRows","text":"","code":"if (FALSE) { # \\dontrun{ removeEmptyRows(prot, \"DomArch\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove Tails — removeTails","title":"Remove Tails — removeTails","text":"Remove tails/singletons function ... Certain low frequency domain architectures can removed. original data frame returned corresponding cleaned column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove Tails — removeTails","text":"","code":"removeTails(prot, by_column = \"DomArch\", keep_domains = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove Tails — removeTails","text":"prot data frame containing 'DomArch', 'GenContext', 'ClustName' columns. by_column Default column 'DomArch'. Can also take 'ClustName', 'GenContext' input. keep_domains Default False Keeps tail entries contain query domains.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove Tails — removeTails","text":"original data frame singletons removed specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove Tails — removeTails","text":"","code":"if (FALSE) { # \\dontrun{ removeTails(prot, \"DomArch\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":null,"dir":"Reference","previous_headings":"","what":"Rename the labels of fasta files — renameFA","title":"Rename the labels of fasta files — renameFA","text":"Rename labels fasta files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rename the labels of fasta files — renameFA","text":"","code":"renameFA(fa_path, outpath, replacement_function = mapAcc2Name, ...)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rename the labels of fasta files — renameFA","text":"fa_path Path fasta file outpath Path write altered fasta file replacement_function Function apply lines starting '>' ... Additional arguments pass replacement_function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rename the labels of fasta files — renameFA","text":"character vector modified lines FASTA file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rename the labels of fasta files — renameFA","text":"","code":"if (FALSE) { # \\dontrun{ renameFA(\"path/to/input.fasta\", \"path/to/output.fasta\", mapAcc2Name, acc2name) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Rename the labels of fasta files — rename_fasta","title":"Rename the labels of fasta files — rename_fasta","text":"Rename labels fasta files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rename the labels of fasta files — rename_fasta","text":"","code":"rename_fasta(fa_path, outpath, replacement_function = map_acc2name, ...)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rename the labels of fasta files — rename_fasta","text":"fa_path Path fasta file outpath Path write altered fasta file replacement_function Function apply lines starting '>' ... Additional arguments pass replacement_function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rename the labels of fasta files — rename_fasta","text":"Character vector containing modified lines Fasta file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rename the labels of fasta files — rename_fasta","text":"","code":"if (FALSE) { # \\dontrun{ rename_fasta(\"input.fasta\", \"output.fasta\", replacement_function = map_acc2name, acc2name = acc2name_table) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace QMs — replaceQuestionMarks","title":"Replace QMs — replaceQuestionMarks","text":"Replace consecutive '?' separated '->', '<-' '||' 'X(s)' Replace '?' 'X'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace QMs — replaceQuestionMarks","text":"","code":"replaceQuestionMarks(prot, by_column = \"GenContext\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace QMs — replaceQuestionMarks","text":"prot DataTable operate by_column Column operate ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace QMs — replaceQuestionMarks","text":"original data frame specified column updated. consecutive '?' characters replaced 'X(s)', individual '?' characters replaced 'X'.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Replace QMs — replaceQuestionMarks","text":"","code":"if (FALSE) { # \\dontrun{ replaceQuestionMarks() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":null,"dir":"Reference","previous_headings":"","what":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"function processes genomic context data frame reverse direction operons based specific patterns GenContext column. handles elements represented \">\" \"<\" restructures genomic context flipping direction operons preserving relationships indicated \"=\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"","code":"reverseOperonSeq(prot)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"prot data.frame data frame containing least column named 'GenContext', represents genomic contexts need reversed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"data.frame input data frame 'GenContext' column updated t o reflect reversed operons.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"","code":"if (FALSE) { # \\dontrun{ # Example genomic context data frame ## Rework example data, does not pass R-CMD Check prot <- data.frame(GenContext = c(\"A>B\", \"C<D\", \"E=F*G\", \"H>I\"))  reversed_prot <- reverseOperonSeq(prot) reversed_prot } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":null,"dir":"Reference","previous_headings":"","what":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"function executes Delta-BLAST search using specified parameters database. sets BLAST database path, runs Delta-BLAST command given query, outputs results.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"","code":"runDeltaBlast(   runDeltaBlast,   db_search_path,   db = \"refseq\",   query,   evalue = \"1e-5\",   out,   num_alignments,   num_threads = 1 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"db_search_path Path BLAST databases. db Name BLAST database search (default \"refseq\"). query Path input query file. evalue E-value threshold reporting matches (default \"1e-5\"). Path output file results saved. num_alignments Number alignments report. num_threads Number threads use search (default 1). deltablast_path Path Delta-BLAST executable.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"function return value; outputs results specified file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"","code":"if (FALSE) { # \\dontrun{ runDeltaBlast(runDeltaBlast, db_search_path) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":null,"dir":"Reference","previous_headings":"","what":"runIPRScan — runIPRScan","title":"runIPRScan — runIPRScan","text":"Run InterProScan given FASTA file save results output file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"runIPRScan — runIPRScan","text":"","code":"runIPRScan(filepath_fasta, filepath_out, appl = c(\"Pfam\", \"Gene3D\"))"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"runIPRScan — runIPRScan","text":"filepath_fasta string representing path input FASTA file. filepath_out string representing base path output file. appl character vector specifying InterProScan applications use (e.g., \"Pfam\", \"Gene3D\"). Default c(\"Pfam\", \"Gene3D\").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"runIPRScan — runIPRScan","text":"data frame containing results InterProScan output TSV file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"runIPRScan — runIPRScan","text":"","code":"if (FALSE) { # \\dontrun{ results <- runIPRScan(     filepath_fasta = \"path/to/your_fasta_file.fasta\",     filepath_out = \"path/to/output_file\",     appl = c(\"Pfam\", \"Gene3D\") ) results } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":null,"dir":"Reference","previous_headings":"","what":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"function executes RPS-BLAST search generate domain architectures specified proteins. sets BLAST database path, runs RPS-BLAST command provided query, outputs results.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"","code":"runRPSBlast(   rpsblast_path,   db_search_path,   db = \"refseq\",   query,   evalue = \"1e-5\",   out,   num_threads = 1 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"rpsblast_path Path RPS-BLAST executable. db_search_path Path BLAST databases. db Name BLAST database search (default \"refseq\"). query Path input query file. evalue E-value threshold reporting matches (default \"1e-5\"). Path output file results saved. num_threads Number threads use search (default 1).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"function return value; outputs results specified file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"","code":"if (FALSE) { # \\dontrun{ runRSPBlast(rpsblast_path, db_search_path, query, out) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick Longer Duplicate — selectLongestDuplicate","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"Pick Longer Duplicate","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"","code":"selectLongestDuplicate(prot, column)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"prot data frame containing data, least one column named 'AccNum' identification duplicates. column name column longest entry among duplicates selected.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"data frame containing longest entries among duplicates based specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"","code":"if (FALSE) { # \\dontrun{ selectLongestDuplicate() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":null,"dir":"Reference","previous_headings":"","what":"Sends a ","title":"Sends a ","text":"Sends \"job accepted\" email user job accepted, including details job submission check status.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sends a ","text":"","code":"sendJobStatusEmail(notify_email, job_dir, pin_id, event_type, context = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sends a ","text":"notify_email email address send notification job_dir directory job's arguments stored, job_args.yml pin_id unique identifier job event_type either 'start' 'end', returns corresponding email given type job_results_url URL user can check status job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sends a ","text":"result sendmailR::sendmail() call","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"shortenLineage — shortenLineage","title":"shortenLineage — shortenLineage","text":"function abbreviates lineage names shortening first part string (given delimiter).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"shortenLineage — shortenLineage","text":"","code":"shortenLineage(data, colname = \"Lineage\", abr_len = 1)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"shortenLineage — shortenLineage","text":"data data frame contains column lineage names shortened. colname Character. name column data frame containing lineage strings shortened. Default \"Lineage\". abr_len Integer. number characters retain first letter. set 1, first letter segment delimiter (>) retained. Default 1.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"shortenLineage — shortenLineage","text":"modified data frame specified lineage column shortened.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"shortenLineage — shortenLineage","text":"","code":"if (FALSE) { # \\dontrun{ df <- data.frame(Lineage = c(\"Bacteria>Firmicutes>Clostridia\", \"Archaea>Euryarchaeota>Thermococci\")) shortened_df <- shortenLineage(df, colname = \"Lineage\", abr_len = 1) shortened_df } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":null,"dir":"Reference","previous_headings":"","what":"Sink Reset — sinkReset","title":"Sink Reset — sinkReset","text":"Sink Reset","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sink Reset — sinkReset","text":"","code":"sinkReset()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sink Reset — sinkReset","text":"return, run close outstanding sink()s","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sink Reset — sinkReset","text":"","code":"if (FALSE) { # \\dontrun{ sinkReset() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":null,"dir":"Reference","previous_headings":"","what":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"function processes genomic context strings (GenContext) reverses directional signs based presence equal sign (\"=\").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"","code":"straightenOperonSeq(prot)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"prot vector vector genomic context strings processed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"vector vector length input, genomic element annotated either forward (\"->\") reverse (\"<-\") direction, depending position relative \"=\" symbols.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"","code":"# Example input: Genomic context with directional symbols and an asterisk genomic_context <- c(\"A\", \"B\", \"*\", \"C\", \"D\", \"=\", \"E\", \"F\") straightenOperonSeq(genomic_context) #> [1] \"A->\" \"B->\" \"*->\" \"C->\" \"D->\" \"=\"   \"<-E\" \"<-F\"  # Output: \"A->\", \"B->\", \"*\", \"<-C\", \"<-D\", \"=\", \"E->\", \"F->\""},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":null,"dir":"Reference","previous_headings":"","what":"themeGenes2 — themeGenes2","title":"themeGenes2 — themeGenes2","text":"themeGenes2","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"themeGenes2 — themeGenes2","text":"","code":"themeGenes2()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"themeGenes2 — themeGenes2","text":"ggplot2 theme object.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"themeGenes2 — themeGenes2","text":"","code":"library(ggplot2)  # Create a sample plot using the custom theme ggplot(mtcars, aes(x = wt, y = mpg)) +     geom_point() +     themeGenes2() +     labs(title = \"Car Weight vs MPG\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":null,"dir":"Reference","previous_headings":"","what":"validateCountDF — validateCountDF","title":"validateCountDF — validateCountDF","text":"validateCountDF","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"validateCountDF — validateCountDF","text":"","code":"validateCountDF(var)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"validateCountDF — validateCountDF","text":"var data frame whose columns converted.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"validateCountDF — validateCountDF","text":"data frame non-'n' columns converted character type.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"validateCountDF — validateCountDF","text":"","code":"if (FALSE) { # \\dontrun{ new_df <- .all_non_n_cols_to_char(my_data) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":null,"dir":"Reference","previous_headings":"","what":"plotWordCloud3 — wordcloud3","title":"plotWordCloud3 — wordcloud3","text":"plotWordCloud3","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotWordCloud3 — wordcloud3","text":"","code":"wordcloud3(   data,   size = 1,   minSize = 0,   gridSize = 0,   fontFamily = \"Segoe UI\",   fontWeight = \"bold\",   color = \"random-dark\",   backgroundColor = \"white\",   minRotation = -pi/4,   maxRotation = pi/4,   shuffle = TRUE,   rotateRatio = 0.4,   shape = \"circle\",   ellipticity = 0.65,   widgetsize = NULL,   figPath = NULL,   hoverFunction = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotWordCloud3 — wordcloud3","text":"data Data frame table containing words frequencies word cloud. size Numeric. Scaling factor word sizes (default 1). minSize Numeric. Minimum font size smallest word (default 0). gridSize Numeric. Size grid placing words (default 0). fontFamily Character. Font family use words (default \"Segoe UI\"). fontWeight Character. Font weight words (default \"bold\"). color Character vector. Color words. Use \"random-dark\" random dark colors (default) specify color. backgroundColor Character. Background color word cloud (default \"white\"). minRotation Numeric. Minimum rotation angle words radians (default -π/4). maxRotation Numeric. Maximum rotation angle words radians (default π/4). shuffle Logical. Whether shuffle words (default TRUE). rotateRatio Numeric. Proportion words rotated (default 0.4). shape Character. Shape word cloud (\"circle\" default, can use \"cardioid\", \"star\", \"triangle\", etc.). ellipticity Numeric. Degree ellipticity (default 0.65). widgetsize Numeric vector. Width height widget (default NULL, uses default size). figPath Character. Path image file use mask word cloud (optional). hoverFunction JS function. JavaScript function run hovering words (optional).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotWordCloud3 — wordcloud3","text":"HTML widget object displaying word cloud.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotWordCloud3 — wordcloud3","text":"","code":"if (FALSE) { # \\dontrun{ wordcloud3(data = your_data, size = 1.5, color = \"random-light\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"words2WordCounts — words2WordCounts","title":"words2WordCounts — words2WordCounts","text":"Get word counts (wc) DOMAINS (DA) DOMAIN ARCHITECTURES (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"words2WordCounts — words2WordCounts","text":"","code":"words2WordCounts(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"words2WordCounts — words2WordCounts","text":"string character string containing elements (words) count. typically space-delimited string representing domain architectures genomic contexts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"words2WordCounts — words2WordCounts","text":"tibble (tbl_df) two columns: words column containing individual words (domains domain architectures). freq column containing frequency counts word.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"words2WordCounts — words2WordCounts","text":"","code":"if (FALSE) { # \\dontrun{ tibble::tibble(DomArch = c(\"aaa+bbb\", \"a+b\", \"b+c\", \"b-c\")) |>     elements2Words() |>     words2WordCounts() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"writeMSA_AA2FA — writeMSA_AA2FA","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"MsaAAMultipleAlignment Objects generated calls msaClustalOmega msaMuscle 'msa' package Write MsaAAMultpleAlignment Objects aligned fasta sequence MsaAAMultipleAlignment Objects generated calls msaClustalOmega msaMuscle 'msa' package","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"","code":"writeMSA_AA2FA(alignment, outpath)  writeMSA_AA2FA(alignment, outpath)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"alignment MsaAAMultipleAlignment object written fasta outpath resulting FASTA file written ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"Character string representing content written FASTA file. Character string FASTA content written file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"","code":"if (FALSE) { # \\dontrun{ writeMSA_AA2FA(\"my_sequences.fasta\", outpath = \"aligned_output.fasta\") } # } if (FALSE) { # \\dontrun{ # Example usage alignment <- alignFasta(\"path/to/sequences.fasta\") writeMSA_AA2FA(alignment, \"path/to/aligned_sequences.fasta\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":null,"dir":"Reference","previous_headings":"","what":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"Write table 2 columns: 1) process 2) median seconds","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"","code":"writeProcessRuntime2TSV(dir_job_results, filepath)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"dir_job_results chr path MolEvolvR job_results filepath path save tsv file","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"tbl_df 2 columns: 1) process 2) median seconds example: writeProcessRuntime2TSV( \"/data/scratch/janani/molevolvr_out/\", \"/data/scratch/janani/molevolvr_out/log_tbl.tsv\" )","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":null,"dir":"Reference","previous_headings":"","what":"writeProcessRuntime2YML — writeProcessRuntime2YML","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"Compute median process runtimes, write YAML list processes median runtimes seconds path specified 'filepath'. default value filepath value env var MOLEVOLVR_PROC_WEIGHTS, getProcessRuntimeWeights() also uses default read location.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"","code":"writeProcessRuntime2YML(dir_job_results, filepath = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"dir_job_results chr path MolEvolvR job_results directory filepath chr path save YAML file; NULL, uses ./molevol_scripts/log_data/job_proc_weights.yml","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"","code":"if (FALSE) { # \\dontrun{ writeProcessRuntime2YML(     \"/data/scratch/janani/molevolvr_out/\",     \"/data/scratch/janani/molevolvr_out/log_tbl.yml\" ) } # }"}]
+[{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement janani.ravi@cuanschutz.edu. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to MolEvolvR","title":"Contributing to MolEvolvR","text":"outlines propose change MolEvolvR. detailed discussion contributing tidyverse packages, please see development contributing guide code review principles.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to MolEvolvR","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to MolEvolvR","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed). See guide create great issue advice.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to MolEvolvR","text":"Fork package clone onto computer. haven’t done , recommend using usethis. Install load usethis package : Clone fork MolEvolvR package using: Install BiocManager Bioconductor: Install development dependencies ensure package passes R CMD check using devtools: R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using: Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number.","code":"install.packages(\"usethis\")  library(\"usethis\") usethis::create_from_github(\"JRaviLab/MolEvolvR\", fork = TRUE) if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\") BiocManager::install(version = \"3.19\") install.packages(\"devtools\")  library(\"devtools\")  devtools::install_dev_deps()  devtools::check() usethis::pr_init(\"brief-description-of-change\")"},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to MolEvolvR","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. Lint Code: Ensure code adheres style guidelines using lintr: use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":"install.packages(\"lintr\")  library(\"lintr\")  lintr::lint(\"path/to/your/file.R\")"},{"path":"https://jravilab.github.io/MolEvolvR/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to MolEvolvR","text":"Please note MolEvolvR project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"BSD 3-clause License","title":"BSD 3-clause License","text":"Copyright (c) 2024 MolEvolvR authors rights reserved. Redistribution use source binary forms, without modification, permitted provided following conditions met: Redistributions source code must retain copyright notice, list conditions following disclaimer. Redistributions binary form must reproduce copyright notice, list conditions following disclaimer documentation /materials provided distribution. Neither name copyright holder names contributors may used endorse promote products derived software without specific prior written permission. SOFTWARE PROVIDED COPYRIGHT HOLDERS CONTRIBUTORS “” EXPRESS IMPLIED WARRANTIES, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE DISCLAIMED. EVENT SHALL COPYRIGHT HOLDER CONTRIBUTORS LIABLE DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, CONSEQUENTIAL DAMAGES (INCLUDING, LIMITED , PROCUREMENT SUBSTITUTE GOODS SERVICES; LOSS USE, DATA, PROFITS; BUSINESS INTERRUPTION) HOWEVER CAUSED THEORY LIABILITY, WHETHER CONTRACT, STRICT LIABILITY, TORT (INCLUDING NEGLIGENCE OTHERWISE) ARISING WAY USE SOFTWARE, EVEN ADVISED POSSIBILITY DAMAGE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Janani Ravi. Author, maintainer. David Mayer. Author. Evan Brenner. Author. Faisal Alquaddoomi. Author. Samuel Chen. Contributor. Lo Sosinski. Contributor. Joseph Burke. Contributor. Jacob Krol. Contributor.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ravi J, Mayer D, Brenner E, Alquaddoomi F (2024). MolEvolvR: Molecular Evolution Phylogeny. R package version 0.99.9, https://jravilab.github.io/MolEvolvR/, https://github.com/jravilab/molevolvr.","code":"@Manual{,   title = {MolEvolvR: Molecular Evolution and Phylogeny},   author = {Janani Ravi and David Mayer and Evan Brenner and Faisal Alquaddoomi},   year = {2024},   note = {R package version 0.99.9, https://jravilab.github.io/MolEvolvR/},   url = {https://github.com/jravilab/molevolvr}, }"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"molevolvr-","dir":"","previous_headings":"","what":"Molecular Evolution and Phylogeny","title":"Molecular Evolution and Phylogeny","text":"MolEvolvR R-package provides framework characterizing proteins using molecular evolution phylogeny. Check pkgdown page : jravilab.github.io/MolEvolvR","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Molecular Evolution and Phylogeny","text":"can install development version MolEvolvR GitHub :","code":"# Install Bioconductor if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\") BiocManager::install(version = \"3.19\")  # Install Development Version of MolEvolvR BiocManager::install(\"JRaviLab/MolEvolvR\")"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"loading-the-package","dir":"","previous_headings":"Installation","what":"Loading the package","title":"Molecular Evolution and Phylogeny","text":"","code":"library(MolEvolvR)"},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Molecular Evolution and Phylogeny","text":"basic example shows analyze favorite protein:","code":"library(MolEvolvR) ## basic example code ## ⏳ Stay tuned!"},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"related-molevolvr-codebases","dir":"","previous_headings":"Companion repos & projects","what":"Related MolEvolvR codebases","title":"Molecular Evolution and Phylogeny","text":"MolEvolvR web-app 1.0 | 🔒Repo | Live web-app | Preprint | Case studies MolEvolvR web-app 2.0 | 🔒Repo","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"specific-use-cases","dir":"","previous_headings":"Companion repos & projects","what":"Specific use cases","title":"Molecular Evolution and Phylogeny","text":"PSP evolution across tree life | 🔒Repo | Live web-app | PubMed Bacterial phage defense system, avcDI | Repo | PubMed DciA evolution across bacteria | Repo | PubMed Internalins Listeria | Repo | PubMed","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"current-contributors","dir":"","previous_headings":"","what":"Current contributors","title":"Molecular Evolution and Phylogeny","text":"David Mayer | R-package, back-end Faisal Alquaddoomi | Front-end 1.0, back-end Evan Brenner | MolEvolvR functionality Vince Rubinetti | Front-end 2.0 Dave Bunten | Data management, engineering Janani Ravi | PI","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"contribution-guidelines","dir":"","previous_headings":"Current contributors","what":"Contribution guidelines","title":"Molecular Evolution and Phylogeny","text":"welcome contributions community! ensure smooth collaborative process, please follow guidelines. Outreachy interns, please check pointers get started. 📜 License","code":""},{"path":"https://jravilab.github.io/MolEvolvR/index.html","id":"code-of-conduct","dir":"","previous_headings":"Current contributors","what":"Code of Conduct","title":"Molecular Evolution and Phylogeny","text":"Please note MolEvolvR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/outreachy_guidelines.html","id":null,"dir":"","previous_headings":"","what":"Getting started","title":"Getting started","text":"Welcome aboard, Outreachy intern! 🙌 JRaviLab Onboarding Visit MolEvolvR package repository; please start README doc repository. Read companion MolEvolvR web-app preprint . Follow instructions repo README install MolEvolvR, starting bioconductor installation instructions. Make sure can build package R CMD build run tests devtools. Check open issues, select task labeled Outreachy, ask assigned . Create branch specific task submit PR (“pull request”), respond feedback reviewers.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/outreachy_guidelines.html","id":"resources","dir":"","previous_headings":"","what":"Resources","title":"Getting started","text":"💻Code Learn R Git/GitHub basics 🗣️Scientific Communication 👥Lab Culture & working JRaviLab | Expectations Contact 📧 Janani Ravi | Email","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"Function map GCA_ID TaxID, TaxID Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"","code":"GCA2Lineage(   prot_data,   assembly_path = \"/data/research/jravilab/common_data/assembly_summary_genbank.txt\",   lineagelookup_path = \"/data/research/jravilab/common_data/lineage_lookup.tsv\",   acc_col = \"AccNum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"prot_data Dataframe containing column GCA_ID assembly_path String path assembly_summary path file can generated using \"downloadAssemblySummary()\" function lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using \"createLineageLookup()\" function acc_col Character. name column prot_data containing accession numbers. Default \"AccNum\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"dataframe containing merged information GCA_IDs, TaxIDs, corresponding lineage phylum level. dataframe include information input prot_data lineage data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"Currently configured kingdom phylum","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/GCA2Lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to map GCA_ID to TaxID, and TaxID to Lineage — GCA2Lineage","text":"","code":"if (FALSE) { # \\dontrun{ result <- GCA2Lineage(prot_data = my_prot_data,                        assembly_path = \"path/to/assembly_summary.txt\",                        lineagelookup_path = \"path/to/lineage_lookup.tsv\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"IPG2Lineage — IPG2Lineage","title":"IPG2Lineage — IPG2Lineage","text":"Takes resulting file efetch run ipg database Takes resulting file efetch run ipg database append lineage, taxid columns","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"IPG2Lineage — IPG2Lineage","text":"","code":"IPG2Lineage(   accessions,   ipg_file,   refseq_assembly_path,   genbank_assembly_path,   lineagelookup_path )  IPG2Lineage(   accessions,   ipg_file,   refseq_assembly_path,   genbank_assembly_path,   lineagelookup_path )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"IPG2Lineage — IPG2Lineage","text":"accessions Character vector protein accessions ipg_file Path file containing results efetch run ipg database. protein accession 'accessions' contained file refseq_assembly_path String. Path RefSeq assembly summary file. genbank_assembly_path String. Path GenBank assembly summary file. lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using \"createLineageLookup()\" function assembly_path String path assembly_summary path file can generated using downloadAssemblySummary function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"IPG2Lineage — IPG2Lineage","text":"data.table lineage information provided protein accessions. data table containing protein accessions along corresponding TaxIDs lineage information.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"IPG2Lineage — IPG2Lineage","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/IPG2Lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"IPG2Lineage — IPG2Lineage","text":"","code":"if (FALSE) { # \\dontrun{ IPG2Lineage() } # }  if (FALSE) { # \\dontrun{ lins <- IPG2Lineage(   accessions = c(\"P12345\", \"Q67890\"),   ipg_file = \"path/to/ipg_results.txt\",   refseq_assembly_path = \"path/to/refseq_assembly_summary.txt\",   genbank_assembly_path = \"path/to/genbank_assembly_summary.txt\",   lineagelookup_path = \"path/to/lineage_lookup.tsv\" ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"MolEvolvR Summary — MolEvolvR_summary","title":"MolEvolvR Summary — MolEvolvR_summary","text":"collection summary functions MolEvolvR package. Function summarize retrieve counts Domains & Domains+Lineage Function retrieve counts many lineages DomArch appears Creates data frame totalcount column function designed sum counts column either Genomic Context Domain Architecture creates totalcount column sums.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MolEvolvR Summary — MolEvolvR_summary","text":"","code":"summarizeByLineage(prot = \"prot\", column = \"DomArch\", by = \"Lineage\", query)  summarizeDomArch_ByLineage(x)  summarizeDomArch(x)  summarizeGenContext_ByDomArchLineage(x)  summarizeGenContext_ByLineage(x)  summarizeGenContext(x)  totalGenContextOrDomArchCounts(   prot,   column = \"DomArch\",   lineage_col = \"Lineage\",   cutoff = 90,   RowsCutoff = FALSE,   digits = 2 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MolEvolvR Summary — MolEvolvR_summary","text":"prot data frame must contain columns: count column Character. column summarize, default \"DomArch\". string representing grouping column (e.g., Lineage). Default \"Lineage\". query string specifying query pattern filtering target column. Use \"\" skip filtering include rows. x dataframe tibble containing data. must columns named GenContext, DomArch, Lineage. lineage_col Character. name lineage column, default \"Lineage\". cutoff Numeric. Cutoff total count. Counts cutoff value shown. Default 0. RowsCutoff Logical. TRUE, filters based cumulative percentage cutoff. Default FALSE. digits Numeric. Number decimal places percentage columns. Default 2.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MolEvolvR Summary — MolEvolvR_summary","text":"tibble summarizing counts occurrences elements column, grouped column. result includes number occurrences (count) arranged descending order count. tibble summarizing counts unique domain architectures (DomArch) per lineage (Lineage). resulting table contains three columns: DomArch, Lineage, count, indicates frequency domain architecture lineage. results arranged descending order count. tibble summarizing unique DomArch, along following columns: totalcount: total occurrences DomArch across lineages. totallin: total number unique lineages DomArch appears. results arranged descending order totallin totalcount. tibble summarizing unique combination GenContext, DomArch, Lineage, along following columns: GenContext: genomic context entry. DomArch: domain architecture entry. Lineage: lineage associated entry. count: total number occurrences combination GenContext, DomArch, Lineage. results arranged descending order count. Describe return, detail tibble summarizing unique combination GenContext Lineage, along following columns: GenContext: genomic context entry. Lineage: lineage associated entry. count: total number occurrences combination GenContext Lineage. results arranged descending order count. data frame following columns: {{ column }}: Unique values specified column. totalcount: total count occurrences unique value specified column. IndividualCountPercent: percentage totalcount relative overall count. CumulativePercent: cumulative percentage total counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"MolEvolvR Summary — MolEvolvR_summary","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/MolEvolvR_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"MolEvolvR Summary — MolEvolvR_summary","text":"","code":"if (FALSE) { # \\dontrun{ library(tidyverse) tibble(DomArch = c(\"a+b\", \"a+b\", \"b+c\", \"a+b\"), Lineage = c(\"l1\", \"l1\", \"l1\", \"l2\")) |>     summarizeByLineage(query = \"all\") } # }  if (FALSE) { # \\dontrun{ summarizeDomArch_ByLineage() } # } if (FALSE) { # \\dontrun{ summarizeDomArch() } # } if (FALSE) { # \\dontrun{ summarizeGenContext_ByDomArchLineage } # } if (FALSE) { # \\dontrun{ summarizeGenContext_ByLineage() } # } if (FALSE) { # \\dontrun{ summarizeGenContext() } # } if (FALSE) { # \\dontrun{ totalGenContextOrDomArchCounts(pspa - gc_lin_counts, 0, \"GC\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"acc2FA — acc2FA","title":"acc2FA — acc2FA","text":"converts protein accession numbers fasta format. Resulting fasta file written outpath. converts protein accession numbers fasta format. Resulting fasta file written outpath. acc2FA converts protein accession numbers fasta format. Resulting fasta file written outpath.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"acc2FA — acc2FA","text":"","code":"acc2FA(accessions, outpath, plan = \"sequential\")  acc2FA(accessions, outpath, plan = \"sequential\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"acc2FA — acc2FA","text":"accessions Character vector containing protein accession numbers generate fasta sequences . Function may work vectors length > 10,000 outpath str. Location fasta file written . plan Character. plan use processing. Default \"sequential\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"acc2FA — acc2FA","text":"logical value indicating whether retrieval conversion successful. Returns TRUE successful FALSE otherwise. Fasta file written specified outpath.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"acc2FA — acc2FA","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"acc2FA — acc2FA","text":"","code":"if (FALSE) { # \\dontrun{ acc2FA(accessions = c(\"ACU53894.1\", \"APJ14606.1\", \"ABK37082.1\"), outpath = \"my_proteins.fasta\") Entrez:accessions <- rep(\"ANY95992.1\", 201) |> acc2FA(outpath = \"entrez.fa\") EBI:accessions <- c(\"P12345\", \"Q9UHC1\", \"O15530\", \"Q14624\", \"P0DTD1\") |> acc2FA(outpath = \"ebi.fa\") } # } if (FALSE) { # \\dontrun{ acc2FA(accessions = c(\"ACU53894.1\", \"APJ14606.1\", \"ABK37082.1\"), outpath = \"my_proteins.fasta\") Entrez:accessions <- rep(\"ANY95992.1\", 201) |> acc2FA(outpath = \"entrez.fa\") EBI:accessions <- c(\"P12345\", \"Q9UHC1\", \"O15530\", \"Q14624\", \"P0DTD1\") |> acc2FA(outpath = \"ebi.fa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":null,"dir":"Reference","previous_headings":"","what":"acc2Lineage — acc2Lineage","title":"acc2Lineage — acc2Lineage","text":"function combines 'efetchIPG()' 'IPG2Lineage()' map set protein accessions assembly (GCA_ID), tax ID, lineage. Function map protein accession numbers lineage function combines 'efetchIPG()' 'IPG2Lineage()' map set protein accessions assembly (GCA_ID), tax ID, lineage.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"acc2Lineage — acc2Lineage","text":"","code":"acc2Lineage(   accessions,   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )  acc2Lineage(   accessions,   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"acc2Lineage — acc2Lineage","text":"accessions Character vector protein accessions assembly_path String path assembly_summary path file can generated using \"downloadAssemblySummary()\" function lineagelookup_path String path lineage lookup file (taxid lineage mapping). file can generated using ipgout_path Path write results efetch run accessions ipg database. NULL, file written. Defaults NULL plan Character. Specifies execution plan parallel processing. Default \"multicore\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"acc2Lineage — acc2Lineage","text":"data.table contains lineage information, mapping protein accessions tax IDs lineages. dataframe containing lineage information mapped given protein accessions. dataframe includes relevant columns TaxID, GCA_ID, Protein, Protein Name, Species, Lineage.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"acc2Lineage — acc2Lineage","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/acc2Lineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"acc2Lineage — acc2Lineage","text":"","code":"if (FALSE) { # \\dontrun{ acc2Lineage() } # } if (FALSE) { # \\dontrun{ lineage_data <- acc2Lineage(   accessions = c(\"P12345\", \"Q67890\"),   assembly_path = \"path/to/assembly_summary.txt\",   lineagelookup_path = \"path/to/lineage_lookup.tsv\",   ipgout_path = \"path/to/output.txt\" ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":null,"dir":"Reference","previous_headings":"","what":"addLeaves2Alignment — addLeaves2Alignment","title":"addLeaves2Alignment — addLeaves2Alignment","text":"Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures. Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addLeaves2Alignment — addLeaves2Alignment","text":"","code":"addLeaves2Alignment(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   reduced = FALSE )  addLeaves2Alignment(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   reduced = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addLeaves2Alignment — addLeaves2Alignment","text":"aln_file Character. Path file. Input tab-delimited file + alignment file accnum & alignment. Default 'pspa_snf7.aln' lin_file Character. Path file. Protein file accession + number lineage mapping. Default 'pspa.txt' reduced Boolean. TRUE, reduced data frame generated one sequence per lineage. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addLeaves2Alignment — addLeaves2Alignment","text":"data frame containing enriched alignment data lineage information. data frame containing combined alignment lineage information.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"addLeaves2Alignment — addLeaves2Alignment","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"addLeaves2Alignment — addLeaves2Alignment","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"addLeaves2Alignment — addLeaves2Alignment","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLeaves2Alignment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addLeaves2Alignment — addLeaves2Alignment","text":"","code":"if (FALSE) { # \\dontrun{ addLeaves2Alignment(\"pspa_snf7.aln\", \"pspa.txt\") } # } if (FALSE) { # \\dontrun{ addLeaves2Alignment(\"pspa_snf7.aln\", \"pspa.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"addLineage — addLineage","title":"addLineage — addLineage","text":"addLineage addLineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addLineage — addLineage","text":"","code":"addLineage(   df,   acc_col = \"AccNum\",   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )  addLineage(   df,   acc_col = \"AccNum\",   assembly_path,   lineagelookup_path,   ipgout_path = NULL,   plan = \"multicore\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addLineage — addLineage","text":"df Dataframe containing accession numbers. dataframe column specified acc_col contains accession numbers. acc_col Character. name column df containing accession numbers. Default \"AccNum\". assembly_path String. path assembly summary file generated using downloadAssemblySummary() function. lineagelookup_path String. path lineage lookup file (taxid lineage mapping) generated using create_lineage_lookup() function. ipgout_path String. Optional path save intermediate output files. Default NULL. plan Character. Specifies execution plan parallel processing. Default \"multicore\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addLineage — addLineage","text":"data.frame combines original df lineage information. dataframe combines original dataframe df lineage information retrieved based provided accession numbers.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addLineage — addLineage","text":"","code":"if (FALSE) { # \\dontrun{ addLineage() } # } if (FALSE) { # \\dontrun{ enriched_df <- addLineage(df = my_data,                            acc_col = \"AccNum\",                            assembly_path = \"path/to/assembly_summary.txt\",                            lineagelookup_path = \"path/to/lineage_lookup.tsv\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":null,"dir":"Reference","previous_headings":"","what":"addName — addName","title":"addName — addName","text":"function adds new 'Name' column comprised components Kingdom, Phylum, Genus, species, well accession function adds new 'Name' column comprised components Kingdom, Phylum, Genus, species, well accession","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addName — addName","text":"","code":"addName(   data,   accnum_col = \"AccNum\",   spec_col = \"Species\",   lin_col = \"Lineage\",   lin_sep = \">\",   out_col = \"Name\" )  addName(   data,   accnum_col = \"AccNum\",   spec_col = \"Species\",   lin_col = \"Lineage\",   lin_sep = \">\",   out_col = \"Name\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addName — addName","text":"data Data add name column accnum_col Column containing accession numbers spec_col Column containing species lin_col Column containing lineage lin_sep Character separating lineage levels out_col Column contains new 'Name' derived Species, Lineage, AccNum info","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addName — addName","text":"Original data 'Name' column Original data 'Name' column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"addName — addName","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addName.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addName — addName","text":"","code":"# Example usage of the addName function data <- data.frame(   AccNum = c(\"ACC123\", \"ACC456\"),   Species = c(\"Homo sapiens\", \"Mus musculus\"),   Lineage = c(\"Eukaryota>Chordata\", \"Eukaryota>Chordata\") ) enriched_data <- addName(data) enriched_data #>   AccNum      Species            Lineage                     Name #> 1 ACC123 Homo sapiens Eukaryota>Chordata  EChorda_Hsapiens_ACC123 #> 2 ACC456 Mus musculus Eukaryota>Chordata EChorda_Mmusculus_ACC456 if (FALSE) { # \\dontrun{ addName(data_frame) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":null,"dir":"Reference","previous_headings":"","what":"addTaxID — addTaxID","title":"addTaxID — addTaxID","text":"addTaxID","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addTaxID — addTaxID","text":"","code":"addTaxID(data, acc_col = \"AccNum\", version = T)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addTaxID — addTaxID","text":"data data frame data table containing protein accession numbers. acc_col string specifying column name data contains accession numbers. Defaults \"AccNum\". version logical indicating whether remove last two characters accession numbers TaxID retrieval. Defaults TRUE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addTaxID — addTaxID","text":"data table includes original data along new column containing corresponding TaxIDs.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/addTaxID.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addTaxID — addTaxID","text":"","code":"if (FALSE) { # \\dontrun{ # Create a sample data table with accession numbers sample_data <- data.table(AccNum = c(\"ABC123.1\", \"XYZ456.1\", \"LMN789.2\")) enriched_data <- addTaxID(sample_data, acc_col = \"AccNum\", version = TRUE) enriched_data } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":null,"dir":"Reference","previous_headings":"","what":"alignFasta — alignFasta","title":"alignFasta — alignFasta","text":"Perform Multiple Sequence Alignment FASTA file. Perform Multiple Sequence Alignment FASTA file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"alignFasta — alignFasta","text":"","code":"alignFasta(fasta_file, tool = \"Muscle\", outpath = NULL)  alignFasta(fasta_file, tool = \"Muscle\", outpath = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"alignFasta — alignFasta","text":"fasta_file Path FASTA file aligned tool Type alignment tool use. One three options: \"Muscle\", \"ClustalO\", \"ClustalW\" outpath Path write resulting alignment FASTA file. NULL, file written","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"alignFasta — alignFasta","text":"aligned fasta sequence MsaAAMultipleAlignment object aligned fasta sequence MsaAAMultipleAlignment object","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"alignFasta — alignFasta","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/alignFasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"alignFasta — alignFasta","text":"","code":"if (FALSE) { # \\dontrun{ aligned_sequences <- alignFasta(\"my_sequences.fasta\", tool = \"Muscle\", outpath = \"aligned_output.fasta\") } # } if (FALSE) { # \\dontrun{ # Example usage aligned_sequences <- alignFasta(\"path/to/sequences.fasta\", tool = \"ClustalO\", outpath = \"path/to/aligned_sequences.fasta\") aligned_sequences } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":null,"dir":"Reference","previous_headings":"","what":"assignJobQueue — assignJobQueue","title":"assignJobQueue — assignJobQueue","text":"Decision function assign job queue","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"assignJobQueue — assignJobQueue","text":"","code":"assignJobQueue(t_sec_estimate, t_cutoff = 21600)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"assignJobQueue — assignJobQueue","text":"t_sec_estimate estimated number seconds job process (calculateEstimatedWallTimeFromOpts    ()) t_long threshold value defines lower bound assigning job \"long queue\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/assignJobQueue.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"assignJobQueue — assignJobQueue","text":"string \"short\" \"long\" example: calculateEstimatedWallTimeFromOpts\t(c(\"homology_search\", \"domain_architecture\"), 3) |> assignJobQueue()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"Given MolEvolvR advanced options number inputs, calculate total estimated walltime job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"","code":"calculateEstimatedWallTimeFromOpts(   advanced_opts,   n_inputs = 1L,   n_hits = NULL,   verbose = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"advanced_opts character vector MolEvolvR advanced options (see mapOption2Process options) n_inputs total number input proteins","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateEstimatedWallTimeFromOpts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateEstimatedWallTimeFromOpts — calculateEstimatedWallTimeFromOpts","text":"total estimated number seconds job process (walltime) example: calculateEstimatedWallTimeFromOpts\t(c(\"homology_search\", \"domain_architecture\"), n_inputs = 3, n_hits = 50L)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateProcessRuntime — calculateProcessRuntime","title":"calculateProcessRuntime — calculateProcessRuntime","text":"Scrape MolEvolvR logs calculate median processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateProcessRuntime — calculateProcessRuntime","text":"","code":"calculateProcessRuntime(dir_job_results)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateProcessRuntime — calculateProcessRuntime","text":"dir_job_results chr path MolEvolvR job_results directory","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/calculateProcessRuntime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateProcessRuntime — calculateProcessRuntime","text":"list names: processes; values: median runtime (seconds) see molevol_scripts/R/metrics.R info functions called examples:  dir_job_results <- \"/data/scratch/janani/molevolvr_out\" list_proc_medians <- calculateProcessRuntime(dir_job_results) outside container environment common_root <- \"/data/molevolvr_transfer/molevolvr_dev\" dir_job_results <- \"/data/molevolvr_transfer/molevolvr_dev/job_results\" list_proc_medians <- calculateProcessRuntime(dir_job_results)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean Cluster File — cleanClusterFile","title":"Clean Cluster File — cleanClusterFile","text":"Reads cleans cluster file function reads space-separated cluster file converts cleaned data frame.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean Cluster File — cleanClusterFile","text":"","code":"cleanClusterFile(path, writepath = NULL, query)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean Cluster File — cleanClusterFile","text":"path character path cluster file cleaned writepath character designating tsv file cleaned cluster file written . value NULL file written. Default NULL query character identifying query file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean Cluster File — cleanClusterFile","text":"cleaned cluster data frame returned tsv file written \"writepath\" parameter used.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusterFile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean Cluster File — cleanClusterFile","text":"","code":"if (FALSE) { # \\dontrun{ cleanClusterFile(\"data/pspa.op_ins_cls\", writepath = NULL, query = \"pspa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Clust — cleanClusters","title":"Cleanup Clust — cleanClusters","text":"Cleanup cluster file Cleans cluster file removing rows contain query cluster. function removes irrelevant rows contain query protein within ClustName column. return value cleaned data frame.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Clust — cleanClusters","text":"","code":"cleanClusters(   prot,   domains_rename,   domains_keep,   condenseRepeatedDomains = TRUE,   removeTails = FALSE,   removeEmptyRows = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Clust — cleanClusters","text":"prot data frame must contain columns Query ClustName. domains_rename data frame containing domain names replaced column 'old' corresponding replacement values column 'new'. domains_keep data frame containing domain names retained. condenseRepeatedDomains Boolean. TRUE, repeated domains 'ClustName' condensed. Default TRUE. removeTails Boolean. TRUE, 'ClustName' filtered based domains keep/remove. Default FALSE. removeEmptyRows Boolean. TRUE, rows empty/unnecessary values 'ClustName' removed. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Clust — cleanClusters","text":"Cleaned data frame","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanClusters.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Clust — cleanClusters","text":"","code":"if (FALSE) { # \\dontrun{ cleanClusters(prot, TRUE, FALSE, domains_keep, domains_rename) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup DomArch — cleanDomainArchitecture","title":"Cleanup DomArch — cleanDomainArchitecture","text":"Cleanup Domain Architectures Cleans DomArch column replacing/removing certain domains function cleans DomArch column one data frame renaming certain domains according second data frame. Certain domains can removed according additional data frame. original data frame returned clean DomArchs column old domains DomArchs.old column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup DomArch — cleanDomainArchitecture","text":"","code":"cleanDomainArchitecture(   prot,   old = \"DomArch.orig\",   new = \"DomArch\",   domains_keep,   domains_rename,   condenseRepeatedDomains = TRUE,   removeTails = FALSE,   removeEmptyRows = F,   domains_ignore = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup DomArch — cleanDomainArchitecture","text":"prot data frame containing 'DomArch' column old name original column containing domain architecture. Defaults \"DomArch.orig\". new name cleaned column created. Defaults \"DomArch\". domains_keep data frame containing domain names retained. domains_rename data frame containing domain names replaced column 'old' corresponding replacement values column 'new'. condenseRepeatedDomains Boolean. TRUE, repeated domains 'DomArch' condensed. Default TRUE. removeTails Boolean. TRUE, 'ClustName' filtered based domains keep/remove. Default FALSE. removeEmptyRows Boolean. TRUE, rows empty/unnecessary values 'DomArch' removed. Default FALSE. domains_ignore data frame containing domain names removed column called 'domains'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup DomArch — cleanDomainArchitecture","text":"original data frame returned clean DomArchs column old domains DomArchs.old column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanDomainArchitecture.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup DomArch — cleanDomainArchitecture","text":"","code":"if (FALSE) { # \\dontrun{ cleanDomainArchitecture(prot, TRUE, FALSE,  omains_keep, domains_rename, domains_ignore = NULL) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup FASTA Header — cleanFAHeaders","title":"Cleanup FASTA Header — cleanFAHeaders","text":"Parse accesion numbers fasta add suffix ith occurence handle duplicates","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup FASTA Header — cleanFAHeaders","text":"","code":"cleanFAHeaders(fasta)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup FASTA Header — cleanFAHeaders","text":"fasta XStringSet object representing sequences FASTA file. sequence names (headers) adjusted uniqueness sanitized.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup FASTA Header — cleanFAHeaders","text":"XStringSet fasta adjusted names (headers)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanFAHeaders.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup FASTA Header — cleanFAHeaders","text":"","code":"if (FALSE) { # \\dontrun{ AAStringSet(c(\"xxx\" = \"ATCG\", \"xxx\" = \"GGGC\")) |>     cleanFAHeaders() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup GeneDesc — cleanGeneDescription","title":"Cleanup GeneDesc — cleanGeneDescription","text":"Cleanup GeneDesc","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup GeneDesc — cleanGeneDescription","text":"","code":"cleanGeneDescription(prot, column)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup GeneDesc — cleanGeneDescription","text":"prot data frame containing gene descriptions. column name column gene descriptions pulled cleanup.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup GeneDesc — cleanGeneDescription","text":"Return trailing period occurs GeneDesc column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGeneDescription.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup GeneDesc — cleanGeneDescription","text":"","code":"if (FALSE) { # \\dontrun{ cleanGeneDescription() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Genomic Contexts — cleanGenomicContext","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"Cleans GenContext column data frame removing certain characters rows. function removes empty rows based 'GenContext' column. cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"","code":"cleanGenomicContext(   prot,   domains_rename = data.frame(old = character(0), new = character(0), stringsAsFactors =     F),   condenseRepeatedDomains = TRUE,   remove_asterisk = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"prot data frame contains columns 'GenContext.orig' domains_rename data frame containing domain names replaced column 'old' replacement column 'new'. Defaults empty data frame new old column non domains renamed condenseRepeatedDomains Boolean. TRUE, repeated domains 'GenContext' condensed. Default TRUE. remove_asterisk Boolean. TRUE, asterisks 'ClustName' removed. Default TRUE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanGenomicContext.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Genomic Contexts — cleanGenomicContext","text":"","code":"if (FALSE) { # \\dontrun{ cleanGenomicContext(prot, domains_rename, T, F) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Lineage — cleanLineage","title":"Cleanup Lineage — cleanLineage","text":"Cleanup Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Lineage — cleanLineage","text":"","code":"cleanLineage(prot, lins_rename)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Lineage — cleanLineage","text":"prot data frame containing 'Lineage' column needs cleaned . lins_rename data frame two columns: 'old' containing terms replaced 'new' containing corresponding replacement terms.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Lineage — cleanLineage","text":"original data frame 'Lineage' column updated based provided replacements.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Lineage — cleanLineage","text":"","code":"if (FALSE) { # \\dontrun{ cleanLineage() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":null,"dir":"Reference","previous_headings":"","what":"Cleanup Species — cleanSpecies","title":"Cleanup Species — cleanSpecies","text":"Cleanup Species Cleans species column data frame removing certain characters rows. function removes unneccessary characters 'Species' column. cleaned version data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cleanup Species — cleanSpecies","text":"","code":"cleanSpecies(prot, removeEmptyRows = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cleanup Species — cleanSpecies","text":"prot data frame contains columns 'Species'. removeEmptyRows Boolean. TRUE, rows empty/unnecessary values 'Species' removed. Default false.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cleanup Species — cleanSpecies","text":"original data frame Species cleaned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanSpecies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cleanup Species — cleanSpecies","text":"","code":"if (FALSE) { # \\dontrun{ cleanSpecies(prot, TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean String — cleanString","title":"Clean String — cleanString","text":"Keep alphanumerics, \"\", \"+\", \".\" strings substitute spaces \"\". Used MolEvolvR codebase cleanup domain architecture values","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean String — cleanString","text":"","code":"cleanString(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean String — cleanString","text":"string","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean String — cleanString","text":"string string alphanumerics, \"_\", \"+\", \".\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/cleanString.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean String — cleanString","text":"","code":"if (FALSE) { # \\dontrun{ cleanString() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":null,"dir":"Reference","previous_headings":"","what":"Download the combined assembly summaries of genbank and refseq — combineFiles","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"Download combined assembly summaries genbank refseq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"","code":"combineFiles(   inpath = c(\"../molevol_data/project_data/phage_defense/\"),   pattern = \"*full_analysis.tsv\",   delim = \"\\t\",   skip = 0,   col_names = T )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"inpath Character. master directory path files reside. search recursive (.e., look subdirectories well). pattern Character. search pattern identify files combined. Default \"*full_analysis.tsv\". delim Character. delimiter used input files. Default tab (\"\"). skip Integer. number lines skip beginning file. Default 0. col_names Logical character vector. TRUE, first row file treated column names. Alternatively, character vector can provided specify custom column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"data frame containing combined contents matched files. row include new column \"ByFile\" indicating source file data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFiles.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download the combined assembly summaries of genbank and refseq — combineFiles","text":"","code":"if (FALSE) { # \\dontrun{ combined_data <- combineFiles(inpath = \"../molevol_data/project_data/phage_defense/\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Combining full_analysis files — combineFullAnalysis","title":"Combining full_analysis files — combineFullAnalysis","text":"Combining full_analysis files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combining full_analysis files — combineFullAnalysis","text":"","code":"combineFullAnalysis(inpath, ret = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combining full_analysis files — combineFullAnalysis","text":"inpath Character. path directory containing .full_analysis.tsv files combined. ret Logical. TRUE, function return combined data frame. Default FALSE, meaning write file return data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combining full_analysis files — combineFullAnalysis","text":"ret TRUE, data frame containing combined data input files. ret FALSE, function writes combined data TSV file named cln_combined.tsv specified directory returns NULL.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineFullAnalysis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combining full_analysis files — combineFullAnalysis","text":"","code":"if (FALSE) { # \\dontrun{ combined_data <- combineFullAnalysis(\"path/to/full_analysis/files\", ret = TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":null,"dir":"Reference","previous_headings":"","what":"Combining clean ipr files — combineIPR","title":"Combining clean ipr files — combineIPR","text":"Combining clean ipr files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combining clean ipr files — combineIPR","text":"","code":"combineIPR(inpath, ret = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combining clean ipr files — combineIPR","text":"inpath Character. path directory containing .iprscan_cln.tsv files combined. ret Logical. TRUE, function return combined data frame. Default FALSE, meaning write file return data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combining clean ipr files — combineIPR","text":"ret TRUE, data frame containing combined data input files. ret FALSE, function writes combined data TSV file named ipr_combined.tsv specified directory returns NULL.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/combineIPR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combining clean ipr files — combineIPR","text":"","code":"if (FALSE) { # \\dontrun{ combineIPR <- combine_ipr(\"path/to/ipr/files\", ret = TRUE) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":null,"dir":"Reference","previous_headings":"","what":"condenseRepeatedDomains — condenseRepeatedDomains","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"Condense repeated domains Condenses repeated domains specified column. function identifies repeated domains condenses (s). ?? Certain domains can removed according additional data frame. original data frame returned corresponding cleaned column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"","code":"condenseRepeatedDomains(prot, by_column = \"DomArch\", excluded_prots = c())"},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"prot data frame containing 'DomArch', 'GenContext', 'ClustName' columns. by_column Column repeats condensed domain+domain -> domain(s). excluded_prots Vector strings condenseRepeatedDomains reduce (s). Defaults c()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"data frame condensed repeated domains specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/condenseRepeatedDomains.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"condenseRepeatedDomains — condenseRepeatedDomains","text":"","code":"if (FALSE) { # \\dontrun{ condenseRepeatedDomains(prot, \"DomArch\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":null,"dir":"Reference","previous_headings":"","what":"Changing case to 'Title Case' — convert2TitleCase","title":"Changing case to 'Title Case' — convert2TitleCase","text":"Translate string Title Case w/ delimitter. Translate string Title Case w/ delimitter. Changing case 'Title Case'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Changing case to 'Title Case' — convert2TitleCase","text":"","code":"convert2TitleCase(text, delimitter)  to_titlecase(text, delimitter)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Changing case to 'Title Case' — convert2TitleCase","text":"x Character vector. y Delimitter. Default space (\" \").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Changing case to 'Title Case' — convert2TitleCase","text":"Character vector input strings converted title case. character vector title case.","code":""},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Changing case to 'Title Case' — convert2TitleCase","text":"Andrie, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convert2TitleCase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Changing case to 'Title Case' — convert2TitleCase","text":"","code":"# Convert a single string to title case convert2TitleCase(\"hello world\") # Returns \"Hello World\" #> [1] \"Hello World\"  convert2TitleCase(\"hello world\") #> [1] \"Hello World\" convert2TitleCase(\"this is a test\", \"_\") #> [1] \"This is a test\""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"convertAlignment2FA — convertAlignment2FA","title":"convertAlignment2FA — convertAlignment2FA","text":"Adding Leaves alignment file w/ accessions Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertAlignment2FA — convertAlignment2FA","text":"","code":"convertAlignment2FA(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   fa_outpath = \"\",   reduced = FALSE )  convertAlignment2FA(   aln_file = \"\",   lin_file = \"data/rawdata_tsv/all_semiclean.txt\",   fa_outpath = \"\",   reduced = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertAlignment2FA — convertAlignment2FA","text":"aln_file Character. Path file. Input tab-delimited file + alignment file accnum & alignment. Default 'pspa_snf7.aln' lin_file Character. Path file. Protein file accession + number lineage mapping. Default 'pspa.txt' fa_outpath Character. Path written fasta file. Default 'NULL' reduced Boolean. TRUE, fasta file contain one sequence per lineage. Default 'FALSE'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertAlignment2FA — convertAlignment2FA","text":"character string representing FASTA formatted sequences. fa_outpath provided, FASTA also saved specified file. Character string containing Fasta formatted sequences. fa_outpath specified, function also writes sequences Fasta file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"convertAlignment2FA — convertAlignment2FA","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"convertAlignment2FA — convertAlignment2FA","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"convertAlignment2FA — convertAlignment2FA","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convertAlignment2FA — convertAlignment2FA","text":"","code":"if (FALSE) { # \\dontrun{ addLeaves2Alignment(\"pspa_snf7.aln\", \"pspa.txt\") } # }  if (FALSE) { # \\dontrun{ convertAlignment2FA(\"pspa_snf7.aln\", \"pspa.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":null,"dir":"Reference","previous_headings":"","what":"convertAlignment2Trees — convertAlignment2Trees","title":"convertAlignment2Trees — convertAlignment2Trees","text":"Generate Trees fasta files \"data/alns\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertAlignment2Trees — convertAlignment2Trees","text":"","code":"convertAlignment2Trees(aln_path = here(\"data/alns/\"))"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertAlignment2Trees — convertAlignment2Trees","text":"aln_path Path directory containing alignment FASTA files (.fa) trees generated. Default \"data/alns/\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertAlignment2Trees — convertAlignment2Trees","text":"return value. function generates tree files (.tre) alignment file specified directory.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertAlignment2Trees.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convertAlignment2Trees — convertAlignment2Trees","text":"","code":"if (FALSE) { # \\dontrun{ generate_trees(here(\"data/alns/\")) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":null,"dir":"Reference","previous_headings":"","what":"convertFA2Tree — convertFA2Tree","title":"convertFA2Tree — convertFA2Tree","text":"convertFA2Tree","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertFA2Tree — convertFA2Tree","text":"","code":"convertFA2Tree(   fa_path = here(\"data/alns/pspa_snf7.fa\"),   tre_path = here(\"data/alns/pspa_snf7.tre\"),   fasttree_path = here(\"src/FastTree\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertFA2Tree — convertFA2Tree","text":"fa_path Path input FASTA alignment file (.fa). Default path \"data/alns/pspa_snf7.fa\". tre_path Path output file generated tree (.tre) saved. Default path \"data/alns/pspa_snf7.tre\". fasttree_path Path FastTree executable, used generate phylogenetic tree. Default \"src/FastTree\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertFA2Tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertFA2Tree — convertFA2Tree","text":"return value. function generates tree file (.tre) input FASTA file.","code":""},{"path":[]},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"Using table returned createIPRScanDomainTable, construct domain fasta single accession number original fasta (.e., original fasta argument createIPRScanDomainTable())","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"","code":"convertIPRScanDomainTable2FA(df_iprscan_domains)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"df_iprscan_domains tbl_df return value createIPRScanDomainTable","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"AAStringSet domain fasta containing domains single protein original fasta passed argument createIPRScanDomainTable()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/convertIPRScanDomainTable2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable()) — convertIPRScanDomainTable2FA","text":"","code":"if (FALSE) { # \\dontrun{ path_molevol_scripts <- file.path(Sys.getenv(\"DEV\", unset = \"/data/molevolvr_transfer/molevolvr_dev\"), \"molevol_scripts\") setwd(path_molevol_scripts) source(\"R/fa2domain.R\") fasta <- Biostrings::readAAStringSet(\"./tests/example_protein.fa\") df_iprscan <- readIPRScanTSV(\"./tests/example_iprscan_valid.tsv\") accnum <- df_iprscan$AccNum[1] df_iprscan_domains <- createIPRScanDomainTable(accnum, fasta, df_iprscan) fasta_domains <- df_iprscan_domains |> convertIPRScanDomainTable2FA() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":null,"dir":"Reference","previous_headings":"","what":"countByColumn — countByColumn","title":"countByColumn — countByColumn","text":"Function obtain element counts (DA, GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"countByColumn — countByColumn","text":"","code":"countByColumn(prot = prot, column = \"DomArch\", min.freq = 1)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"countByColumn — countByColumn","text":"prot data frame containing dataset analyze, typically multiple columns including one specified column parameter. column character string specifying name column analyze. default \"DomArch\". min.freq integer specifying minimum frequency element must included output. Default 1.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"countByColumn — countByColumn","text":"tibble two columns: column unique elements specified column (e.g., \"DomArch\"). freq frequency element, .e., number times element appears specified column. tibble filtered include elements frequency greater equal min.freq include elements NA values starting hyphen (\"-\").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/countByColumn.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"countByColumn — countByColumn","text":"","code":"if (FALSE) { # \\dontrun{ countByColumn(prot = my_data, column = \"DomArch\", min.freq = 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Domain Network — createBinaryDomainNetwork","title":"Domain Network — createBinaryDomainNetwork","text":"function creates domain network 'DomArch' column. Domains part 'domains_of_interest' different node color domains. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Domain Network — createBinaryDomainNetwork","text":"","code":"createBinaryDomainNetwork(   prot,   column = \"DomArch\",   domains_of_interest,   cutoff = 70,   layout = \"nice\",   query_color = adjustcolor(\"yellow\", alpha.f = 0.5),   partner_color = adjustcolor(\"skyblue\", alpha.f = 0.5),   border_color = adjustcolor(\"grey\", alpha.f = 0.8),   IsDirected = T )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Domain Network — createBinaryDomainNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. domains_of_interest Character vector specifying domains interest. cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" query_color Color nodes domains domains_of_interest vector colored partner_color Color nodes part domains_of_interest vector colored border_color Color borders nodes. IsDirected network directed? Set false eliminate arrows","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Domain Network — createBinaryDomainNetwork","text":"network visualization domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createBinaryDomainNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Domain Network — createBinaryDomainNetwork","text":"","code":"if (FALSE) { # \\dontrun{ createBinaryDomainNetwork(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Domain Network — createDomainNetwork","title":"Domain Network — createDomainNetwork","text":"function creates domain network 'DomArch' column. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Domain Network — createDomainNetwork","text":"","code":"createDomainNetwork(   prot,   column = \"DomArch\",   domains_of_interest,   cutoff = 70,   layout = \"nice\",   query_color = adjustcolor(\"green\", alpha.f = 0.5) )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Domain Network — createDomainNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. domains_of_interest Character vector specifying domains interest. cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" query_color Character. Color represent queried domain network.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Domain Network — createDomainNetwork","text":"network visualization domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createDomainNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Domain Network — createDomainNetwork","text":"","code":"if (FALSE) { # \\dontrun{ createDomainNetwork(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":null,"dir":"Reference","previous_headings":"","what":"createFA2Tree — createFA2Tree","title":"createFA2Tree — createFA2Tree","text":"Generating phylogenetic tree alignment file '.fa'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createFA2Tree — createFA2Tree","text":"","code":"createFA2Tree(   fa_file = \"data/alns/pspa_snf7.fa\",   out_file = \"data/alns/pspa_snf7.tre\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createFA2Tree — createFA2Tree","text":"fa_file Character. Path alignment FASTA file (.fa) phylogenetic tree generated. Default 'pspa_snf7.fa'. out_file Path output file generated tree (.tre) saved. Default \"data/alns/pspa_snf7.tre\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createFA2Tree — createFA2Tree","text":"return value. function generates phylogenetic tree file (.tre) based different approaches like Neighbor Joining, UPGMA, Maximum Likelihood.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createFA2Tree — createFA2Tree","text":"alignment file need two columns: 1. accession + number 2. alignment. protein homolog accession lineage mapping + file ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"createFA2Tree — createFA2Tree","text":"Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"createFA2Tree — createFA2Tree","text":"Janani Ravi, MolEcologist","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createFA2Tree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createFA2Tree — createFA2Tree","text":"","code":"if (FALSE) { # \\dontrun{ generate_aln2tree(\"pspa_snf7.fa\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Genomic Context Directed Network — createGenomicContextNetwork","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"function creates Genomic Context network 'GenContext' column. network Genomic Context returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"","code":"createGenomicContextNetwork(   prot,   domains_of_interest,   column = \"GenContext\",   cutoff = 40,   layout = \"grid\",   directed = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"prot data frame contains column 'GenContext'. domains_of_interest Character vector domains interest. column Name column containing Genomic Context nodes edges generated. cutoff Integer. use GenContexts occur cutoff percentage total count layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\" \"nice\" directed network directed?","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"plot genomic context network.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createGenomicContextNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Genomic Context Directed Network — createGenomicContextNetwork","text":"","code":"if (FALSE) { # \\dontrun{ gc_directed_network(pspa, column = \"GenContext\", cutoff = 55) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":null,"dir":"Reference","previous_headings":"","what":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"given accession number, get domain sequences using interproscan output table & original FASTA file","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"","code":"createIPRScanDomainTable(   accnum,   fasta,   df_iprscan,   analysis = c(\"Pfam\", \"Gene3D\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"accnum chr single accession number original fasta (fasta param) used search sequence's domains (df_iprscan param) fasta AAStringSet original fasta file fed interproscan df_iprscan tbl_df output TSV interproscan, read tibble readIPRScanTSV() analysis chr domain databases extract sequences ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"tbl_df table domain sequence new identifier column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createIPRScanDomainTable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file — createIPRScanDomainTable","text":"","code":"if (FALSE) { # \\dontrun{ path_molevol_scripts <- file.path(Sys.getenv(\"DEV\", unset = \"/data/molevolvr_transfer/molevolvr_dev\"), \"molevol_scripts\") setwd(path_molevol_scripts) source(\"R/fa2domain.R\") fasta <- Biostrings::readAAStringSet(\"./tests/example_protein.fa\") df_iprscan <- readIPRScanTSV(\"./tests/example_iprscan_valid.tsv\") accnum <- df_iprscan$AccNum[1] df_iprscan_domains <- createIPRScanDomainTable(accnum, fasta, df_iprscan) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":null,"dir":"Reference","previous_headings":"","what":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"'base_url' parameter set environment variable 'BASE_URL' available, defaults \"http://jravilab.org/molevolvr/\" .","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"","code":"createJobResultsURL(   pin_id,   base_url = Sys.getenv(\"BASE_URL\", unset = \"http://jravilab.org/molevolvr/\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"pin_id unique identifier job base_url base URL MolEvolvR web app","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobResultsURL.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Given a pin_id, returns the URL where the user can check the status of their job — createJobResultsURL","text":"URL user can check status job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":null,"dir":"Reference","previous_headings":"","what":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"Produces mail message can sent user job accepted. Used sendJobStatusEmail() method.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"","code":"createJobStatusEmailMessage(   job_dir,   pin_id,   job_results_url,   event_type,   context )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"job_dir directory job's arguments stored, job_args.yml pin_id unique identifier job job_results_url URL user can check status job event_type either 'start' 'end', returns corresponding email given type context list additional values, e.g. job runtime info, can used template emails","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createJobStatusEmailMessage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method. — createJobStatusEmailMessage","text":"result sendmailR::sendmail() call","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":null,"dir":"Reference","previous_headings":"","what":"createLineageLookup — createLineageLookup","title":"createLineageLookup — createLineageLookup","text":"Create look table goes TaxID, Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createLineageLookup — createLineageLookup","text":"","code":"createLineageLookup(   lineage_file = here(\"data/rankedlineage.dmp\"),   outfile,   taxonomic_rank = \"phylum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createLineageLookup — createLineageLookup","text":"lineage_file Path rankedlineage.dmp file containing taxid's corresponding taxonomic rank. rankedlineage.dmp can downloaded https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/ outfile File resulting lineage lookup table written taxonomic_rank upperbound taxonomic rank lineage includes. lineaege include superkingdom>...>taxonomic_rank. Choices include: \"supperkingdom\", \"phylum\",   \"class\",\"order\", \"family\", \"genus\", \"species\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createLineageLookup — createLineageLookup","text":"tibble containing tax IDs respective lineages specified taxonomic rank, saved tab-separated file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"createLineageLookup — createLineageLookup","text":"Samuel Chen","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createLineageLookup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createLineageLookup — createLineageLookup","text":"","code":"if (FALSE) { # \\dontrun{ createLineageLookup(lineage_file = \"data/rankedlineage.dmp\",                       outfile = \"data/lineage_lookup.tsv\",                       taxonomic_rank = \"family\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to generate MSA using kalign — createMSA_Kalign","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"Function generate MSA using kalign","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"","code":"createMSA_Kalign(fa_file = \"\", outfile = \"\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"fa_file Character. path input FASTA file containing protein sequences. outfile Character. path output file alignment saved.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"list containing alignment object output file path.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_Kalign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to generate MSA using kalign — createMSA_Kalign","text":"","code":"if (FALSE) { # \\dontrun{ createMSA_Kalign(fa_file = \"path/to/sequences.fasta\",                   outfile = \"path/to/alignment.txt\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Sequence Alignment — createMSA_PDF","title":"Multiple Sequence Alignment — createMSA_PDF","text":"Generates multiple sequence alignment fasta file createMSA_PDF function reads fasta file generates multiple sequence alignment pdf","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Sequence Alignment — createMSA_PDF","text":"","code":"createMSA_PDF(   fasta_path,   out_path = NULL,   lowerbound = NULL,   upperbound = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Sequence Alignment — createMSA_PDF","text":"fasta_path Character. path location fasta file read. out_path Character. path location output pdf write. Default NULL. value NULL, pdf written directory fasta file. lowerbound Numeric. column determines starting location MSA. Default NULL. value NULL, entire multiple sequence alignment printed. upperbound Numeric. column determines ending location MSA. Default NULL. value NULL, entire multiple sequence alignment printed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Sequence Alignment — createMSA_PDF","text":"PDF file containing multiple sequence alignment.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createMSA_PDF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multiple Sequence Alignment — createMSA_PDF","text":"","code":"if (FALSE) { # \\dontrun{ createMSA_PDF(fasta_path = \"path/to/your/file.fasta\",          out_path = \"path/to/output/alignment.pdf\",          lowerbound = 10,          upperbound = 200) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":null,"dir":"Reference","previous_headings":"","what":"createRepresentativeAccNum — createRepresentativeAccNum","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"Function generate vector one Accession number per distinct observation 'reduced' column Function generate vector one Accession number per distinct observation 'reduced' column","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"","code":"createRepresentativeAccNum(   prot_data,   reduced = \"Lineage\",   accnum_col = \"AccNum\" )  createRepresentativeAccNum(   prot_data,   reduced = \"Lineage\",   accnum_col = \"AccNum\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"prot_data Data frame containing Accession Numbers reduced Column prot_data distinct observations generated . One accession number assigned observations accnum_col Column prot_data contains Accession Numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"character vector containing one Accession number per distinct observation specified reduced column. character vector containing representative accession numbers, one distinct observation specified 'reduced' column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createRepresentativeAccNum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createRepresentativeAccNum — createRepresentativeAccNum","text":"","code":"if (FALSE) { # \\dontrun{ createRepresentativeAccNum(prot) } # } if (FALSE) { # \\dontrun{ # Example usage with a data frame called `protein_data` createRepresentativeAccNum <- RepresentativeAccNums(prot_data = protein_data,                                                     reduced = \"Lineage\",                                                     accnum_col = \"AccNum\") representative_accessions } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"function creates domain network 'DomArch' column. network domains returned based shared domain architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"","code":"createUndirectedGenomicContextNetwork(   prot,   column = \"GenContext\",   domains_of_interest,   cutoff_type = \"Lineage\",   cutoff = 1,   layout = \"grid\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"prot data frame contains column 'DomArch'. column Name column containing Domain architecture nodes edges generated. domains_of_interest Character vector specifying domains interest. cutoff_type Character. Used determine data filtered. Either \"Total Count\" filter total amount times domain architecture occurs cutoff Integer. use domains occur cutoff total counts cutoff_type \"Total Count\". use domains appear cutoff greater lineages cutoff_type Lineage. layout Character. Layout type used network. Options : \"circle\" \"random\" \"auto\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"plot domain architecture network.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createUndirectedGenomicContextNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createUndirectedGenomicContextNetwork — createUndirectedGenomicContextNetwork","text":"","code":"if (FALSE) { # \\dontrun{ createUndirectedGenomicContextNetwork(pspa, column = \"DomArch\",  domains_of_interest = c(\"Domain1\", \"Domain2\"),  cutoff_type = \"Total Count\", cutoff = 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":null,"dir":"Reference","previous_headings":"","what":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"Wordclouds predominant domains (DAs) DAs (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"","code":"createWordCloud2Element(   query_data = \"prot\",   colname = \"DomArch\",   cutoff = 70,   UsingRowsCutoff = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default \"prot\". colname Character. name column query_data generate word cloud . Default \"DomArch\". cutoff Numeric. cutoff value filtering elements based frequency. Default 70. UsingRowsCutoff Logical. Whether use row-based cutoff instead frequency cutoff. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"word cloud plot showing frequency elements selected column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloud2Element.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wordclouds for the predominant domains, domain architectures. — createWordCloud2Element","text":"","code":"if (FALSE) { # \\dontrun{ createWordCloudElement(prot, \"da2doms\", 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":null,"dir":"Reference","previous_headings":"","what":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"Wordclouds predominant domains (DAs) DAs (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"","code":"createWordCloudElement(   query_data = \"prot\",   colname = \"DomArch\",   cutoff = 70,   UsingRowsCutoff = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default \"prot\". colname Character. name column query_data generate word cloud . Default \"DomArch\". cutoff Numeric. cutoff value filtering elements based frequency. Default 70. UsingRowsCutoff Logical. Whether use row-based cutoff instead frequency cutoff. Default FALSE.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"word cloud plot showing frequency elements selected column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/createWordCloudElement.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wordclouds for the predominant domains, domain architectures — createWordCloudElement","text":"","code":"if (FALSE) { # \\dontrun{ createWordCloudElement(prot, \"da2doms\", 10) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":null,"dir":"Reference","previous_headings":"","what":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"Download combined assembly summaries genbank refseq","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"","code":"downloadAssemblySummary(   outpath,   keep = c(\"assembly_accession\", \"taxid\", \"species_taxid\", \"organism_name\") )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"outpath String path assembly summary file written keep Character vector containing columns retained downloaded","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"tab-separated file containing assembly summary. function notreturn value writes output directly specified file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/downloadAssemblySummary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download the combined assembly summaries of genbank and refseq — downloadAssemblySummary","text":"","code":"if (FALSE) { # \\dontrun{ downloadAssemblySummary(outpath = \"assembly_summary.tsv\",      keep = c(\"assembly_accession\", \"taxid\", \"organism_name\")) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":null,"dir":"Reference","previous_headings":"","what":"efetchIPG — efetchIPG","title":"efetchIPG — efetchIPG","text":"Perform efetch ipg database write results out_path Perform efetch ipg database write results out_path","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"efetchIPG — efetchIPG","text":"","code":"efetchIPG(accessions, out_path, plan = \"multicore\")  efetchIPG(accessions, out_path, plan = \"multicore\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"efetchIPG — efetchIPG","text":"accessions Character vector containing accession numbers query ipg database out_path Path write efetch results plan Character. Specifies execution plan parallel processing. Default \"multicore\". accnums Character vector containing accession numbers query ipg database","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"efetchIPG — efetchIPG","text":"return value. function writes fetched results out_path. function return value writes efetch results directly specified out_path.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"efetchIPG — efetchIPG","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/efetchIPG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"efetchIPG — efetchIPG","text":"","code":"if (FALSE) { # \\dontrun{ efetchIPG() } # } if (FALSE) { # \\dontrun{ efetchIPG(   accessions = c(\"P12345\", \"Q67890\", \"A12345\"),   out_path = \"path/to/efetch_results.xml\" ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":null,"dir":"Reference","previous_headings":"","what":"elements2Words — elements2Words","title":"elements2Words — elements2Words","text":"Break string ELEMENTS WORDS domain architecture (DA) genomic context (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"elements2Words — elements2Words","text":"","code":"elements2Words(prot, column = \"DomArch\", conversion_type = \"da2doms\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"elements2Words — elements2Words","text":"prot dataframe containing dataset analyze. specified column contains string elements processed. column character string specifying name column analyze. Default \"DomArch\". conversion_type character string specifying type conversion. Two options available: da2doms Convert domain architectures individual domains replacing + symbols spaces. gc2da Convert genomic context domain architectures replacing directional symbols (<-, ->, |) spaces.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"elements2Words — elements2Words","text":"single string elements delimited spaces. function performs necessary substitutions based conversion_type cleans extraneous characters like newlines, tabs, multiple spaces.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/elements2Words.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"elements2Words — elements2Words","text":"","code":"if (FALSE) { # \\dontrun{ tibble::tibble(DomArch = c(\"aaa+bbb\",  \"a+b\", \"b+c\", \"b-c\")) |> elements2Words() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":null,"dir":"Reference","previous_headings":"","what":"make accnums unique — ensureUniqAccNum","title":"make accnums unique — ensureUniqAccNum","text":"Append index occurence suffix accession number (character vector) making unique","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"make accnums unique — ensureUniqAccNum","text":"","code":"ensureUniqAccNum(accnums)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"make accnums unique — ensureUniqAccNum","text":"accnums chr vector accession numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"make accnums unique — ensureUniqAccNum","text":"chr vector adjusted, unique accession numbers","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/ensureUniqAccNum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"make accnums unique — ensureUniqAccNum","text":"","code":"if (FALSE) { # \\dontrun{ c(\"xxx\", \"xxx\", \"xxx\", \"yyy\", \"yyy\") |>     ensureUniqAccNum() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":null,"dir":"Reference","previous_headings":"","what":"extractAccNum — extractAccNum","title":"extractAccNum — extractAccNum","text":"extractAccNum","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"extractAccNum — extractAccNum","text":"","code":"extractAccNum(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"extractAccNum — extractAccNum","text":"string string extract accession number. string may contain accession information delimited | spaces.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"extractAccNum — extractAccNum","text":"Describe return, detail","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/extractAccNum.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"extractAccNum — extractAccNum","text":"","code":"if (FALSE) { # \\dontrun{ extractAccNum() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":null,"dir":"Reference","previous_headings":"","what":"filterByDomains — filterByDomains","title":"filterByDomains — filterByDomains","text":"filterByDomains filters data frame identifying exact domain matches either keeping removing rows identified domain","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filterByDomains — filterByDomains","text":"","code":"filterByDomains(   prot,   column = \"DomArch\",   doms_keep = c(),   doms_remove = c(),   ignore.case = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filterByDomains — filterByDomains","text":"prot Dataframe filter column Column search domains (DomArch column) doms_keep Vector domains must identified within column order observation kept doms_remove Vector domains , found within observation, removed ignore.case matching non case sensitive","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"filterByDomains — filterByDomains","text":"Filtered data frame","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"filterByDomains — filterByDomains","text":"need make domains 'regex safe', handled function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"filterByDomains — filterByDomains","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByDomains.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"filterByDomains — filterByDomains","text":"","code":"if (FALSE) { # \\dontrun{ filterByDomains() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":null,"dir":"Reference","previous_headings":"","what":"filterByFrequency — filterByFrequency","title":"filterByFrequency — filterByFrequency","text":"Function filter based frequencies","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filterByFrequency — filterByFrequency","text":"","code":"filterByFrequency(x, min.freq)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filterByFrequency — filterByFrequency","text":"x tibble (tbl_df) containing least two columns: one elements (e.g., words) one frequency (e.g., freq). min.freq numeric value specifying minimum frequency threshold. elements frequencies greater equal value retained.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"filterByFrequency — filterByFrequency","text":"tibble structure x, filtered include rows frequency greater equal min.freq.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/filterByFrequency.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"filterByFrequency — filterByFrequency","text":"","code":"if (FALSE) { # \\dontrun{ filterByFrequency() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":null,"dir":"Reference","previous_headings":"","what":"findParalogs — findParalogs","title":"findParalogs — findParalogs","text":"Creates data frame paralogs.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"findParalogs — findParalogs","text":"","code":"findParalogs(prot)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"findParalogs — findParalogs","text":"prot data frame filtered Query, containing columns Species Lineage","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"findParalogs — findParalogs","text":"returns dataframe containing paralogs counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"findParalogs — findParalogs","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/findParalogs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"findParalogs — findParalogs","text":"","code":"if (FALSE) { # \\dontrun{ findParalogs(pspa) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":null,"dir":"Reference","previous_headings":"","what":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"Format job arguments html-formatted key/value pairs, including email","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"","code":"formatJobArgumentsHTML(job_args)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"job_args list job arguments, e.g. read job_args.yml file","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"list HTML-formatted key/value pairs","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/formatJobArgumentsHTML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format job arguments into html-formatted key/value pairs, for including in an email — formatJobArgumentsHTML","text":"","code":"if (FALSE) { # \\dontrun{ formatJobArgumentsHTML(\"/data/scratch/janani/molevolvr_out/Ba5sV1_full\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"generateAllAlignments2FA — generateAllAlignments2FA","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"Adding Leaves alignment file w/ accessions Adding Leaves alignment files w/ accessions & DAs? Adding Leaves alignment file w/ accessions Adding Leaves alignment files w/ accessions & DAs?","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"","code":"generateAllAlignments2FA(   aln_path = here(\"data/rawdata_aln/\"),   fa_outpath = here(\"data/alns/\"),   lin_file = here(\"data/rawdata_tsv/all_semiclean.txt\"),   reduced = F )  generateAllAlignments2FA(   aln_path = here(\"data/rawdata_aln/\"),   fa_outpath = here(\"data/alns/\"),   lin_file = here(\"data/rawdata_tsv/all_semiclean.txt\"),   reduced = F )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"aln_path Character. Path alignment files. Default '(\"data/rawdata_aln/\")' fa_outpath Character. Path file. Master protein file AccNum & lineages. Default '(\"data/rawdata_tsv/all_semiclean.txt\")' lin_file Character. Path written fasta file. Default '(\"data/alns/\")'. reduced Boolean. TRUE, fasta file contain one sequence per lineage. Default 'FALSE'.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"NULL. function saves output FASTA files specified directory. NULL. function saves output FASTA files specified directory.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"alignment files need two columns separated spaces: AccNum 2. alignment. protein homolog file AccNum, Species, Lineages. alignment files need two columns separated spaces: AccNum 2. alignment. protein homolog file AccNum, Species, Lineages.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"Please refer source code alternate + file formats /column names. Please refer source code alternate + file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/generateAllAlignments2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"generateAllAlignments2FA — generateAllAlignments2FA","text":"","code":"if (FALSE) { # \\dontrun{ generateAllAlignments2FA() } # } if (FALSE) { # \\dontrun{ generateAllAlignments2FA() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":null,"dir":"Reference","previous_headings":"","what":"getAccNumFromFA — getAccNumFromFA","title":"getAccNumFromFA — getAccNumFromFA","text":"getAccNumFromFA getAccNumFromFA","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getAccNumFromFA — getAccNumFromFA","text":"","code":"getAccNumFromFA(fasta_file)  getAccNumFromFA(fasta_file)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getAccNumFromFA — getAccNumFromFA","text":"fasta_file Character. Path FASTA file accession numbers extracted.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getAccNumFromFA — getAccNumFromFA","text":"character vector containing extracted accession numbers. character vector containing extracted accession numbers.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getAccNumFromFA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getAccNumFromFA — getAccNumFromFA","text":"","code":"if (FALSE) { # \\dontrun{ getAccNumFromFA(\"my_sequences.fasta\") } # } if (FALSE) { # \\dontrun{ # Example usage accnums <- getAccNumFromFA(\"path/to/sequences.fasta\") accnums } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":null,"dir":"Reference","previous_headings":"","what":"getDomainsFromFA — getDomainsFromFA","title":"getDomainsFromFA — getDomainsFromFA","text":"getDomainsFromFA","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getDomainsFromFA — getDomainsFromFA","text":"","code":"getDomainsFromFA(   fasta,   df_iprscan,   analysis = c(\"Pfam\", \"Gene3D\"),   verbose = FALSE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getDomainsFromFA — getDomainsFromFA","text":"fasta AAStringSet protein (AA) fasta df_iprscan tbl_df interproscan results original fasta analysis chr domain databases extract sequences ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getDomainsFromFA — getDomainsFromFA","text":"fasta_domains AAStringSet fasta domains","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getDomainsFromFA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getDomainsFromFA — getDomainsFromFA","text":"","code":"if (FALSE) { # \\dontrun{ path_molevol_scripts <- file.path(Sys.getenv(\"DEV\", unset = \"/data/molevolvr_transfer/molevolvr_dev\"), \"molevol_scripts\") setwd(path_molevol_scripts) source(\"R/fa2domain.R\") fasta <- Biostrings::readAAStringSet(\"./tests/example_protein.fa\") df_iprscan <- readIPRScanTSV(\"./tests/example_iprscan_valid.tsv\") getDomainsFromFA(fasta, df_iprscan) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColNames.html","id":null,"dir":"Reference","previous_headings":"","what":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","title":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","text":"Constructor function interproscan column names (based upon global variable written molevol_scripts/R/colnames_molevol.R)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColNames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","text":"","code":"getIPRScanColNames()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColNames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColNames","text":"chr interproscan column names used throughout molevolvr","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColTypes.html","id":null,"dir":"Reference","previous_headings":"","what":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","title":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","text":"construct column types reading interproscan output TSVs (based upon global variable written molevol_scripts/R/colnames_molevol.R)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColTypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","text":"","code":"getIPRScanColTypes()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getIPRScanColTypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R) — getIPRScanColTypes","text":"collector named vector type expecatations interproscan columns","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":null,"dir":"Reference","previous_headings":"","what":"getProcessRuntimeWeights — getProcessRuntimeWeights","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"Quickly get runtime weights MolEvolvR backend processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"","code":"getProcessRuntimeWeights(medians_yml_path = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"dir_job_results chr path MolEvolvR job_results directory","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getProcessRuntimeWeights.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getProcessRuntimeWeights — getProcessRuntimeWeights","text":"list names: processes; values: median runtime (seconds) example: writeProcessRuntime2YML()","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":null,"dir":"Reference","previous_headings":"","what":"getTopAccByLinDomArch — getTopAccByLinDomArch","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"Group lineage + DA take top 20","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"","code":"getTopAccByLinDomArch(   infile_full,   DA_col = \"DomArch.Pfam\",   lin_col = \"Lineage_short\",   n = 20,   query )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"infile_full data frame containing full dataset lineage domain architecture information. DA_col string representing name domain architecture column. Default \"DomArch.Pfam\". lin_col string representing name lineage column. Default \"Lineage_short\". n integer specifying number top accession numbers return. Default 20. query string filtering specific query name. \"\", data matching query processed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"vector top N accession numbers (AccNum) based counts grouped lineage domain architecture.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/getTopAccByLinDomArch.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getTopAccByLinDomArch — getTopAccByLinDomArch","text":"","code":"if (FALSE) { # \\dontrun{ top_accessions <- getTopAccByLinDomArch(infile_full = my_data, DA_col = \"DomArch.Pfam\", lin_col = \"Lineage_short\", n = 20, query = \"specific_query_name\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":null,"dir":"Reference","previous_headings":"","what":"mapAcc2Name — mapAcc2Name","title":"mapAcc2Name — mapAcc2Name","text":"Default renameFA() replacement function. Maps accession number name Default rename_fasta() replacement function. Maps accession number name","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mapAcc2Name — mapAcc2Name","text":"","code":"mapAcc2Name(line, acc2name, acc_col = \"AccNum\", name_col = \"Name\")  mapAcc2Name(line, acc2name, acc_col = \"AccNum\", name_col = \"Name\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mapAcc2Name — mapAcc2Name","text":"line line fasta file starting '>' acc2name Data Table containing column accession numbers name column acc_col Name column containing Accession numbers name_col Name column containing names accession numbers mapped ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mapAcc2Name — mapAcc2Name","text":"character string representing updated FASTA line, accession number replaced corresponding name. Character string. modified line Fasta file header name instead accession number.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAcc2Name.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"mapAcc2Name — mapAcc2Name","text":"","code":"if (FALSE) { # \\dontrun{ mapAcc2Name(\">P12345 some description\", acc2name, \"AccNum\", \"Name\") } # } if (FALSE) { # \\dontrun{ acc2name_table <- data.table(AccNum = c(\"ACC001\", \"ACC002\"), Name = c(\"Species A\", \"Species B\")) line <- \">ACC001 some additional info\" mapped_line <- mapAcc2Name(line, acc2name_table) mapped_line  # Expected output: \">Species A\" } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":null,"dir":"Reference","previous_headings":"","what":"mapAdvOption2Process — mapAdvOption2Process","title":"mapAdvOption2Process — mapAdvOption2Process","text":"Use MolEvolvR advanced options get associated processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mapAdvOption2Process — mapAdvOption2Process","text":"","code":"mapAdvOption2Process(advanced_opts)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mapAdvOption2Process — mapAdvOption2Process","text":"advanced_opts character vector MolEvolvR advanced options","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapAdvOption2Process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mapAdvOption2Process — mapAdvOption2Process","text":"character vector process names execute given advanced options example: advanced_opts <- c(\"homology_search\", \"domain_architecture\") procs <- mapAdvOption2Process(advanced_opts)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapOption2Process.html","id":null,"dir":"Reference","previous_headings":"","what":"mapOption2Process — mapOption2Process","title":"mapOption2Process — mapOption2Process","text":"Construct list names (MolEvolvR advanced options) point processes","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapOption2Process.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mapOption2Process — mapOption2Process","text":"","code":"mapOption2Process()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/mapOption2Process.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mapOption2Process — mapOption2Process","text":"list names (MolEvolvR advanced options) point processes example: list_opts2procs <- mapOption2Process","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotEstimatedWallTimes.html","id":null,"dir":"Reference","previous_headings":"","what":"plotEstimatedWallTimes — plotEstimatedWallTimes","title":"plotEstimatedWallTimes — plotEstimatedWallTimes","text":"Plot estimated runtimes different advanced options number inputs function just fun; , messy code","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotEstimatedWallTimes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotEstimatedWallTimes — plotEstimatedWallTimes","text":"","code":"plotEstimatedWallTimes()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotEstimatedWallTimes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotEstimatedWallTimes — plotEstimatedWallTimes","text":"line plot object example: p <- plotEstimatedWallTimes() ggplot2::ggsave(filename = \"/data/molevolvr_transfer/molevolvr_ dev/molevol_scripts/docs/estimate_walltimes.png\", plot = p)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":null,"dir":"Reference","previous_headings":"","what":"plotIPR2Viz — plotIPR2Viz","title":"plotIPR2Viz — plotIPR2Viz","text":"plotIPR2Viz","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotIPR2Viz — plotIPR2Viz","text":"","code":"plotIPR2Viz(   infile_ipr = NULL,   infile_full = NULL,   accessions = c(),   analysis = c(\"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"),   group_by = \"Analysis\",   topn = 20,   name = \"Name\",   text_size = 15,   query = \"All\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotIPR2Viz — plotIPR2Viz","text":"infile_ipr path input IPR file (TSV format) containing domain information. infile_full path full input file (TSV format) containing lineage accession information. accessions character vector accession numbers filter analysis. Default empty vector. analysis character vector specifying types analysis include (e.g., \"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"). Default vector analyses. group_by string specifying group visualization. Default \"Analysis\". Options include \"Analysis\" \"Query\". topn integer specifying number top accessions visualize. Default 20. name string representing name use y-axis labels. Default \"Name\". text_size integer specifying text size plot. Default 15. query string filtering specific query name. \"\", data matching query processed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotIPR2Viz — plotIPR2Viz","text":"ggplot object representing domain architecture visualization.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2Viz.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotIPR2Viz — plotIPR2Viz","text":"","code":"if (FALSE) { # \\dontrun{ plot <- plotIPR2Viz(infile_ipr = \"path/to/ipr_file.tsv\",                     infile_full = \"path/to/full_file.tsv\",                     accessions = c(\"ACC123\", \"ACC456\"),                     analysis = c(\"Pfam\", \"TMHMM\"),                     group_by = \"Analysis\",                     topn = 20,                     name = \"Gene Name\",                     text_size = 15,                     query = \"All\") plot } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":null,"dir":"Reference","previous_headings":"","what":"plotIPR2VizWeb — plotIPR2VizWeb","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"plotIPR2VizWeb","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"","code":"plotIPR2VizWeb(   infile_ipr,   accessions,   analysis = c(\"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"),   group_by = \"Analysis\",   name = \"Name\",   text_size = 15,   legend_name = \"ShortName\",   cols = 5,   rows = 10 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"infile_ipr path input IPR file (TSV format) containing domain information. accessions character vector accession numbers filter analysis. analysis character vector specifying types analysis include (e.g., \"Pfam\", \"Phobius\", \"TMHMM\", \"Gene3D\"). Default vector analyses. group_by string specifying group visualization. Default \"Analysis\". Options include \"Analysis\" \"Query\". name string representing name use y-axis labels. Default \"Name\". text_size integer specifying text size plot. Default 15. legend_name string representing column use legend labels. Default \"ShortName\". cols integer specifying number columns facet wrap. Default 5. rows integer specifying number rows legend. Default 10.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"ggplot object representing domain architecture visualization web display.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotIPR2VizWeb.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotIPR2VizWeb — plotIPR2VizWeb","text":"","code":"if (FALSE) { # \\dontrun{ plot <- plotIPR2VizWeb(infile_ipr = \"path/to/ipr_file.tsv\",                        accessions = c(\"ACC123\", \"ACC456\"),                        analysis = c(\"Pfam\", \"TMHMM\"),                        group_by = \"Analysis\",                        name = \"Gene Name\",                        text_size = 15,                        legend_name = \"ShortName\",                        cols = 5,                        rows = 10) plot } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"Lineage plot Domains, Domain Architectures Genomic Contexts. Heatmap.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"","code":"plotLineageDA(   query_data = \"prot\",   colname = \"DomArch\",   cutoff = 90,   RowsCutoff = FALSE,   color = \"default\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default prot (variable w/ protein data). colname Column name query_data: \"DomArch.norep\", \"GenContext.norep\", \"DomArch.PFAM.norep\" \"DomArch.LADB.norep\". Default \"DomArch.norep\". cutoff Numeric. Cutoff word frequency. Default 90. RowsCutoff Boolean. TRUE, applies row cutoff remove data rows based certain condition. Default FALSE. color Color heatmap. One six options: \"default\", \"magma\", \"inferno\", \"plasma\", \"viridis\", \"cividis\"","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"LineageDA plot object.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages — plotLineageDA","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageDA(toast_rack_data, 10, \"DomArch.norep\", \"da2doms\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"Lineage Domain Repeats Plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"","code":"plotLineageDomainRepeats(query_data, colname)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"query_data Data frame containing protein homolog data, including relevant domain architectures lineages. colname Character. name column query_data contains domain architectures structural information.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"ggplot object representing heatmap (tile plot) domain repeat counts across different lineages, color intensity representing occurrence domains.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageDomainRepeats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Domain Repeats Plot — plotLineageDomainRepeats","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageDomainRepeats() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":null,"dir":"Reference","previous_headings":"","what":"plotLineageHeatmap — plotLineageHeatmap","title":"plotLineageHeatmap — plotLineageHeatmap","text":"Generate lineage plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotLineageHeatmap — plotLineageHeatmap","text":"","code":"plotLineageHeatmap(prot, domains_of_interest, level = 3, label.size = 8)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotLineageHeatmap — plotLineageHeatmap","text":"prot Data frame containing DomArch Lineage Columns domains_of_interest Vector domains check presence lineages level max depth Lineage. ie) = Kingdom, 2 = Phylum, 3 = class ... label.size Size text labels","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotLineageHeatmap — plotLineageHeatmap","text":"ggplot object representing heatmap (tile plot) domain repeat counts across different lineages, color intensity representing occurrence domains.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"plotLineageHeatmap — plotLineageHeatmap","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageHeatmap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotLineageHeatmap — plotLineageHeatmap","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageHeatmap(psp_data,     c(         \"PspA\", \"Snf7\", \"Classical-AAA\", \"PspF\", \"PspB\", \"PspC\", \"ClgR\", \"PspM\",         \"Thioredoxin\", \"PspN_N\", \"DUF3046\", \"LiaI-LiaF-TM\", \"Toast_rack\", \"REC\",         \"HISKIN\", \"HAAS\", \"SHOCT-bihelical\", \"SHOCT-like\", \"Tfu_1009\", \"PspAA\",         \"Spermine_synth\", \"TM-Flotillin\", \"Band-7\", \"Betapropeller\",         \"MacB_PCD\", \"FTSW_RODA_SPOVE\", \"Cest_Tir\", \"SIGMA-HTH\", \"GNTR-HTH\",         \"DUF2089-HTH\", \"PadR-HTH\", \"RHH\", \"ZnR\"     ),     level = 2 ) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Plot for top neighbors — plotLineageNeighbors","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"Lineage plot top neighbors obtained DAs Genomic Contexts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"","code":"plotLineageNeighbors(   query_data = \"prot\",   query = \"pspa\",   colname = \"GenContext.norep\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default pspa_data. query Name query protein/domain. Default \"pspa\". colname Column name query_data. Default \"GenContext.norep\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"ggplot object representing heatmap (tile plot) lineage versus top neighboring domain architectures, color intensity representing frequency occurrences.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageNeighbors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Plot for top neighbors — plotLineageNeighbors","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageNeighbors(pspa_data, pspa, \"GenContext.norep\", \"da2doms\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"Lineage plot queries. Heatmap.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"","code":"plotLineageQuery(   query_data = all,   queries,   colname = \"ClustName\",   cutoff,   color = \"default\" )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default prot (variable w/ protein data). queries Character Vector containing queries used categories. colname Character. column used filtering based queries. Default \"ClustName\". cutoff Numeric. cutoff value filtering rows based total count. Rows values cutoff excluded. color Character. Defines color palette used heatmap. Default red gradient.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"ggplot object representing heatmap (tile plot) showing relationship queries lineages, intensity color representing count matching records.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"Janani Ravi, Samuel Chen","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageQuery.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageQuery(prot, c(\"PspA\", \"PspB\", \"PspC\", \"PspM\", \"PspN\"), 95) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":null,"dir":"Reference","previous_headings":"","what":"Lineage Sunburst — plotLineageSunburst","title":"Lineage Sunburst — plotLineageSunburst","text":"Lineage Sunburst","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lineage Sunburst — plotLineageSunburst","text":"","code":"plotLineageSunburst(   prot,   lineage_column = \"Lineage\",   type = \"sunburst\",   levels = 2,   colors = NULL,   legendOrder = NULL,   showLegend = TRUE,   maxLevels = 5 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lineage Sunburst — plotLineageSunburst","text":"prot Data frame containing lineage column sunburst plot generated lineage_column String. Name lineage column within data frame. Defaults \"Lineage\" type String, either \"sunburst\" \"sund2b\". type \"sunburst\", sunburst plot lineage levels Integer. Number levels sunburst . colors vector colors sunburst plot. NULL, default colors used. legendOrder String vector. order legend. legendOrder NULL, showLegend Boolean. TRUE, legend enabled component first renders. maxLevels Integer, maximum number levels display sunburst; 5 default, NULL disable legend descending order top level hierarchy. rendered. type sund2b, sund2b plot rendered.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lineage Sunburst — plotLineageSunburst","text":"sunburst sund2b plot based input lineage data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotLineageSunburst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lineage Sunburst — plotLineageSunburst","text":"","code":"if (FALSE) { # \\dontrun{ plotLineageSunburst(prot, lineage_column = \"Lineage\", type = \"sunburst\", levels = 3) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"Stacked Lineage Plot — plotStackedLineage","title":"Stacked Lineage Plot — plotStackedLineage","text":"Stacked Lineage Plot","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stacked Lineage Plot — plotStackedLineage","text":"","code":"plotStackedLineage(   prot,   column = \"DomArch\",   cutoff,   Lineage_col = \"Lineage\",   xlabel = \"Domain Architecture\",   reduce_lineage = TRUE,   label.size = 8,   legend.position = c(0.7, 0.4),   legend.text.size = 10,   legend.cols = 2,   legend.size = 0.7,   coord_flip = TRUE,   legend = TRUE )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stacked Lineage Plot — plotStackedLineage","text":"prot Data frame containing protein data including domain architecture lineage information. column Character. name column prot representing domain architectures (default \"DomArch\"). cutoff Numeric. threshold value filtering domain architectures protein counts. Lineage_col Character. name column representing lineage data (default \"Lineage\"). xlabel Character. Label x-axis (default \"Domain Architecture\"). reduce_lineage Logical. Whether shorten lineage names (default TRUE). label.size Numeric. size axis text labels (default 8). legend.position Numeric vector. Coordinates placing legend (default c(0.7, 0.4)). legend.text.size Numeric. Size text legend (default 10). legend.cols Numeric. Number columns legend (default 2). legend.size Numeric. Size legend keys (default 0.7). coord_flip Logical. Whether flip coordinates plot (default TRUE). legend Logical. Whether display legend (default TRUE).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stacked Lineage Plot — plotStackedLineage","text":"ggplot object representing stacked bar plot showing distribution protein domain architectures across lineages.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotStackedLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stacked Lineage Plot — plotStackedLineage","text":"","code":"if (FALSE) { # \\dontrun{ plotStackedLineage() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an interactive plotly from count data — plotSunburst","title":"Create an interactive plotly from count data — plotSunburst","text":"functions help quickly create interactive hierarchical plots categorical data. expect summary data created dplyr::count() produce either sunburst plot (plotSunburst()) treemap plot (plotTreemap())","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an interactive plotly from count data — plotSunburst","text":"","code":"plotSunburst(count_data, fill_by_n = FALSE, sort_by_n = FALSE, maxdepth = 2)  plotTreemap(count_data, fill_by_n = FALSE, sort_by_n = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an interactive plotly from count data — plotSunburst","text":"count_data data frame containing data. fill_by_n Logical indicating fill color based counts. sort_by_n Logical indicating data sorted counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotSunburst.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an interactive plotly from count data — plotSunburst","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union starwars_count <- count(starwars, species, eye_color, name)  # sunburst plot plotSunburst(starwars_count)  {\"x\":{\"visdat\":{\"17092f34d3e0\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"17092f34d3e0\",\"attrs\":{\"17092f34d3e0\":{\"ids\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.white\",\"Aleena.->.unknown.->.Ratts Tyerel\",\"Besalisk.->.yellow.->.Dexter Jettster\",\"Cerean.->.yellow.->.Ki-Adi-Mundi\",\"Chagrian.->.blue.->.Mas Amedda\",\"Clawdite.->.yellow.->.Zam Wesell\",\"Droid.->.black.->.BB8\",\"Droid.->.red.->.IG-88\",\"Droid.->.red.->.R2-D2\",\"Droid.->.red.->.R5-D4\",\"Droid.->.red, blue.->.R4-P17\",\"Droid.->.yellow.->.C-3PO\",\"Dug.->.orange.->.Sebulba\",\"Ewok.->.brown.->.Wicket Systri Warrick\",\"Geonosian.->.yellow.->.Poggle the Lesser\",\"Gungan.->.orange.->.Jar Jar Binks\",\"Gungan.->.orange.->.Roos Tarpals\",\"Gungan.->.orange.->.Rugor Nass\",\"Human.->.blue.->.Anakin Skywalker\",\"Human.->.blue.->.Beru Whitesun Lars\",\"Human.->.blue.->.Cliegg Lars\",\"Human.->.blue.->.Finis Valorum\",\"Human.->.blue.->.Jocasta Nu\",\"Human.->.blue.->.Lobot\",\"Human.->.blue.->.Luke Skywalker\",\"Human.->.blue.->.Mon Mothma\",\"Human.->.blue.->.Owen Lars\",\"Human.->.blue.->.Qui-Gon Jinn\",\"Human.->.blue.->.Ric Olié\",\"Human.->.blue.->.Wilhuff Tarkin\",\"Human.->.blue-gray.->.Obi-Wan Kenobi\",\"Human.->.brown.->.Arvel Crynyd\",\"Human.->.brown.->.Bail Prestor Organa\",\"Human.->.brown.->.Biggs Darklighter\",\"Human.->.brown.->.Boba Fett\",\"Human.->.brown.->.Dooku\",\"Human.->.brown.->.Dormé\",\"Human.->.brown.->.Han Solo\",\"Human.->.brown.->.Jango Fett\",\"Human.->.brown.->.Lando Calrissian\",\"Human.->.brown.->.Leia Organa\",\"Human.->.brown.->.Mace Windu\",\"Human.->.brown.->.Padmé Amidala\",\"Human.->.brown.->.Poe Dameron\",\"Human.->.brown.->.Quarsh Panaka\",\"Human.->.brown.->.Raymus Antilles\",\"Human.->.brown.->.Shmi Skywalker\",\"Human.->.dark.->.Finn\",\"Human.->.hazel.->.Rey\",\"Human.->.hazel.->.Wedge Antilles\",\"Human.->.unknown.->.Captain Phasma\",\"Human.->.yellow.->.Darth Vader\",\"Human.->.yellow.->.Palpatine\",\"Hutt.->.orange.->.Jabba Desilijic Tiure\",\"Iktotchi.->.orange.->.Saesee Tiin\",\"Kaleesh.->.green, yellow.->.Grievous\",\"Kaminoan.->.black.->.Lama Su\",\"Kaminoan.->.black.->.Taun We\",\"Kel Dor.->.black.->.Plo Koon\",\"Mirialan.->.blue.->.Barriss Offee\",\"Mirialan.->.blue.->.Luminara Unduli\",\"Mon Calamari.->.orange.->.Ackbar\",\"Muun.->.gold.->.San Hill\",\"Nautolan.->.black.->.Kit Fisto\",\"Neimodian.->.red.->.Nute Gunray\",\"Pau'an.->.black.->.Tion Medon\",\"Quermian.->.yellow.->.Yarael Poof\",\"Rodian.->.black.->.Greedo\",\"Skakoan.->.unknown.->.Wat Tambor\",\"Sullustan.->.black.->.Nien Nunb\",\"Tholothian.->.blue.->.Adi Gallia\",\"Togruta.->.black.->.Shaak Ti\",\"Toong.->.orange.->.Ben Quadinaros\",\"Toydarian.->.yellow.->.Watto\",\"Trandoshan.->.red.->.Bossk\",\"Twi'lek.->.hazel.->.Ayla Secura\",\"Twi'lek.->.pink.->.Bib Fortuna\",\"Vulptereen.->.yellow.->.Dud Bolt\",\"Wookiee.->.blue.->.Chewbacca\",\"Wookiee.->.blue.->.Tarfful\",\"Xexto.->.black.->.Gasgano\",\"Yoda's species.->.brown.->.Yoda\",\"Zabrak.->.brown.->.Eeth Koth\",\"Zabrak.->.yellow.->.Darth Maul\",\"NA.->.blue.->.Jek Tono Porkins\",\"NA.->.brown.->.Cordé\",\"NA.->.brown.->.Gregar Typho\",\"NA.->.white.->.Sly Moore\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Droid\",\"Droid\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"Zabrak\",\"NA\",\"NA\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.brown\",\"NA.->.white\"],\"labels\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",null,\"unknown\",\"yellow\",\"yellow\",\"blue\",\"yellow\",\"black\",\"red\",\"red, blue\",\"yellow\",\"orange\",\"brown\",\"yellow\",\"orange\",\"blue\",\"blue-gray\",\"brown\",\"dark\",\"hazel\",\"unknown\",\"yellow\",\"orange\",\"orange\",\"green, yellow\",\"black\",\"black\",\"blue\",\"orange\",\"gold\",\"black\",\"red\",\"black\",\"yellow\",\"black\",\"unknown\",\"black\",\"blue\",\"black\",\"orange\",\"yellow\",\"red\",\"hazel\",\"pink\",\"yellow\",\"blue\",\"black\",\"brown\",\"brown\",\"yellow\",\"blue\",\"brown\",\"white\",\"Ratts Tyerel\",\"Dexter Jettster\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Zam Wesell\",\"BB8\",\"IG-88\",\"R2-D2\",\"R5-D4\",\"R4-P17\",\"C-3PO\",\"Sebulba\",\"Wicket Systri Warrick\",\"Poggle the Lesser\",\"Jar Jar Binks\",\"Roos Tarpals\",\"Rugor Nass\",\"Anakin Skywalker\",\"Beru Whitesun Lars\",\"Cliegg Lars\",\"Finis Valorum\",\"Jocasta Nu\",\"Lobot\",\"Luke Skywalker\",\"Mon Mothma\",\"Owen Lars\",\"Qui-Gon Jinn\",\"Ric Olié\",\"Wilhuff Tarkin\",\"Obi-Wan Kenobi\",\"Arvel Crynyd\",\"Bail Prestor Organa\",\"Biggs Darklighter\",\"Boba Fett\",\"Dooku\",\"Dormé\",\"Han Solo\",\"Jango Fett\",\"Lando Calrissian\",\"Leia Organa\",\"Mace Windu\",\"Padmé Amidala\",\"Poe Dameron\",\"Quarsh Panaka\",\"Raymus Antilles\",\"Shmi Skywalker\",\"Finn\",\"Rey\",\"Wedge Antilles\",\"Captain Phasma\",\"Darth Vader\",\"Palpatine\",\"Jabba Desilijic Tiure\",\"Saesee Tiin\",\"Grievous\",\"Lama Su\",\"Taun We\",\"Plo Koon\",\"Barriss Offee\",\"Luminara Unduli\",\"Ackbar\",\"San Hill\",\"Kit Fisto\",\"Nute Gunray\",\"Tion Medon\",\"Yarael Poof\",\"Greedo\",\"Wat Tambor\",\"Nien Nunb\",\"Adi Gallia\",\"Shaak Ti\",\"Ben Quadinaros\",\"Watto\",\"Bossk\",\"Ayla Secura\",\"Bib Fortuna\",\"Dud Bolt\",\"Chewbacca\",\"Tarfful\",\"Gasgano\",\"Yoda\",\"Eeth Koth\",\"Darth Maul\",\"Jek Tono Porkins\",\"Cordé\",\"Gregar Typho\",\"Sly Moore\"],\"values\":[1,1,1,1,1,6,1,1,1,3,35,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,2,4,1,1,1,1,1,1,3,1,1,1,1,1,3,12,1,16,1,2,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],\"hovertext\":[\"column: species<br />value: Aleena<br />n: 1\",\"column: species<br />value: Besalisk<br />n: 1\",\"column: species<br />value: Cerean<br />n: 1\",\"column: species<br />value: Chagrian<br />n: 1\",\"column: species<br />value: Clawdite<br />n: 1\",\"column: species<br />value: Droid<br />n: 6\",\"column: species<br />value: Dug<br />n: 1\",\"column: species<br />value: Ewok<br />n: 1\",\"column: species<br />value: Geonosian<br />n: 1\",\"column: species<br />value: Gungan<br />n: 3\",\"column: species<br />value: Human<br />n: 35\",\"column: species<br />value: Hutt<br />n: 1\",\"column: species<br />value: Iktotchi<br />n: 1\",\"column: species<br />value: Kaleesh<br />n: 1\",\"column: species<br />value: Kaminoan<br />n: 2\",\"column: species<br />value: Kel Dor<br />n: 1\",\"column: species<br />value: Mirialan<br />n: 2\",\"column: species<br />value: Mon Calamari<br />n: 1\",\"column: species<br />value: Muun<br />n: 1\",\"column: species<br />value: Nautolan<br />n: 1\",\"column: species<br />value: Neimodian<br />n: 1\",\"column: species<br />value: Pau'an<br />n: 1\",\"column: species<br />value: Quermian<br />n: 1\",\"column: species<br />value: Rodian<br />n: 1\",\"column: species<br />value: Skakoan<br />n: 1\",\"column: species<br />value: Sullustan<br />n: 1\",\"column: species<br />value: Tholothian<br />n: 1\",\"column: species<br />value: Togruta<br />n: 1\",\"column: species<br />value: Toong<br />n: 1\",\"column: species<br />value: Toydarian<br />n: 1\",\"column: species<br />value: Trandoshan<br />n: 1\",\"column: species<br />value: Twi'lek<br />n: 2\",\"column: species<br />value: Vulptereen<br />n: 1\",\"column: species<br />value: Wookiee<br />n: 2\",\"column: species<br />value: Xexto<br />n: 1\",\"column: species<br />value: Yoda's species<br />n: 1\",\"column: species<br />value: Zabrak<br />n: 2\",\"column: species<br />value: NA<br />n: 4\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 3\",\"column: eye_color<br />value: red, blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 3\",\"column: eye_color<br />value: blue<br />n: 12\",\"column: eye_color<br />value: blue-gray<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 16\",\"column: eye_color<br />value: dark<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 2\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: green, yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: gold<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br 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1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 3\",\"column: eye_color<br />value: blue<br />n: 12\",\"column: eye_color<br />value: blue-gray<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 16\",\"column: eye_color<br />value: dark<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 2\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: green, yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: gold<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 1\",\"column: eye_color<br />value: pink<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 2\",\"column: eye_color<br />value: white<br />n: 1\",\"column: name<br />value: Ratts Tyerel<br />n: 1\",\"column: name<br />value: Dexter Jettster<br />n: 1\",\"column: name<br />value: Ki-Adi-Mundi<br />n: 1\",\"column: name<br />value: Mas Amedda<br />n: 1\",\"column: name<br />value: Zam Wesell<br />n: 1\",\"column: name<br />value: BB8<br />n: 1\",\"column: name<br />value: IG-88<br />n: 1\",\"column: name<br />value: R2-D2<br />n: 1\",\"column: name<br />value: R5-D4<br />n: 1\",\"column: name<br />value: R4-P17<br />n: 1\",\"column: name<br />value: C-3PO<br />n: 1\",\"column: name<br />value: Sebulba<br />n: 1\",\"column: name<br />value: Wicket Systri Warrick<br />n: 1\",\"column: name<br />value: Poggle the Lesser<br />n: 1\",\"column: name<br />value: Jar Jar Binks<br />n: 1\",\"column: name<br />value: Roos Tarpals<br />n: 1\",\"column: name<br />value: Rugor Nass<br />n: 1\",\"column: name<br />value: Anakin Skywalker<br />n: 1\",\"column: name<br />value: Beru Whitesun Lars<br />n: 1\",\"column: name<br />value: Cliegg Lars<br />n: 1\",\"column: name<br />value: Finis Valorum<br />n: 1\",\"column: name<br />value: Jocasta Nu<br />n: 1\",\"column: name<br />value: Lobot<br />n: 1\",\"column: name<br />value: Luke Skywalker<br />n: 1\",\"column: name<br />value: Mon Mothma<br />n: 1\",\"column: name<br />value: Owen Lars<br />n: 1\",\"column: name<br />value: Qui-Gon Jinn<br />n: 1\",\"column: name<br />value: Ric Olié<br />n: 1\",\"column: name<br />value: Wilhuff Tarkin<br />n: 1\",\"column: name<br />value: Obi-Wan Kenobi<br />n: 1\",\"column: name<br />value: Arvel Crynyd<br />n: 1\",\"column: name<br />value: Bail Prestor Organa<br />n: 1\",\"column: name<br />value: Biggs Darklighter<br />n: 1\",\"column: name<br />value: Boba Fett<br />n: 1\",\"column: name<br />value: Dooku<br />n: 1\",\"column: name<br />value: Dormé<br />n: 1\",\"column: name<br />value: Han Solo<br />n: 1\",\"column: name<br />value: Jango Fett<br />n: 1\",\"column: name<br />value: Lando Calrissian<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: Tarfful<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\"],\"sort\":false,\"branchvalues\":\"total\",\"type\":\"sunburst\",\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]} # fill by group size plotSunburst(starwars_count, fill_by_n = TRUE)  {\"x\":{\"visdat\":{\"17091407c52a\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"17091407c52a\",\"attrs\":{\"17091407c52a\":{\"ids\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.white\",\"Aleena.->.unknown.->.Ratts Tyerel\",\"Besalisk.->.yellow.->.Dexter Jettster\",\"Cerean.->.yellow.->.Ki-Adi-Mundi\",\"Chagrian.->.blue.->.Mas Amedda\",\"Clawdite.->.yellow.->.Zam Wesell\",\"Droid.->.black.->.BB8\",\"Droid.->.red.->.IG-88\",\"Droid.->.red.->.R2-D2\",\"Droid.->.red.->.R5-D4\",\"Droid.->.red, blue.->.R4-P17\",\"Droid.->.yellow.->.C-3PO\",\"Dug.->.orange.->.Sebulba\",\"Ewok.->.brown.->.Wicket Systri Warrick\",\"Geonosian.->.yellow.->.Poggle the Lesser\",\"Gungan.->.orange.->.Jar Jar Binks\",\"Gungan.->.orange.->.Roos Tarpals\",\"Gungan.->.orange.->.Rugor Nass\",\"Human.->.blue.->.Anakin Skywalker\",\"Human.->.blue.->.Beru Whitesun Lars\",\"Human.->.blue.->.Cliegg Lars\",\"Human.->.blue.->.Finis Valorum\",\"Human.->.blue.->.Jocasta Nu\",\"Human.->.blue.->.Lobot\",\"Human.->.blue.->.Luke Skywalker\",\"Human.->.blue.->.Mon Mothma\",\"Human.->.blue.->.Owen Lars\",\"Human.->.blue.->.Qui-Gon Jinn\",\"Human.->.blue.->.Ric Olié\",\"Human.->.blue.->.Wilhuff Tarkin\",\"Human.->.blue-gray.->.Obi-Wan Kenobi\",\"Human.->.brown.->.Arvel Crynyd\",\"Human.->.brown.->.Bail Prestor Organa\",\"Human.->.brown.->.Biggs Darklighter\",\"Human.->.brown.->.Boba Fett\",\"Human.->.brown.->.Dooku\",\"Human.->.brown.->.Dormé\",\"Human.->.brown.->.Han Solo\",\"Human.->.brown.->.Jango Fett\",\"Human.->.brown.->.Lando Calrissian\",\"Human.->.brown.->.Leia Organa\",\"Human.->.brown.->.Mace Windu\",\"Human.->.brown.->.Padmé Amidala\",\"Human.->.brown.->.Poe Dameron\",\"Human.->.brown.->.Quarsh Panaka\",\"Human.->.brown.->.Raymus Antilles\",\"Human.->.brown.->.Shmi Skywalker\",\"Human.->.dark.->.Finn\",\"Human.->.hazel.->.Rey\",\"Human.->.hazel.->.Wedge Antilles\",\"Human.->.unknown.->.Captain Phasma\",\"Human.->.yellow.->.Darth Vader\",\"Human.->.yellow.->.Palpatine\",\"Hutt.->.orange.->.Jabba Desilijic Tiure\",\"Iktotchi.->.orange.->.Saesee Tiin\",\"Kaleesh.->.green, yellow.->.Grievous\",\"Kaminoan.->.black.->.Lama Su\",\"Kaminoan.->.black.->.Taun We\",\"Kel Dor.->.black.->.Plo Koon\",\"Mirialan.->.blue.->.Barriss Offee\",\"Mirialan.->.blue.->.Luminara Unduli\",\"Mon Calamari.->.orange.->.Ackbar\",\"Muun.->.gold.->.San Hill\",\"Nautolan.->.black.->.Kit Fisto\",\"Neimodian.->.red.->.Nute Gunray\",\"Pau'an.->.black.->.Tion Medon\",\"Quermian.->.yellow.->.Yarael Poof\",\"Rodian.->.black.->.Greedo\",\"Skakoan.->.unknown.->.Wat Tambor\",\"Sullustan.->.black.->.Nien Nunb\",\"Tholothian.->.blue.->.Adi Gallia\",\"Togruta.->.black.->.Shaak Ti\",\"Toong.->.orange.->.Ben Quadinaros\",\"Toydarian.->.yellow.->.Watto\",\"Trandoshan.->.red.->.Bossk\",\"Twi'lek.->.hazel.->.Ayla Secura\",\"Twi'lek.->.pink.->.Bib Fortuna\",\"Vulptereen.->.yellow.->.Dud Bolt\",\"Wookiee.->.blue.->.Chewbacca\",\"Wookiee.->.blue.->.Tarfful\",\"Xexto.->.black.->.Gasgano\",\"Yoda's species.->.brown.->.Yoda\",\"Zabrak.->.brown.->.Eeth Koth\",\"Zabrak.->.yellow.->.Darth Maul\",\"NA.->.blue.->.Jek Tono Porkins\",\"NA.->.brown.->.Cordé\",\"NA.->.brown.->.Gregar Typho\",\"NA.->.white.->.Sly Moore\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Droid\",\"Droid\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"Zabrak\",\"NA\",\"NA\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.brown\",\"NA.->.white\"],\"labels\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",null,\"unknown\",\"yellow\",\"yellow\",\"blue\",\"yellow\",\"black\",\"red\",\"red, blue\",\"yellow\",\"orange\",\"brown\",\"yellow\",\"orange\",\"blue\",\"blue-gray\",\"brown\",\"dark\",\"hazel\",\"unknown\",\"yellow\",\"orange\",\"orange\",\"green, yellow\",\"black\",\"black\",\"blue\",\"orange\",\"gold\",\"black\",\"red\",\"black\",\"yellow\",\"black\",\"unknown\",\"black\",\"blue\",\"black\",\"orange\",\"yellow\",\"red\",\"hazel\",\"pink\",\"yellow\",\"blue\",\"black\",\"brown\",\"brown\",\"yellow\",\"blue\",\"brown\",\"white\",\"Ratts Tyerel\",\"Dexter Jettster\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Zam Wesell\",\"BB8\",\"IG-88\",\"R2-D2\",\"R5-D4\",\"R4-P17\",\"C-3PO\",\"Sebulba\",\"Wicket Systri Warrick\",\"Poggle the Lesser\",\"Jar 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Calrissian<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: Tarfful<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\"],\"sort\":false,\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"colorbar\":{\"bgcolor\":\"\"},\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"branchvalues\":\"total\",\"type\":\"sunburst\",\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]} # treemap plot, ordered by group size plotTreemap(starwars_count, sort_by_n = TRUE)  {\"x\":{\"visdat\":{\"170976bbfab1\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"170976bbfab1\",\"attrs\":{\"170976bbfab1\":{\"ids\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.white\",\"Aleena.->.unknown.->.Ratts Tyerel\",\"Besalisk.->.yellow.->.Dexter Jettster\",\"Cerean.->.yellow.->.Ki-Adi-Mundi\",\"Chagrian.->.blue.->.Mas Amedda\",\"Clawdite.->.yellow.->.Zam Wesell\",\"Droid.->.black.->.BB8\",\"Droid.->.red.->.IG-88\",\"Droid.->.red.->.R2-D2\",\"Droid.->.red.->.R5-D4\",\"Droid.->.red, blue.->.R4-P17\",\"Droid.->.yellow.->.C-3PO\",\"Dug.->.orange.->.Sebulba\",\"Ewok.->.brown.->.Wicket Systri Warrick\",\"Geonosian.->.yellow.->.Poggle the Lesser\",\"Gungan.->.orange.->.Jar Jar Binks\",\"Gungan.->.orange.->.Roos Tarpals\",\"Gungan.->.orange.->.Rugor Nass\",\"Human.->.blue.->.Anakin Skywalker\",\"Human.->.blue.->.Beru Whitesun Lars\",\"Human.->.blue.->.Cliegg Lars\",\"Human.->.blue.->.Finis Valorum\",\"Human.->.blue.->.Jocasta Nu\",\"Human.->.blue.->.Lobot\",\"Human.->.blue.->.Luke Skywalker\",\"Human.->.blue.->.Mon Mothma\",\"Human.->.blue.->.Owen Lars\",\"Human.->.blue.->.Qui-Gon Jinn\",\"Human.->.blue.->.Ric Olié\",\"Human.->.blue.->.Wilhuff Tarkin\",\"Human.->.blue-gray.->.Obi-Wan Kenobi\",\"Human.->.brown.->.Arvel Crynyd\",\"Human.->.brown.->.Bail Prestor Organa\",\"Human.->.brown.->.Biggs Darklighter\",\"Human.->.brown.->.Boba Fett\",\"Human.->.brown.->.Dooku\",\"Human.->.brown.->.Dormé\",\"Human.->.brown.->.Han Solo\",\"Human.->.brown.->.Jango Fett\",\"Human.->.brown.->.Lando Calrissian\",\"Human.->.brown.->.Leia Organa\",\"Human.->.brown.->.Mace Windu\",\"Human.->.brown.->.Padmé Amidala\",\"Human.->.brown.->.Poe Dameron\",\"Human.->.brown.->.Quarsh Panaka\",\"Human.->.brown.->.Raymus Antilles\",\"Human.->.brown.->.Shmi Skywalker\",\"Human.->.dark.->.Finn\",\"Human.->.hazel.->.Rey\",\"Human.->.hazel.->.Wedge Antilles\",\"Human.->.unknown.->.Captain Phasma\",\"Human.->.yellow.->.Darth Vader\",\"Human.->.yellow.->.Palpatine\",\"Hutt.->.orange.->.Jabba Desilijic Tiure\",\"Iktotchi.->.orange.->.Saesee Tiin\",\"Kaleesh.->.green, yellow.->.Grievous\",\"Kaminoan.->.black.->.Lama Su\",\"Kaminoan.->.black.->.Taun We\",\"Kel Dor.->.black.->.Plo Koon\",\"Mirialan.->.blue.->.Barriss Offee\",\"Mirialan.->.blue.->.Luminara Unduli\",\"Mon Calamari.->.orange.->.Ackbar\",\"Muun.->.gold.->.San Hill\",\"Nautolan.->.black.->.Kit Fisto\",\"Neimodian.->.red.->.Nute Gunray\",\"Pau'an.->.black.->.Tion Medon\",\"Quermian.->.yellow.->.Yarael Poof\",\"Rodian.->.black.->.Greedo\",\"Skakoan.->.unknown.->.Wat Tambor\",\"Sullustan.->.black.->.Nien Nunb\",\"Tholothian.->.blue.->.Adi Gallia\",\"Togruta.->.black.->.Shaak Ti\",\"Toong.->.orange.->.Ben Quadinaros\",\"Toydarian.->.yellow.->.Watto\",\"Trandoshan.->.red.->.Bossk\",\"Twi'lek.->.hazel.->.Ayla Secura\",\"Twi'lek.->.pink.->.Bib Fortuna\",\"Vulptereen.->.yellow.->.Dud Bolt\",\"Wookiee.->.blue.->.Chewbacca\",\"Wookiee.->.blue.->.Tarfful\",\"Xexto.->.black.->.Gasgano\",\"Yoda's species.->.brown.->.Yoda\",\"Zabrak.->.brown.->.Eeth Koth\",\"Zabrak.->.yellow.->.Darth Maul\",\"NA.->.blue.->.Jek Tono Porkins\",\"NA.->.brown.->.Cordé\",\"NA.->.brown.->.Gregar Typho\",\"NA.->.white.->.Sly Moore\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Droid\",\"Droid\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",\"Zabrak\",\"NA\",\"NA\",\"NA\",\"Aleena.->.unknown\",\"Besalisk.->.yellow\",\"Cerean.->.yellow\",\"Chagrian.->.blue\",\"Clawdite.->.yellow\",\"Droid.->.black\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red\",\"Droid.->.red, blue\",\"Droid.->.yellow\",\"Dug.->.orange\",\"Ewok.->.brown\",\"Geonosian.->.yellow\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Gungan.->.orange\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue\",\"Human.->.blue-gray\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.brown\",\"Human.->.dark\",\"Human.->.hazel\",\"Human.->.hazel\",\"Human.->.unknown\",\"Human.->.yellow\",\"Human.->.yellow\",\"Hutt.->.orange\",\"Iktotchi.->.orange\",\"Kaleesh.->.green, yellow\",\"Kaminoan.->.black\",\"Kaminoan.->.black\",\"Kel Dor.->.black\",\"Mirialan.->.blue\",\"Mirialan.->.blue\",\"Mon Calamari.->.orange\",\"Muun.->.gold\",\"Nautolan.->.black\",\"Neimodian.->.red\",\"Pau'an.->.black\",\"Quermian.->.yellow\",\"Rodian.->.black\",\"Skakoan.->.unknown\",\"Sullustan.->.black\",\"Tholothian.->.blue\",\"Togruta.->.black\",\"Toong.->.orange\",\"Toydarian.->.yellow\",\"Trandoshan.->.red\",\"Twi'lek.->.hazel\",\"Twi'lek.->.pink\",\"Vulptereen.->.yellow\",\"Wookiee.->.blue\",\"Wookiee.->.blue\",\"Xexto.->.black\",\"Yoda's species.->.brown\",\"Zabrak.->.brown\",\"Zabrak.->.yellow\",\"NA.->.blue\",\"NA.->.brown\",\"NA.->.brown\",\"NA.->.white\"],\"labels\":[\"Aleena\",\"Besalisk\",\"Cerean\",\"Chagrian\",\"Clawdite\",\"Droid\",\"Dug\",\"Ewok\",\"Geonosian\",\"Gungan\",\"Human\",\"Hutt\",\"Iktotchi\",\"Kaleesh\",\"Kaminoan\",\"Kel Dor\",\"Mirialan\",\"Mon Calamari\",\"Muun\",\"Nautolan\",\"Neimodian\",\"Pau'an\",\"Quermian\",\"Rodian\",\"Skakoan\",\"Sullustan\",\"Tholothian\",\"Togruta\",\"Toong\",\"Toydarian\",\"Trandoshan\",\"Twi'lek\",\"Vulptereen\",\"Wookiee\",\"Xexto\",\"Yoda's species\",\"Zabrak\",null,\"unknown\",\"yellow\",\"yellow\",\"blue\",\"yellow\",\"black\",\"red\",\"red, blue\",\"yellow\",\"orange\",\"brown\",\"yellow\",\"orange\",\"blue\",\"blue-gray\",\"brown\",\"dark\",\"hazel\",\"unknown\",\"yellow\",\"orange\",\"orange\",\"green, yellow\",\"black\",\"black\",\"blue\",\"orange\",\"gold\",\"black\",\"red\",\"black\",\"yellow\",\"black\",\"unknown\",\"black\",\"blue\",\"black\",\"orange\",\"yellow\",\"red\",\"hazel\",\"pink\",\"yellow\",\"blue\",\"black\",\"brown\",\"brown\",\"yellow\",\"blue\",\"brown\",\"white\",\"Ratts Tyerel\",\"Dexter Jettster\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Zam Wesell\",\"BB8\",\"IG-88\",\"R2-D2\",\"R5-D4\",\"R4-P17\",\"C-3PO\",\"Sebulba\",\"Wicket Systri Warrick\",\"Poggle the Lesser\",\"Jar Jar Binks\",\"Roos Tarpals\",\"Rugor Nass\",\"Anakin Skywalker\",\"Beru Whitesun Lars\",\"Cliegg Lars\",\"Finis Valorum\",\"Jocasta Nu\",\"Lobot\",\"Luke Skywalker\",\"Mon Mothma\",\"Owen Lars\",\"Qui-Gon Jinn\",\"Ric Olié\",\"Wilhuff Tarkin\",\"Obi-Wan Kenobi\",\"Arvel Crynyd\",\"Bail Prestor Organa\",\"Biggs Darklighter\",\"Boba Fett\",\"Dooku\",\"Dormé\",\"Han Solo\",\"Jango Fett\",\"Lando Calrissian\",\"Leia Organa\",\"Mace Windu\",\"Padmé Amidala\",\"Poe Dameron\",\"Quarsh Panaka\",\"Raymus Antilles\",\"Shmi Skywalker\",\"Finn\",\"Rey\",\"Wedge Antilles\",\"Captain Phasma\",\"Darth Vader\",\"Palpatine\",\"Jabba Desilijic Tiure\",\"Saesee Tiin\",\"Grievous\",\"Lama Su\",\"Taun We\",\"Plo Koon\",\"Barriss Offee\",\"Luminara Unduli\",\"Ackbar\",\"San Hill\",\"Kit Fisto\",\"Nute Gunray\",\"Tion Medon\",\"Yarael Poof\",\"Greedo\",\"Wat Tambor\",\"Nien Nunb\",\"Adi Gallia\",\"Shaak Ti\",\"Ben Quadinaros\",\"Watto\",\"Bossk\",\"Ayla Secura\",\"Bib Fortuna\",\"Dud Bolt\",\"Chewbacca\",\"Tarfful\",\"Gasgano\",\"Yoda\",\"Eeth Koth\",\"Darth Maul\",\"Jek Tono Porkins\",\"Cordé\",\"Gregar Typho\",\"Sly Moore\"],\"values\":[1,1,1,1,1,6,1,1,1,3,35,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,2,4,1,1,1,1,1,1,3,1,1,1,1,1,3,12,1,16,1,2,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],\"hovertext\":[\"column: species<br />value: Aleena<br />n: 1\",\"column: species<br />value: Besalisk<br />n: 1\",\"column: species<br />value: Cerean<br />n: 1\",\"column: species<br />value: Chagrian<br />n: 1\",\"column: species<br />value: Clawdite<br />n: 1\",\"column: species<br />value: Droid<br />n: 6\",\"column: species<br />value: Dug<br />n: 1\",\"column: species<br />value: Ewok<br />n: 1\",\"column: species<br />value: Geonosian<br />n: 1\",\"column: species<br />value: Gungan<br />n: 3\",\"column: species<br />value: Human<br />n: 35\",\"column: species<br />value: Hutt<br />n: 1\",\"column: species<br />value: Iktotchi<br />n: 1\",\"column: species<br />value: Kaleesh<br />n: 1\",\"column: species<br />value: Kaminoan<br />n: 2\",\"column: species<br />value: Kel Dor<br />n: 1\",\"column: species<br />value: Mirialan<br />n: 2\",\"column: species<br />value: Mon Calamari<br />n: 1\",\"column: species<br />value: Muun<br />n: 1\",\"column: species<br />value: Nautolan<br />n: 1\",\"column: species<br />value: Neimodian<br />n: 1\",\"column: species<br />value: Pau'an<br />n: 1\",\"column: species<br />value: Quermian<br />n: 1\",\"column: species<br />value: Rodian<br />n: 1\",\"column: species<br />value: Skakoan<br />n: 1\",\"column: species<br />value: Sullustan<br />n: 1\",\"column: species<br />value: Tholothian<br />n: 1\",\"column: species<br />value: Togruta<br />n: 1\",\"column: species<br />value: Toong<br />n: 1\",\"column: species<br />value: Toydarian<br />n: 1\",\"column: species<br />value: Trandoshan<br />n: 1\",\"column: species<br />value: Twi'lek<br />n: 2\",\"column: species<br />value: Vulptereen<br />n: 1\",\"column: species<br />value: Wookiee<br />n: 2\",\"column: species<br />value: Xexto<br />n: 1\",\"column: species<br />value: Yoda's species<br />n: 1\",\"column: species<br />value: Zabrak<br />n: 2\",\"column: species<br />value: NA<br />n: 4\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 3\",\"column: eye_color<br />value: red, blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 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species<br />value: Toydarian<br />n: 1\",\"column: species<br />value: Trandoshan<br />n: 1\",\"column: species<br />value: Twi'lek<br />n: 2\",\"column: species<br />value: Vulptereen<br />n: 1\",\"column: species<br />value: Wookiee<br />n: 2\",\"column: species<br />value: Xexto<br />n: 1\",\"column: species<br />value: Yoda's species<br />n: 1\",\"column: species<br />value: Zabrak<br />n: 2\",\"column: species<br />value: NA<br />n: 4\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 3\",\"column: eye_color<br />value: red, blue<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 3\",\"column: eye_color<br />value: blue<br />n: 12\",\"column: eye_color<br />value: blue-gray<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 16\",\"column: eye_color<br />value: dark<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 2\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: green, yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: gold<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: unknown<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: orange<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: red<br />n: 1\",\"column: eye_color<br />value: hazel<br />n: 1\",\"column: eye_color<br />value: pink<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 2\",\"column: eye_color<br />value: black<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 1\",\"column: eye_color<br />value: yellow<br />n: 1\",\"column: eye_color<br />value: blue<br />n: 1\",\"column: eye_color<br />value: brown<br />n: 2\",\"column: eye_color<br />value: white<br />n: 1\",\"column: name<br />value: Ratts Tyerel<br />n: 1\",\"column: name<br />value: Dexter Jettster<br />n: 1\",\"column: name<br />value: Ki-Adi-Mundi<br />n: 1\",\"column: name<br />value: Mas Amedda<br />n: 1\",\"column: name<br />value: Zam Wesell<br />n: 1\",\"column: name<br />value: BB8<br />n: 1\",\"column: name<br />value: IG-88<br />n: 1\",\"column: name<br />value: R2-D2<br />n: 1\",\"column: name<br />value: R5-D4<br />n: 1\",\"column: name<br />value: R4-P17<br />n: 1\",\"column: name<br />value: C-3PO<br />n: 1\",\"column: name<br />value: Sebulba<br />n: 1\",\"column: name<br />value: Wicket Systri Warrick<br />n: 1\",\"column: name<br />value: Poggle the Lesser<br />n: 1\",\"column: name<br />value: Jar Jar Binks<br />n: 1\",\"column: name<br />value: Roos Tarpals<br />n: 1\",\"column: name<br />value: Rugor Nass<br />n: 1\",\"column: name<br />value: Anakin Skywalker<br />n: 1\",\"column: name<br />value: Beru Whitesun Lars<br />n: 1\",\"column: name<br />value: Cliegg Lars<br />n: 1\",\"column: name<br />value: Finis Valorum<br />n: 1\",\"column: name<br />value: Jocasta Nu<br />n: 1\",\"column: name<br />value: Lobot<br />n: 1\",\"column: name<br />value: Luke Skywalker<br />n: 1\",\"column: name<br />value: Mon Mothma<br />n: 1\",\"column: name<br />value: Owen Lars<br />n: 1\",\"column: name<br />value: Qui-Gon Jinn<br />n: 1\",\"column: name<br />value: Ric Olié<br />n: 1\",\"column: name<br />value: Wilhuff Tarkin<br />n: 1\",\"column: name<br />value: Obi-Wan Kenobi<br />n: 1\",\"column: name<br />value: Arvel Crynyd<br />n: 1\",\"column: name<br />value: Bail Prestor Organa<br />n: 1\",\"column: name<br />value: Biggs Darklighter<br />n: 1\",\"column: name<br />value: Boba Fett<br />n: 1\",\"column: name<br />value: Dooku<br />n: 1\",\"column: name<br />value: Dormé<br />n: 1\",\"column: name<br />value: Han Solo<br />n: 1\",\"column: name<br />value: Jango Fett<br />n: 1\",\"column: name<br />value: Lando Calrissian<br />n: 1\",\"column: name<br />value: Leia Organa<br />n: 1\",\"column: name<br />value: Mace Windu<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: Raymus Antilles<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Wedge Antilles<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Saesee Tiin<br />n: 1\",\"column: name<br />value: Grievous<br />n: 1\",\"column: name<br />value: Lama Su<br />n: 1\",\"column: name<br />value: Taun We<br />n: 1\",\"column: name<br />value: Plo Koon<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Kit Fisto<br />n: 1\",\"column: name<br />value: Nute Gunray<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Adi Gallia<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Chewbacca<br />n: 1\",\"column: name<br />value: Tarfful<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\",\"column: name<br />value: Eeth Koth<br />n: 1\",\"column: name<br />value: Darth Maul<br />n: 1\",\"column: name<br />value: Jek Tono Porkins<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\"],\"sort\":true,\"branchvalues\":\"total\",\"hoverinfo\":[\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\"],\"type\":\"treemap\",\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]} # display al charchaters by homeworld starwars %>%     count(homeworld, name) %>%     plotTreemap(sort_by_n = TRUE)  {\"x\":{\"visdat\":{\"17095690eab9\":[\"function () \",\"plotlyVisDat\"]},\"cur_data\":\"17095690eab9\",\"attrs\":{\"17095690eab9\":{\"ids\":[\"Alderaan\",\"Aleen Minor\",\"Bespin\",\"Bestine IV\",\"Cato Neimoidia\",\"Cerea\",\"Champala\",\"Chandrila\",\"Concord Dawn\",\"Corellia\",\"Coruscant\",\"Dathomir\",\"Dorin\",\"Endor\",\"Eriadu\",\"Geonosis\",\"Glee Anselm\",\"Haruun Kal\",\"Iktotch\",\"Iridonia\",\"Kalee\",\"Kamino\",\"Kashyyyk\",\"Malastare\",\"Mirial\",\"Mon Cala\",\"Muunilinst\",\"Naboo\",\"Nal Hutta\",\"Ojom\",\"Quermia\",\"Rodia\",\"Ryloth\",\"Serenno\",\"Shili\",\"Skako\",\"Socorro\",\"Stewjon\",\"Sullust\",\"Tatooine\",\"Toydaria\",\"Trandosha\",\"Troiken\",\"Tund\",\"Umbara\",\"Utapau\",\"Vulpter\",\"Zolan\",\"NA\",\"Alderaan.->.Bail Prestor Organa\",\"Alderaan.->.Leia Organa\",\"Alderaan.->.Raymus Antilles\",\"Aleen Minor.->.Ratts Tyerel\",\"Bespin.->.Lobot\",\"Bestine IV.->.Jek Tono Porkins\",\"Cato Neimoidia.->.Nute Gunray\",\"Cerea.->.Ki-Adi-Mundi\",\"Champala.->.Mas Amedda\",\"Chandrila.->.Mon Mothma\",\"Concord Dawn.->.Jango Fett\",\"Corellia.->.Han Solo\",\"Corellia.->.Wedge Antilles\",\"Coruscant.->.Adi Gallia\",\"Coruscant.->.Finis Valorum\",\"Coruscant.->.Jocasta Nu\",\"Dathomir.->.Darth Maul\",\"Dorin.->.Plo Koon\",\"Endor.->.Wicket Systri Warrick\",\"Eriadu.->.Wilhuff Tarkin\",\"Geonosis.->.Poggle the Lesser\",\"Glee Anselm.->.Kit Fisto\",\"Haruun Kal.->.Mace Windu\",\"Iktotch.->.Saesee Tiin\",\"Iridonia.->.Eeth Koth\",\"Kalee.->.Grievous\",\"Kamino.->.Boba Fett\",\"Kamino.->.Lama Su\",\"Kamino.->.Taun We\",\"Kashyyyk.->.Chewbacca\",\"Kashyyyk.->.Tarfful\",\"Malastare.->.Sebulba\",\"Mirial.->.Barriss Offee\",\"Mirial.->.Luminara Unduli\",\"Mon Cala.->.Ackbar\",\"Muunilinst.->.San Hill\",\"Naboo.->.Cordé\",\"Naboo.->.Dormé\",\"Naboo.->.Gregar Typho\",\"Naboo.->.Jar Jar Binks\",\"Naboo.->.Padmé Amidala\",\"Naboo.->.Palpatine\",\"Naboo.->.Quarsh Panaka\",\"Naboo.->.R2-D2\",\"Naboo.->.Ric Olié\",\"Naboo.->.Roos Tarpals\",\"Naboo.->.Rugor Nass\",\"Nal Hutta.->.Jabba Desilijic Tiure\",\"Ojom.->.Dexter Jettster\",\"Quermia.->.Yarael Poof\",\"Rodia.->.Greedo\",\"Ryloth.->.Ayla Secura\",\"Ryloth.->.Bib Fortuna\",\"Serenno.->.Dooku\",\"Shili.->.Shaak Ti\",\"Skako.->.Wat Tambor\",\"Socorro.->.Lando Calrissian\",\"Stewjon.->.Obi-Wan Kenobi\",\"Sullust.->.Nien Nunb\",\"Tatooine.->.Anakin Skywalker\",\"Tatooine.->.Beru Whitesun Lars\",\"Tatooine.->.Biggs Darklighter\",\"Tatooine.->.C-3PO\",\"Tatooine.->.Cliegg Lars\",\"Tatooine.->.Darth Vader\",\"Tatooine.->.Luke Skywalker\",\"Tatooine.->.Owen Lars\",\"Tatooine.->.R5-D4\",\"Tatooine.->.Shmi Skywalker\",\"Toydaria.->.Watto\",\"Trandosha.->.Bossk\",\"Troiken.->.Gasgano\",\"Tund.->.Ben Quadinaros\",\"Umbara.->.Sly Moore\",\"Utapau.->.Tion Medon\",\"Vulpter.->.Dud Bolt\",\"Zolan.->.Zam Wesell\",\"NA.->.Arvel Crynyd\",\"NA.->.BB8\",\"NA.->.Captain Phasma\",\"NA.->.Finn\",\"NA.->.IG-88\",\"NA.->.Poe Dameron\",\"NA.->.Qui-Gon Jinn\",\"NA.->.R4-P17\",\"NA.->.Rey\",\"NA.->.Yoda\"],\"parents\":[\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Alderaan\",\"Alderaan\",\"Alderaan\",\"Aleen Minor\",\"Bespin\",\"Bestine IV\",\"Cato Neimoidia\",\"Cerea\",\"Champala\",\"Chandrila\",\"Concord Dawn\",\"Corellia\",\"Corellia\",\"Coruscant\",\"Coruscant\",\"Coruscant\",\"Dathomir\",\"Dorin\",\"Endor\",\"Eriadu\",\"Geonosis\",\"Glee Anselm\",\"Haruun Kal\",\"Iktotch\",\"Iridonia\",\"Kalee\",\"Kamino\",\"Kamino\",\"Kamino\",\"Kashyyyk\",\"Kashyyyk\",\"Malastare\",\"Mirial\",\"Mirial\",\"Mon Cala\",\"Muunilinst\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Naboo\",\"Nal Hutta\",\"Ojom\",\"Quermia\",\"Rodia\",\"Ryloth\",\"Ryloth\",\"Serenno\",\"Shili\",\"Skako\",\"Socorro\",\"Stewjon\",\"Sullust\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Tatooine\",\"Toydaria\",\"Trandosha\",\"Troiken\",\"Tund\",\"Umbara\",\"Utapau\",\"Vulpter\",\"Zolan\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\",\"NA\"],\"labels\":[\"Alderaan\",\"Aleen Minor\",\"Bespin\",\"Bestine IV\",\"Cato Neimoidia\",\"Cerea\",\"Champala\",\"Chandrila\",\"Concord Dawn\",\"Corellia\",\"Coruscant\",\"Dathomir\",\"Dorin\",\"Endor\",\"Eriadu\",\"Geonosis\",\"Glee Anselm\",\"Haruun Kal\",\"Iktotch\",\"Iridonia\",\"Kalee\",\"Kamino\",\"Kashyyyk\",\"Malastare\",\"Mirial\",\"Mon Cala\",\"Muunilinst\",\"Naboo\",\"Nal Hutta\",\"Ojom\",\"Quermia\",\"Rodia\",\"Ryloth\",\"Serenno\",\"Shili\",\"Skako\",\"Socorro\",\"Stewjon\",\"Sullust\",\"Tatooine\",\"Toydaria\",\"Trandosha\",\"Troiken\",\"Tund\",\"Umbara\",\"Utapau\",\"Vulpter\",\"Zolan\",null,\"Bail Prestor Organa\",\"Leia Organa\",\"Raymus Antilles\",\"Ratts Tyerel\",\"Lobot\",\"Jek Tono Porkins\",\"Nute Gunray\",\"Ki-Adi-Mundi\",\"Mas Amedda\",\"Mon Mothma\",\"Jango Fett\",\"Han Solo\",\"Wedge Antilles\",\"Adi Gallia\",\"Finis Valorum\",\"Jocasta Nu\",\"Darth Maul\",\"Plo Koon\",\"Wicket Systri Warrick\",\"Wilhuff Tarkin\",\"Poggle the Lesser\",\"Kit Fisto\",\"Mace Windu\",\"Saesee Tiin\",\"Eeth Koth\",\"Grievous\",\"Boba Fett\",\"Lama Su\",\"Taun We\",\"Chewbacca\",\"Tarfful\",\"Sebulba\",\"Barriss Offee\",\"Luminara Unduli\",\"Ackbar\",\"San Hill\",\"Cordé\",\"Dormé\",\"Gregar Typho\",\"Jar Jar Binks\",\"Padmé Amidala\",\"Palpatine\",\"Quarsh Panaka\",\"R2-D2\",\"Ric Olié\",\"Roos Tarpals\",\"Rugor Nass\",\"Jabba Desilijic Tiure\",\"Dexter 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Tarfful<br />n: 1\",\"column: name<br />value: Sebulba<br />n: 1\",\"column: name<br />value: Barriss Offee<br />n: 1\",\"column: name<br />value: Luminara Unduli<br />n: 1\",\"column: name<br />value: Ackbar<br />n: 1\",\"column: name<br />value: San Hill<br />n: 1\",\"column: name<br />value: Cordé<br />n: 1\",\"column: name<br />value: Dormé<br />n: 1\",\"column: name<br />value: Gregar Typho<br />n: 1\",\"column: name<br />value: Jar Jar Binks<br />n: 1\",\"column: name<br />value: Padmé Amidala<br />n: 1\",\"column: name<br />value: Palpatine<br />n: 1\",\"column: name<br />value: Quarsh Panaka<br />n: 1\",\"column: name<br />value: R2-D2<br />n: 1\",\"column: name<br />value: Ric Olié<br />n: 1\",\"column: name<br />value: Roos Tarpals<br />n: 1\",\"column: name<br />value: Rugor Nass<br />n: 1\",\"column: name<br />value: Jabba Desilijic Tiure<br />n: 1\",\"column: name<br />value: Dexter Jettster<br />n: 1\",\"column: name<br />value: Yarael Poof<br />n: 1\",\"column: name<br />value: Greedo<br />n: 1\",\"column: name<br />value: Ayla Secura<br />n: 1\",\"column: name<br />value: Bib Fortuna<br />n: 1\",\"column: name<br />value: Dooku<br />n: 1\",\"column: name<br />value: Shaak Ti<br />n: 1\",\"column: name<br />value: Wat Tambor<br />n: 1\",\"column: name<br />value: Lando Calrissian<br />n: 1\",\"column: name<br />value: Obi-Wan Kenobi<br />n: 1\",\"column: name<br />value: Nien Nunb<br />n: 1\",\"column: name<br />value: Anakin Skywalker<br />n: 1\",\"column: name<br />value: Beru Whitesun Lars<br />n: 1\",\"column: name<br />value: Biggs Darklighter<br />n: 1\",\"column: name<br />value: C-3PO<br />n: 1\",\"column: name<br />value: Cliegg Lars<br />n: 1\",\"column: name<br />value: Darth Vader<br />n: 1\",\"column: name<br />value: Luke Skywalker<br />n: 1\",\"column: name<br />value: Owen Lars<br />n: 1\",\"column: name<br />value: R5-D4<br />n: 1\",\"column: name<br />value: Shmi Skywalker<br />n: 1\",\"column: name<br />value: Watto<br />n: 1\",\"column: name<br />value: Bossk<br />n: 1\",\"column: name<br />value: Gasgano<br />n: 1\",\"column: name<br />value: Ben Quadinaros<br />n: 1\",\"column: name<br />value: Sly Moore<br />n: 1\",\"column: name<br />value: Tion Medon<br />n: 1\",\"column: name<br />value: Dud Bolt<br />n: 1\",\"column: name<br />value: Zam Wesell<br />n: 1\",\"column: name<br />value: Arvel Crynyd<br />n: 1\",\"column: name<br />value: BB8<br />n: 1\",\"column: name<br />value: Captain Phasma<br />n: 1\",\"column: name<br />value: Finn<br />n: 1\",\"column: name<br />value: IG-88<br />n: 1\",\"column: name<br />value: Poe Dameron<br />n: 1\",\"column: name<br />value: Qui-Gon Jinn<br />n: 1\",\"column: name<br />value: R4-P17<br />n: 1\",\"column: name<br />value: Rey<br />n: 1\",\"column: name<br />value: Yoda<br />n: 1\"],\"sort\":true,\"branchvalues\":\"total\",\"hoverinfo\":[\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\",\"text\"],\"type\":\"treemap\",\"marker\":{\"color\":\"rgba(31,119,180,1)\",\"line\":{\"color\":\"rgba(255,255,255,1)\"}},\"frame\":null}],\"highlight\":{\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.20000000000000001,\"selected\":{\"opacity\":1},\"debounce\":0},\"shinyEvents\":[\"plotly_hover\",\"plotly_click\",\"plotly_selected\",\"plotly_relayout\",\"plotly_brushed\",\"plotly_brushing\",\"plotly_clickannotation\",\"plotly_doubleclick\",\"plotly_deselect\",\"plotly_afterplot\",\"plotly_sunburstclick\"],\"base_url\":\"https://plot.ly\"},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":null,"dir":"Reference","previous_headings":"","what":"UpSet Plot — plotUpSet","title":"UpSet Plot — plotUpSet","text":"UpSet plot Domain Architectures vs Domains Genomic Contexts vs Domain Architectures.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UpSet Plot — plotUpSet","text":"","code":"plotUpSet(   query_data = \"toast_rack.sub\",   colname = \"DomArch\",   cutoff = 90,   RowsCutoff = FALSE,   text.scale = 1.5,   point.size = 2.2,   line.size = 0.8 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"UpSet Plot — plotUpSet","text":"query_data Data frame protein homologs usual 11 columns + additional word columns (0/1 format). Default toast_rack.sub colname Column name query_data: \"DomArch.norep\", \"GenContext.norep\", \"DomArch.PFAM.norep\" \"DomArch.LADB.norep\". Default \"DomArch.norep\". cutoff Numeric. Cutoff word frequency. Default 90. RowsCutoff Boolean. TRUE, applies row cutoff remove data rows based certain condition. Default FALSE. text.scale Allows scaling axis title, tick lables, numbers intersection size bars. text.scale can either take universal scale form integer, vector specific scales format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers bars) point.size Numeric. Sets size points UpSet plot. Default 2.2. line.size Numeric. Sets line width UpSet plot. Default 0.8.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UpSet Plot — plotUpSet","text":"UpSet plot object. plot visualizes intersections sets based provided colname query_data.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"UpSet Plot — plotUpSet","text":"\"da2doms\" need file DA.doms.wc well column query_data$DomArch.norep \"gc2da\", need file GC.DA.wc well column query_data$GenContext.norep","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"UpSet Plot — plotUpSet","text":"Please refer source code alternate file formats /column names.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"UpSet Plot — plotUpSet","text":"Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/plotUpSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"UpSet Plot — plotUpSet","text":"","code":"if (FALSE) { # \\dontrun{ plotUpSet(pspa.sub, 10, \"da2doms\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":null,"dir":"Reference","previous_headings":"","what":"prepareColumnParams — prepareColumnParams","title":"prepareColumnParams — prepareColumnParams","text":"prepareColumnParams","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prepareColumnParams — prepareColumnParams","text":"","code":"prepareColumnParams(count_data, fill_by_n, sort_by_n)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prepareColumnParams — prepareColumnParams","text":"count_data data frame containing data. fill_by_n Logical indicating fill color based counts. sort_by_n Logical indicating data sorted counts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"prepareColumnParams — prepareColumnParams","text":"data frame parameters treemap visualization.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareColumnParams.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prepareColumnParams — prepareColumnParams","text":"","code":"if (FALSE) { # \\dontrun{ count_data <- data.frame(Category = c(\"A\", \"B\", \"C\"),                           n = c(10, 20, 15)) params <- prepareColumnParams(count_data, fill_by_n = TRUE, sort_by_n = FALSE) params } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":null,"dir":"Reference","previous_headings":"","what":"prepareSingleColumnParams — prepareSingleColumnParams","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"prepareSingleColumnParams","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"","code":"prepareSingleColumnParams(df, col_num, root)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"df data frame containing data processed. col_num integer representing column number process. root string representing root node treemap.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"data frame containing parameters specified column treemap visualization.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/prepareSingleColumnParams.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"prepareSingleColumnParams — prepareSingleColumnParams","text":"","code":"if (FALSE) { # \\dontrun{ df <- data.frame(Category = c(\"A\", \"A\", \"B\", \"B\", \"C\"),                  n = c(10, 20, 30, 40, 50)) params <- prepareSingleColumnParams(df, col_num = 1, root = \"Root\") params } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":null,"dir":"Reference","previous_headings":"","what":"proteinAcc2TaxID — proteinAcc2TaxID","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"proteinAcc2TaxID","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"","code":"proteinAcc2TaxID(accnums, suffix, out_path, return_dt = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"accnums character vector protein accession numbers mapped TaxIDs. suffix string suffix used name output file generated script. out_path string specifying directory output file saved. return_dt logical indicating whether return result data table. Defaults FALSE. TRUE, output file read data table returned.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"return_dt TRUE, data table containing mapping protein accession numbers TaxIDs. FALSE, function returns NULL.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"proteinAcc2TaxID — proteinAcc2TaxID","text":"","code":"if (FALSE) { # \\dontrun{ # Example accession numbers accessions <- c(\"ABC123\", \"XYZ456\", \"LMN789\") tax_data <- proteinAcc2TaxID(accessions, suffix = \"example\", out_path = \"/path/to/output\", return_dt = TRUE) tax_data } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":null,"dir":"Reference","previous_headings":"","what":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"Perform elink go protein database taxonomy database write resulting file taxid lineage out_path","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"","code":"proteinAcc2TaxID_old(accessions, out_path, plan = \"multicore\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"accessions character vector containing accession numbers query protein database. out_path string specifying path results query written. set NULL, temporary directory used. plan character string specifies execution plan parallel processing. default \"multicore\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"function return value. writes results specified output path.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/proteinAcc2TaxID_old.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"proteinAcc2TaxID_old — proteinAcc2TaxID_old","text":"","code":"if (FALSE) { # \\dontrun{ accessions <- c(\"ABC123\", \"XYZ456\", \"LMN789\") proteinAcc2TaxID_old(accessions, out_path = \"/path/to/output\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":null,"dir":"Reference","previous_headings":"","what":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"Read interproscan output TSV standardized column names types","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"","code":"readIPRScanTSV(filepath)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"filepath chr path interproscan output TSV","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/readIPRScanTSV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read an interproscan output TSV with standardized column names and types — readIPRScanTSV","text":"tbl_df interproscan output table","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove Asterisk — removeAsterisks","title":"Remove Asterisk — removeAsterisks","text":"Remove asterisks column data Used removing * GenContext columns","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove Asterisk — removeAsterisks","text":"","code":"removeAsterisks(query_data, colname = \"GenContext\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove Asterisk — removeAsterisks","text":"query_data data frame containing data processed. colname name column asterisks removed. Defaults \"GenContext\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove Asterisk — removeAsterisks","text":"original data frame asterisks removed specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeAsterisks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove Asterisk — removeAsterisks","text":"","code":"if (FALSE) { # \\dontrun{ removeAsterisks() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove Empty — removeEmptyRows","title":"Remove Empty — removeEmptyRows","text":"Remove empty rows column Removes empty rows specified column. function ... original data frame returned corresponding cleaned column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove Empty — removeEmptyRows","text":"","code":"removeEmptyRows(prot, by_column = \"DomArch\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove Empty — removeEmptyRows","text":"prot data frame containing 'DomArch', 'Species', 'GenContext', 'ClustName' columns. by_column Column empty rows removed domain+domain -> domain(s). Default column 'DomArch'. Can also take following input, 'Species', 'GenContext', 'ClustName'.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove Empty — removeEmptyRows","text":"tibble rows removed specified column contains \"-\", \"NA\", empty string.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeEmptyRows.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove Empty — removeEmptyRows","text":"","code":"if (FALSE) { # \\dontrun{ removeEmptyRows(prot, \"DomArch\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove Tails — removeTails","title":"Remove Tails — removeTails","text":"Remove tails/singletons function ... Certain low frequency domain architectures can removed. original data frame returned corresponding cleaned column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove Tails — removeTails","text":"","code":"removeTails(prot, by_column = \"DomArch\", keep_domains = FALSE)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove Tails — removeTails","text":"prot data frame containing 'DomArch', 'GenContext', 'ClustName' columns. by_column Default column 'DomArch'. Can also take 'ClustName', 'GenContext' input. keep_domains Default False Keeps tail entries contain query domains.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove Tails — removeTails","text":"original data frame singletons removed specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/removeTails.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove Tails — removeTails","text":"","code":"if (FALSE) { # \\dontrun{ removeTails(prot, \"DomArch\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":null,"dir":"Reference","previous_headings":"","what":"Rename the labels of fasta files — renameFA","title":"Rename the labels of fasta files — renameFA","text":"Rename labels fasta files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rename the labels of fasta files — renameFA","text":"","code":"renameFA(fa_path, outpath, replacement_function = mapAcc2Name, ...)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rename the labels of fasta files — renameFA","text":"fa_path Path fasta file outpath Path write altered fasta file replacement_function Function apply lines starting '>' ... Additional arguments pass replacement_function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rename the labels of fasta files — renameFA","text":"character vector modified lines FASTA file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/renameFA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rename the labels of fasta files — renameFA","text":"","code":"if (FALSE) { # \\dontrun{ renameFA(\"path/to/input.fasta\", \"path/to/output.fasta\", mapAcc2Name, acc2name) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Rename the labels of fasta files — rename_fasta","title":"Rename the labels of fasta files — rename_fasta","text":"Rename labels fasta files","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rename the labels of fasta files — rename_fasta","text":"","code":"rename_fasta(fa_path, outpath, replacement_function = map_acc2name, ...)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rename the labels of fasta files — rename_fasta","text":"fa_path Path fasta file outpath Path write altered fasta file replacement_function Function apply lines starting '>' ... Additional arguments pass replacement_function","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rename the labels of fasta files — rename_fasta","text":"Character vector containing modified lines Fasta file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/rename_fasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rename the labels of fasta files — rename_fasta","text":"","code":"if (FALSE) { # \\dontrun{ rename_fasta(\"input.fasta\", \"output.fasta\", replacement_function = map_acc2name, acc2name = acc2name_table) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace QMs — replaceQuestionMarks","title":"Replace QMs — replaceQuestionMarks","text":"Replace consecutive '?' separated '->', '<-' '||' 'X(s)' Replace '?' 'X'","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace QMs — replaceQuestionMarks","text":"","code":"replaceQuestionMarks(prot, by_column = \"GenContext\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace QMs — replaceQuestionMarks","text":"prot DataTable operate by_column Column operate ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace QMs — replaceQuestionMarks","text":"original data frame specified column updated. consecutive '?' characters replaced 'X(s)', individual '?' characters replaced 'X'.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/replaceQuestionMarks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Replace QMs — replaceQuestionMarks","text":"","code":"if (FALSE) { # \\dontrun{ replaceQuestionMarks() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":null,"dir":"Reference","previous_headings":"","what":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"function processes genomic context data frame reverse direction operons based specific patterns GenContext column. handles elements represented \">\" \"<\" restructures genomic context flipping direction operons preserving relationships indicated \"=\".","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"","code":"reverseOperonSeq(prot)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"prot data.frame data frame containing least column named 'GenContext', represents genomic contexts need reversed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"data.frame input data frame 'GenContext' column updated t o reflect reversed operons.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/reverseOperonSeq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq — reverseOperonSeq","text":"","code":"if (FALSE) { # \\dontrun{ # Example genomic context data frame ## Rework example data, does not pass R-CMD Check prot <- data.frame(GenContext = c(\"A>B\", \"C<D\", \"E=F*G\", \"H>I\"))  reversed_prot <- reverseOperonSeq(prot) reversed_prot } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":null,"dir":"Reference","previous_headings":"","what":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"function executes Delta-BLAST search using specified parameters database. sets BLAST database path, runs Delta-BLAST command given query, outputs results.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"","code":"runDeltaBlast(   runDeltaBlast,   db_search_path,   db = \"refseq\",   query,   evalue = \"1e-5\",   out,   num_alignments,   num_threads = 1 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"db_search_path Path BLAST databases. db Name BLAST database search (default \"refseq\"). query Path input query file. evalue E-value threshold reporting matches (default \"1e-5\"). Path output file results saved. num_alignments Number alignments report. num_threads Number threads use search (default 1). deltablast_path Path Delta-BLAST executable.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"function return value; outputs results specified file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runDeltaBlast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run DELTABLAST to find homologs for proteins of interest — runDeltaBlast","text":"","code":"if (FALSE) { # \\dontrun{ runDeltaBlast(runDeltaBlast, db_search_path) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":null,"dir":"Reference","previous_headings":"","what":"runIPRScan — runIPRScan","title":"runIPRScan — runIPRScan","text":"Run InterProScan given FASTA file save results output file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"runIPRScan — runIPRScan","text":"","code":"runIPRScan(filepath_fasta, filepath_out, appl = c(\"Pfam\", \"Gene3D\"))"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"runIPRScan — runIPRScan","text":"filepath_fasta string representing path input FASTA file. filepath_out string representing base path output file. appl character vector specifying InterProScan applications use (e.g., \"Pfam\", \"Gene3D\"). Default c(\"Pfam\", \"Gene3D\").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"runIPRScan — runIPRScan","text":"data frame containing results InterProScan output TSV file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runIPRScan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"runIPRScan — runIPRScan","text":"","code":"if (FALSE) { # \\dontrun{ results <- runIPRScan(     filepath_fasta = \"path/to/your_fasta_file.fasta\",     filepath_out = \"path/to/output_file\",     appl = c(\"Pfam\", \"Gene3D\") ) results } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":null,"dir":"Reference","previous_headings":"","what":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"function executes RPS-BLAST search generate domain architectures specified proteins. sets BLAST database path, runs RPS-BLAST command provided query, outputs results.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"","code":"runRPSBlast(   rpsblast_path,   db_search_path,   db = \"refseq\",   query,   evalue = \"1e-5\",   out,   num_threads = 1 )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"rpsblast_path Path RPS-BLAST executable. db_search_path Path BLAST databases. db Name BLAST database search (default \"refseq\"). query Path input query file. evalue E-value threshold reporting matches (default \"1e-5\"). Path output file results saved. num_threads Number threads use search (default 1).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"function return value; outputs results specified file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/runRPSBlast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Run RPSBLAST to generate domain architectures for proteins of interest — runRPSBlast","text":"","code":"if (FALSE) { # \\dontrun{ runRSPBlast(rpsblast_path, db_search_path, query, out) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":null,"dir":"Reference","previous_headings":"","what":"Pick Longer Duplicate — selectLongestDuplicate","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"Pick Longer Duplicate","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"","code":"selectLongestDuplicate(prot, column)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"prot data frame containing data, least one column named 'AccNum' identification duplicates. column name column longest entry among duplicates selected.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"data frame containing longest entries among duplicates based specified column.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/selectLongestDuplicate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pick Longer Duplicate — selectLongestDuplicate","text":"","code":"if (FALSE) { # \\dontrun{ selectLongestDuplicate() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":null,"dir":"Reference","previous_headings":"","what":"Sends a ","title":"Sends a ","text":"Sends \"job accepted\" email user job accepted, including details job submission check status.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sends a ","text":"","code":"sendJobStatusEmail(notify_email, job_dir, pin_id, event_type, context = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sends a ","text":"notify_email email address send notification job_dir directory job's arguments stored, job_args.yml pin_id unique identifier job event_type either 'start' 'end', returns corresponding email given type job_results_url URL user can check status job","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sendJobStatusEmail.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sends a ","text":"result sendmailR::sendmail() call","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":null,"dir":"Reference","previous_headings":"","what":"shortenLineage — shortenLineage","title":"shortenLineage — shortenLineage","text":"function abbreviates lineage names shortening first part string (given delimiter).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"shortenLineage — shortenLineage","text":"","code":"shortenLineage(data, colname = \"Lineage\", abr_len = 1)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"shortenLineage — shortenLineage","text":"data data frame contains column lineage names shortened. colname Character. name column data frame containing lineage strings shortened. Default \"Lineage\". abr_len Integer. number characters retain first letter. set 1, first letter segment delimiter (>) retained. Default 1.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"shortenLineage — shortenLineage","text":"modified data frame specified lineage column shortened.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/shortenLineage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"shortenLineage — shortenLineage","text":"","code":"if (FALSE) { # \\dontrun{ df <- data.frame(Lineage = c(\"Bacteria>Firmicutes>Clostridia\", \"Archaea>Euryarchaeota>Thermococci\")) shortened_df <- shortenLineage(df, colname = \"Lineage\", abr_len = 1) shortened_df } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":null,"dir":"Reference","previous_headings":"","what":"Sink Reset — sinkReset","title":"Sink Reset — sinkReset","text":"Sink Reset","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sink Reset — sinkReset","text":"","code":"sinkReset()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sink Reset — sinkReset","text":"return, run close outstanding sink()s","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/sinkReset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sink Reset — sinkReset","text":"","code":"if (FALSE) { # \\dontrun{ sinkReset() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":null,"dir":"Reference","previous_headings":"","what":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"function processes genomic context strings (GenContext) reverses directional signs based presence equal sign (\"=\").","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"","code":"straightenOperonSeq(prot)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"prot vector vector genomic context strings processed.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"vector vector length input, genomic element annotated either forward (\"->\") reverse (\"<-\") direction, depending position relative \"=\" symbols.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/straightenOperonSeq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"straightenOperonSeq: Reverse Equalities in Genomic Context — straightenOperonSeq","text":"","code":"# Example input: Genomic context with directional symbols and an asterisk genomic_context <- c(\"A\", \"B\", \"*\", \"C\", \"D\", \"=\", \"E\", \"F\") straightenOperonSeq(genomic_context) #> [1] \"A->\" \"B->\" \"*->\" \"C->\" \"D->\" \"=\"   \"<-E\" \"<-F\"  # Output: \"A->\", \"B->\", \"*\", \"<-C\", \"<-D\", \"=\", \"E->\", \"F->\""},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":null,"dir":"Reference","previous_headings":"","what":"themeGenes2 — themeGenes2","title":"themeGenes2 — themeGenes2","text":"themeGenes2","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"themeGenes2 — themeGenes2","text":"","code":"themeGenes2()"},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"themeGenes2 — themeGenes2","text":"ggplot2 theme object.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/themeGenes2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"themeGenes2 — themeGenes2","text":"","code":"library(ggplot2)  # Create a sample plot using the custom theme ggplot(mtcars, aes(x = wt, y = mpg)) +     geom_point() +     themeGenes2() +     labs(title = \"Car Weight vs MPG\")"},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":null,"dir":"Reference","previous_headings":"","what":"validateCountDF — validateCountDF","title":"validateCountDF — validateCountDF","text":"validateCountDF","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"validateCountDF — validateCountDF","text":"","code":"validateCountDF(var)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"validateCountDF — validateCountDF","text":"var data frame whose columns converted.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"validateCountDF — validateCountDF","text":"data frame non-'n' columns converted character type.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/validateCountDF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"validateCountDF — validateCountDF","text":"","code":"if (FALSE) { # \\dontrun{ new_df <- .all_non_n_cols_to_char(my_data) } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":null,"dir":"Reference","previous_headings":"","what":"plotWordCloud3 — wordcloud3","title":"plotWordCloud3 — wordcloud3","text":"plotWordCloud3","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plotWordCloud3 — wordcloud3","text":"","code":"wordcloud3(   data,   size = 1,   minSize = 0,   gridSize = 0,   fontFamily = \"Segoe UI\",   fontWeight = \"bold\",   color = \"random-dark\",   backgroundColor = \"white\",   minRotation = -pi/4,   maxRotation = pi/4,   shuffle = TRUE,   rotateRatio = 0.4,   shape = \"circle\",   ellipticity = 0.65,   widgetsize = NULL,   figPath = NULL,   hoverFunction = NULL )"},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plotWordCloud3 — wordcloud3","text":"data Data frame table containing words frequencies word cloud. size Numeric. Scaling factor word sizes (default 1). minSize Numeric. Minimum font size smallest word (default 0). gridSize Numeric. Size grid placing words (default 0). fontFamily Character. Font family use words (default \"Segoe UI\"). fontWeight Character. Font weight words (default \"bold\"). color Character vector. Color words. Use \"random-dark\" random dark colors (default) specify color. backgroundColor Character. Background color word cloud (default \"white\"). minRotation Numeric. Minimum rotation angle words radians (default -π/4). maxRotation Numeric. Maximum rotation angle words radians (default π/4). shuffle Logical. Whether shuffle words (default TRUE). rotateRatio Numeric. Proportion words rotated (default 0.4). shape Character. Shape word cloud (\"circle\" default, can use \"cardioid\", \"star\", \"triangle\", etc.). ellipticity Numeric. Degree ellipticity (default 0.65). widgetsize Numeric vector. Width height widget (default NULL, uses default size). figPath Character. Path image file use mask word cloud (optional). hoverFunction JS function. JavaScript function run hovering words (optional).","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"plotWordCloud3 — wordcloud3","text":"HTML widget object displaying word cloud.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/wordcloud3.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"plotWordCloud3 — wordcloud3","text":"","code":"if (FALSE) { # \\dontrun{ wordcloud3(data = your_data, size = 1.5, color = \"random-light\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"words2WordCounts — words2WordCounts","title":"words2WordCounts — words2WordCounts","text":"Get word counts (wc) DOMAINS (DA) DOMAIN ARCHITECTURES (GC)","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"words2WordCounts — words2WordCounts","text":"","code":"words2WordCounts(string)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"words2WordCounts — words2WordCounts","text":"string character string containing elements (words) count. typically space-delimited string representing domain architectures genomic contexts.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"words2WordCounts — words2WordCounts","text":"tibble (tbl_df) two columns: words column containing individual words (domains domain architectures). freq column containing frequency counts word.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/words2WordCounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"words2WordCounts — words2WordCounts","text":"","code":"if (FALSE) { # \\dontrun{ tibble::tibble(DomArch = c(\"aaa+bbb\", \"a+b\", \"b+c\", \"b-c\")) |>     elements2Words() |>     words2WordCounts() } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":null,"dir":"Reference","previous_headings":"","what":"writeMSA_AA2FA — writeMSA_AA2FA","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"MsaAAMultipleAlignment Objects generated calls msaClustalOmega msaMuscle 'msa' package Write MsaAAMultpleAlignment Objects aligned fasta sequence MsaAAMultipleAlignment Objects generated calls msaClustalOmega msaMuscle 'msa' package","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"","code":"writeMSA_AA2FA(alignment, outpath)  writeMSA_AA2FA(alignment, outpath)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"alignment MsaAAMultipleAlignment object written fasta outpath resulting FASTA file written ","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"Character string representing content written FASTA file. Character string FASTA content written file.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"Samuel Chen, Janani Ravi","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeMSA_AA2FA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"writeMSA_AA2FA — writeMSA_AA2FA","text":"","code":"if (FALSE) { # \\dontrun{ writeMSA_AA2FA(\"my_sequences.fasta\", outpath = \"aligned_output.fasta\") } # } if (FALSE) { # \\dontrun{ # Example usage alignment <- alignFasta(\"path/to/sequences.fasta\") writeMSA_AA2FA(alignment, \"path/to/aligned_sequences.fasta\") } # }"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":null,"dir":"Reference","previous_headings":"","what":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"Write table 2 columns: 1) process 2) median seconds","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"","code":"writeProcessRuntime2TSV(dir_job_results, filepath)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"dir_job_results chr path MolEvolvR job_results filepath path save tsv file","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2TSV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"writeProcessRuntime2TSV — writeProcessRuntime2TSV","text":"tbl_df 2 columns: 1) process 2) median seconds example: writeProcessRuntime2TSV( \"/data/scratch/janani/molevolvr_out/\", \"/data/scratch/janani/molevolvr_out/log_tbl.tsv\" )","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":null,"dir":"Reference","previous_headings":"","what":"writeProcessRuntime2YML — writeProcessRuntime2YML","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"Compute median process runtimes, write YAML list processes median runtimes seconds path specified 'filepath'. default value filepath value env var MOLEVOLVR_PROC_WEIGHTS, getProcessRuntimeWeights() also uses default read location.","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"","code":"writeProcessRuntime2YML(dir_job_results, filepath = NULL)"},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"dir_job_results chr path MolEvolvR job_results directory filepath chr path save YAML file; NULL, uses ./molevol_scripts/log_data/job_proc_weights.yml","code":""},{"path":"https://jravilab.github.io/MolEvolvR/reference/writeProcessRuntime2YML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"writeProcessRuntime2YML — writeProcessRuntime2YML","text":"","code":"if (FALSE) { # \\dontrun{ writeProcessRuntime2YML(     \"/data/scratch/janani/molevolvr_out/\",     \"/data/scratch/janani/molevolvr_out/log_tbl.yml\" ) } # }"}]