update vignettes

drostlab · Oct 3, 2024 · 49892a2 · 49892a2
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diff --git a/vignettes/Enrichment.R b/vignettes/Enrichment.R
@@ -1,4 +1,4 @@
-## ----eval=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # read expression data (organ specific genes) from Sestak and Domazet-Loso, 2015
 #  Drerio.OrganSpecificExpression <- read_excel("MBE_2015a_Drerio_PhyloMap.xlsx", sheet = 2, skip = 3)
 #  
@@ -13,14 +13,14 @@
 #                 legendName   = "PS")
 #  
 
-## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  PlotEnrichment(Drerio.PhyloMap,
 #                 test.set     = Drerio.Brain.Genes,
 #                 measure      = "log-foldchange",
 #                 use.only.map = TRUE,
 #                 legendName   = "PS")
 
-## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # specify plot.bars = FALSE to retrieve only numeric results
 #  EnrichmentResult <- PlotEnrichment(Drerio.PhyloMap,
 #                                     test.set     = Drerio.Brain.Genes,
@@ -32,12 +32,12 @@
 #  # access p-values quantifying the enrichment for each Phylostratum
 #  EnrichmentResult$p.values
 
-## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # access enrichment matrix storing C_1 and C_2
 #  EnrichmentResult$enrichment.matrix
 #  
 
-## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # complete.bg = TRUE (default) -> retain test.set genes in background set
 #  PlotEnrichment(Drerio.PhyloMap,
 #                 test.set     = Drerio.Brain.Genes,
@@ -46,7 +46,7 @@
 #                 use.only.map = TRUE,
 #                 legendName   = "PS")
 
-## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # complete.bg = FALSE -> remove test.set genes from background set
 #  PlotEnrichment(Drerio.PhyloMap,
 #                 test.set     = Drerio.Brain.Genes,
@@ -55,19 +55,19 @@
 #                 use.only.map = TRUE,
 #                 legendName   = "PS")
 
-## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  PlotEnrichment(Drerio.PhyloMap,
 #                 test.set     = Drerio.Brain.Genes,
 #                 measure      = "foldchange",
 #                 complete.bg  = TRUE,
 #                 use.only.map = TRUE,
 #                 legendName   = "PS")
 
-## ---- eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # retrieve the taxonomy of D. rerio
-#  taxonomy(organism = "Danio rerio")
+#  myTAI::taxonomy(organism = "Danio rerio")
 
-## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # the best parameter setting to visualize this plot:
 #  # png("DrerioBrainSpecificGeneExpression.png",700,400)
 #  PlotGeneSet(ExpressionSet = DrerioPhyloExpressionSet,
@@ -81,14 +81,14 @@
 #  
 #  # dev.off()
 
-## ---- eval = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # select the ExpressionSet subset of Brain specific genes
 #  Brain.PhyloExpressionSet <- SelectGeneSet( ExpressionSet = DrerioPhyloExpressionSet,
 #                                             gene.set      = Drerio.Brain.Genes )
 #  
 #  head(Brain.PhyloExpressionSet)
 
-## ----eval = FALSE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+## ----eval = FALSE-------------------------------------------------------------
 #  # adjust p-values for multiple comparisons with Benjamini & Hochberg (1995)
 #  PlotEnrichment(Drerio.PhyloMap,
 #                 test.set        = Drerio.Brain.Genes,

diff --git a/vignettes/Enrichment.Rmd b/vignettes/Enrichment.Rmd
@@ -353,7 +353,7 @@ PlotEnrichment(Drerio.PhyloMap,
 
 ```
 
-Please consult these reviews ([Biostatistics Handbook](http://www.biostathandbook.com/multiplecomparisons.html), [Gelman et al., 2008](http://www.stat.columbia.edu/~gelman/research/published/multiple2f.pdf), and [Slides](http://www.gs.washington.edu/academics/courses/akey/56008/lecture/lecture10.pdf)) to decide whether or not to apply p-value adjustment
+Please consult these reviews [Gelman et al., 2008](http://www.stat.columbia.edu/~gelman/research/published/multiple2f.pdf), and [Slides](http://www.gs.washington.edu/academics/courses/akey/56008/lecture/lecture10.pdf)) to decide whether or not to apply p-value adjustment
 to your own dataset. 
 
 

diff --git a/vignettes/Enrichment.html b/vignettes/Enrichment.html
@@ -11,7 +11,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 
 
-<meta name="date" content="2023-08-16" />
+<meta name="date" content="2024-10-03" />
 
 <title>Enrichment Analyses</title>
 
@@ -50,7 +50,7 @@
 </style>
 <style type="text/css" data-origin="pandoc">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -61,7 +61,7 @@
 }
 @media print {
 pre > code.sourceCode { white-space: pre-wrap; }
-pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
 }
 pre.numberSource code
 { counter-reset: source-line 0; }
@@ -338,7 +338,7 @@
 
 
 <h1 class="title toc-ignore">Enrichment Analyses</h1>
-<h4 class="date">2023-08-16</h4>
+<h4 class="date">2024-10-03</h4>
 
 
 
@@ -619,9 +619,11 @@ <h2>Interpretation of Enrichment Results</h2>
 <span id="cb13-5"><a href="#cb13-5" tabindex="-1"></a>               <span class="at">use.only.map =</span> <span class="cn">TRUE</span>,</span>
 <span id="cb13-6"><a href="#cb13-6" tabindex="-1"></a>               <span class="at">legendName   =</span> <span class="st">&quot;PS&quot;</span>)</span></code></pre></div>
 <p>Again, we retrieve the <em>D. rerio</em> specific taxonomy
-represented by PS1-14 using the <code>taxonomy()</code> function (see <a href="Introduction.html">Introduction</a> and <a href="Taxonomy.html">Taxonomy</a> for details).</p>
+represented by PS1-14 using the <code>myTAI::taxonomy()</code> function
+(see <a href="Introduction.html">Introduction</a> and
+<code>Taxonomy</code> for details).</p>
 <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="co"># retrieve the taxonomy of D. rerio</span></span>
-<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a><span class="fu">taxonomy</span>(<span class="at">organism =</span> <span class="st">&quot;Danio rerio&quot;</span>)</span></code></pre></div>
+<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a>myTAI<span class="sc">::</span><span class="fu">taxonomy</span>(<span class="at">organism =</span> <span class="st">&quot;Danio rerio&quot;</span>)</span></code></pre></div>
 <pre><code>                    id         name    rank
 1   cellular organisms      no rank  131567
 2            Eukaryota superkingdom    2759
@@ -714,8 +716,7 @@ <h3>Adjust P-values for Multiple Comparisons</h3>
 <span id="cb18-6"><a href="#cb18-6" tabindex="-1"></a>               <span class="at">use.only.map    =</span> <span class="cn">TRUE</span>,</span>
 <span id="cb18-7"><a href="#cb18-7" tabindex="-1"></a>               <span class="at">legendName      =</span> <span class="st">&quot;PS&quot;</span>,</span>
 <span id="cb18-8"><a href="#cb18-8" tabindex="-1"></a>               <span class="at">p.adjust.method =</span> <span class="st">&quot;BH&quot;</span>)</span></code></pre></div>
-<p>Please consult these reviews (<a href="http://www.biostathandbook.com/multiplecomparisons.html">Biostatistics
-Handbook</a>, <a href="http://www.stat.columbia.edu/~gelman/research/published/multiple2f.pdf">Gelman
+<p>Please consult these reviews <a href="http://www.stat.columbia.edu/~gelman/research/published/multiple2f.pdf">Gelman
 et al., 2008</a>, and <a href="http://www.gs.washington.edu/academics/courses/akey/56008/lecture/lecture10.pdf">Slides</a>)
 to decide whether or not to apply p-value adjustment to your own
 dataset.</p>
-Original file line number
+Diff line change
@@ Expand Up / @@ -353,7 +353,7 @@ PlotEnrichment(Drerio.PhyloMap, @@
     ```
-    Please consult these reviews ([Biostatistics Handbook](http://www.biostathandbook.com/multiplecomparisons.html), [Gelman et al., 2008](http://www.stat.columbia.edu/~gelman/research/published/multiple2f.pdf), and [Slides](http://www.gs.washington.edu/academics/courses/akey/56008/lecture/lecture10.pdf)) to decide whether or not to apply p-value adjustment
+    Please consult these reviews [Gelman et al., 2008](http://www.stat.columbia.edu/~gelman/research/published/multiple2f.pdf), and [Slides](http://www.gs.washington.edu/academics/courses/akey/56008/lecture/lecture10.pdf)) to decide whether or not to apply p-value adjustment
     to your own dataset.
@@ Expand Down @@