graphy_v2.py

import pandas as pd
# import numpy as np
# from matplotlib import pyplot as plt
# from matplotlib import gridspec
# from matplotlib.patches import Rectangle
# from matplotlib import rc
# import matplotlib.patches as mpatches
# import subprocess
# from operator import itemgetter
#import seaborn as sns
import itertools
import sys
import os
import spectra
if sys.version_info[0] < 3: 
    from StringIO import StringIO
else:
    from io import StringIO
sys.path.insert(0,'/Users/DarthRNA/Documents/Robin/PythonModules')
sys.path.insert(0,'/Users/DarthRNA/Documents/Robin/HitsSummary')
import clip_tools as ct
from functions import *
from defaults import *

from ipywidgets import interact
import ipywidgets as widgets
from IPython.display import display
from ipywidgets import FloatSlider
from IPython.display import clear_output


updates = "\
3/23/17: Now the tracks are displayed in the order they were selected! <p> \
4/11/17: Added custom section to bedfiles. Covers custom bedfiles, including custom miRNA tracks <p> \
4/27/17: Updated LeftToRight button\
"

###################################################


# Required: Reference. 
# file_utr3 is used in finding the names of genes, 
#    though a bed of entire gene transcripts might be more useful (and should work)
# file_refseq is used to graph the refseq track. 

# file_utr3 = "/Users/DarthRNA/Documents/Robin/genomes/refseq_3utr.bed"
# file_refseq = "/Users/DarthRNA/Documents/Robin/genomes/refseq_names.txt"
# file_targetscan = "/Users/DarthRNA/Documents/Robin/genomes/Targetscan.bed"
# file_refgenebed = '/Users/DarthRNA/Documents/Robin/genomes/refGene.bed'
# default_track_folder = "/Users/DarthRNA/Documents/Robin/GRAPHY_TEST/"


bedfiles_allowed = {"Peaks":{"name":"Peaks",
                             "bedfile":"/Users/DarthRNA/Documents/Robin/FASTUTR/peaks.bed",
                             "bedtype":"bed"},
                    "Targetscan":{"name":"Targetscan",
                                  "bedfile":file_targetscan,
                                  "bedtype":"targetscan"}}



### Lookup 3'UTR by Refseq
df_refseq_3utr = pd.read_table("/Users/DarthRNA/Documents/Robin/genomes/mm10_refseq_3utr.bed",names=['chrom','start','stop','name','score','strand'])
df_refseq_3utr.name = ["_".join(x.split("_")[0:2]) for x in df_refseq_3utr.name]
df_refseq_3utr = df_refseq_3utr.drop_duplicates("name")
df_refseq_3utr = df_refseq_3utr.set_index("name")

###################################################

# Make a genelookup object.
bd = ct.BetweenDict(file_refgenebed)

##############################################

print_plotting_parameters = True

##############################################


legend = True # adds legend box to alignment bam track.
staticaxes = False # keeps axes the same across all bam files. (for normalized data)
LeftToRight = False # Makes all genes read left to right. 
axis_off = False  # Don't show the axis labels.

### FILE OUTPUT OPTIONS ###
#dpi = 300
# figwidth = "scale"  # Can be "scale" or <int>  (15 is a good basic value)
# outputformat = "pdf"
# outputsuffix = ""

# Mostly Untouched Default Variables.



# Set static parameters
limits = "default" # can also be [int_start,int_stop]

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defaultloc = 'chr5:142,903,034-142,906,867'
defaultgeneid = 'Actb'
defaultrefseqid = 'NM_007393'
defaultstrand = "-"

#### Accordian Change File Locations ####
w_default_folder = widgets.Text(
    description='RnaSeq Folder',
    value=default_track_folder,
)
w_default_folder.width="80%"
w_default_folder_valid = widgets.Valid(value=True)
hboxdefaultfolder = widgets.HBox([w_default_folder,w_default_folder_valid])
page1 = widgets.VBox(children=[hboxdefaultfolder])

accord = widgets.Accordion(children=[page1], width="80%")
display(accord)

accord.set_title(0, 'Defaults')


#### Define Widgets ###
lookuptype_widget = widgets.RadioButtons(
    options={'By location':'location','By geneid (3\'UTR only)':"geneid"},
    value='location',
    description='Lookup:',
    disabled=False
)

location_widget = widgets.Text(
    value=defaultloc,
    placeholder='Type something',
    description='Location:',
    disabled=False
)


strand_widget = widgets.RadioButtons(
    options=['+','-'],
    value=defaultstrand,
    description='Strand:',
    disabled=False
)


geneid_widget = widgets.Dropdown(
        options=[defaultgeneid],
        value=defaultgeneid,
        description='GeneID:',
        disabled=False,
        button_style='' # 'success', 'info', 'warning', 'danger' or ''
    )

refseqid_widget = widgets.Dropdown(
        options=[defaultrefseqid],
        value=defaultrefseqid,
        description='RefseqID:',
        disabled=False,
        button_style='' # 'success', 'info', 'warning', 'danger' or ''
    )


## Updating Widgets ##

def update_by_type(*args):
    if lookuptype_widget.value == "location":
        location_widget.value = defaultloc
    if lookuptype_widget.value == "geneid":
        location_widget.value = defaultgeneid

def update_geneid(*args):
    if lookuptype_widget.value == "location":
        chrom,start,stop = ct.easylocation(location_widget.value)
        strand = strand_widget.value
        genelist =  list(get_gene_id(chrom,start,stop,strand,bd,choice='all'))
        if len(genelist)>0:
            geneid_widget.options = genelist
        else:
            geneid_widget.options = ["None"]
    elif lookuptype_widget.value == "geneid":
        geneid_widget.options = [location_widget.value]
        geneid_widget.value = location_widget.value
        

def update_refseqid(*args):
    reflist =  get_refseq_id(file_refseq,geneid_widget.value,choice="all")
    print reflist
    if len(reflist)>0:
        refseqid_widget.options = reflist
    else:
        refseqid_widget.options = ["None"]

lookuptype_widget.observe(update_by_type,'value')
location_widget.observe(update_geneid, 'value')
strand_widget.observe(update_geneid, 'value')
geneid_widget.observe(update_refseqid,'value')

display(widgets.HTML(value="<h5>Updates:</h5><p>" + updates))
display(widgets.HTML(value="<h3>Select Region</h3>"))

### Define INTERACT: All interdependent widgets must be in here ###
def printer(lookuptype,loc, strand, geneid,refseqid):
    print("")
interact(printer,
         lookuptype = lookuptype_widget,
         loc=location_widget,
         strand=strand_widget,
         geneid=geneid_widget,
         refseqid = refseqid_widget,
         continuous_update=False)


### Select File ###
all_files = os.listdir(default_track_folder)
file_types = ["bam","bw"]
file_names = []
for f in all_files:
    if f.split(".")[-1] in file_types:
        file_names.append(f)
file_widget = widgets.SelectMultiple(
    options=file_names,
    disabled=False
)

def update_antisense_check(*args):
    if len(file_widget.value)==0:
        w_as_selectors.layout.display="none"
        w_antisense_check.options = []
    if len(file_widget.value)>0:
        w_as_selectors.layout.display=""
        # Add or remove from antisence_check.options
        options = w_antisense_check.options
        for i in file_widget.value:
            if not i in options:
                options.append(i)
        for i in options:
            if not i in file_widget.value:
                options.remove(i)
        w_antisense_check.options = options



file_widget.observe(update_antisense_check,'value')

w_aschecktitle= widgets.HTML("Are any of these tracks antisense?")
# The antisense_check box is also holding the order of the files selected
w_antisense_check = widgets.SelectMultiple(
    options=[]
)
w_as_selectors = widgets.VBox([w_aschecktitle,w_antisense_check])
w_as_selectors.layout.display="none"

### Style Selectors ###
buttonwidth="15%"
buttonstyle='info'
w_labels = widgets.ToggleButton(
    value=False,
    description='BedLabels',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip='Label each element of a bedtrack',
    width=buttonwidth,
)
w_invert = widgets.ToggleButton(
    value=False,
    description='Left to Right',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Always display genes from left to right regardless of strand.",
    width=buttonwidth,

)
w_legend = widgets.ToggleButton(
    value=True,
    description='Legend',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Show Legend for Seq-Tracks",
    width=buttonwidth,

)
w_stagger = widgets.ToggleButton(
    value=False,
    description='Stagger Bedtracks',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Stagger Bedtracks",
    width=buttonwidth,
)
w_refseq = widgets.ToggleButton(
    value=True,
    description='Show Refseq',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Refseq track?",
    width=buttonwidth,
)
w_shadeBed = widgets.ToggleButton(
    value=False,
    description='Shade Bed',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Highlight bedtrack regions",
    width=buttonwidth,
)
w_staticaxes = widgets.ToggleButton(
    value=True,
    description='Autoscale',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Scale the rnaseq tracks?",
    width=buttonwidth,
)
w_boundingbox = widgets.ToggleButton(
    value=True,
    description='Show BoundingBox',
    button_style=buttonstyle, # 'success', 'info', 'warning', 'danger' or ''
    tooltip="Show axes and border box?",
    width=buttonwidth,
)
formattingwidth ="20%"
w_xscale = widgets.FloatText(
    description="x scale (inches)",
    placeholder="Int",
    tooltip="can enter 0 to autoscale",
    width=formattingwidth,
)
w_fontsize = widgets.FloatText(
    description="Font Size",
    placeholder="Int",
    tooltip="can enter 0 to autoscale",
    value=12,
    width=formattingwidth,
)
w_dpi = widgets.FloatText(
    description="DPI",
    placeholder="300",
    value="300",
    width=formattingwidth,
)
w_fileformat = widgets.Text(
    description="File Format",
    placeholder="Pdf,Svg,PNG",
    value="pdf",
    width=formattingwidth,
)
w_filesuffix = widgets.Text(
    description="File Suffix",
    placeholder="None",
    value="",
    width=formattingwidth,
)

w_outputfolder = widgets.Text(
    value="/Users/DarthRNA/Documents/Robin/TrackImages/",
    description="Output Folder",
    width="80%",
)
w_outputfolder_valid = widgets.Valid(value=True)
hboxoutputfolder = widgets.HBox([w_outputfolder,w_outputfolder_valid])
def output_folder_check(*args):
    if os.path.isdir(w_outputfolder.value) and w_outputfolder.value[-1] == "/" :
        w_outputfolder_valid.value=True
    else:
        w_outputfolder_valid.value=False
w_outputfolder.observe(output_folder_check,'value')


### Color Selectors ###
w_cp1=widgets.ColorPicker(value="#0080ff",width="100px",concise=False)
w_cp2=widgets.ColorPicker(value="#ff0000",width="100px",concise=False)
w_cp3=widgets.ColorPicker(value="#00ff00",width="100px",concise=False)
w_cp4=widgets.ColorPicker(value="#800080",width="100px",concise=False)



selectors_color = widgets.HBox([w_cp1,w_cp2,w_cp3,w_cp4])
selectors1 = widgets.HBox([w_labels,
                           w_invert,
                           w_legend,
                           w_stagger,
                           w_refseq,
                           w_shadeBed,
                           w_staticaxes,
                           w_boundingbox,
                          ])
selectors2 = widgets.HBox([w_xscale,
                           w_fontsize,
                           w_dpi,
                           w_fileformat,
                           w_filesuffix,
                          ])


### MiRNA and Bedtrack Picker ###
bedtracks_widget = widgets.RadioButtons(
    options=["None"] + bedfiles_allowed.keys() + ["Custom","Other"],
    description='Bedfiles:',
    disabled=False
)
other_bedtracks_widget = widgets.Text(
    value=placeholder_file_bedfile,
    description="Other:",
    width="90%"
)
miRNA_widget = widgets.Select(
    options=["None"],
    value="None",
    description = "miRNA Family",
)


def update_miRNAlist(*args):
    miRNAwrapper.layout.display="none"
    otherbedtrackwrapper.layout.display="none"
    def get_targetscan_families(targetscan_file):
        beddb = pd.read_table(targetscan_file,names=["chrom","start","stop","miRNA"],usecols=[0,1,2,3])
        families = beddb.miRNA.unique()
        f = families.tolist()
        return sorted(f[1:])
    if bedtracks_widget.value=="Targetscan":
        miRNA_widget.description = "miRNA Family"
        miRNAwrapper.layout.display=""
        tsfamilies = get_targetscan_families(bedfiles_allowed[bedtracks_widget.value]["bedfile"])
        miRNA_widget.options = ["ALL"] + tsfamilies
    if bedtracks_widget.value=="Other":
        otherbedtrackwrapper.layout.display=""
    if bedtracks_widget.value in ["None","Peaks"]:
        miRNAwrapper.layout.display="none"
        miRNA_widget.options = ["None"]
        miRNA_widget.value = "None"
    if bedtracks_widget.value=="Custom":
        miRNAwrapper.layout.display=""
        if os.path.isdir(w_default_folder.value) and w_default_folder.value[-1] == "/" :
            w_default_folder_valid.value=True
            track_folder = w_default_folder.value
            all_files = os.listdir(track_folder)
            file_names = []
            file_types = ["bed"]
            for f in all_files:
                if f.split(".")[-1] in file_types:
                    file_names.append(f)
            miRNA_widget.options = file_names
            miRNA_widget.description = "Bedfile"
        else:
            w_default_folder_valid.value=False
            file_names = []
            miRNA_widget.options =[]
# def update_bedfile_other(*args):
#     if bedtracks_widget.value == "Other":


bedtracks_widget.observe(update_miRNAlist,'value')
#otherbedtrackwrapper.observe(update_bedfile_other,'value')

display(widgets.HTML(value="<h3>Files</h3>"))
display(bedtracks_widget)
otherbedtrackwrapper = widgets.VBox([other_bedtracks_widget])
display(otherbedtrackwrapper)
otherbedtrackwrapper.layout.display="none"
# Puts miRNA_widget in a VBox that can have its display toggled. 
miRNAwrapper = widgets.VBox([miRNA_widget])
display(miRNAwrapper)
miRNAwrapper.layout.display="none"

def miRNAUpdater(bedfile,miRNApick):
    print(bedfile)

miRNA_widget.layout.display=""
# interact(miRNAUpdater,
#          bedfile=bedtracks_widget,
#          miRNApick = miRNA_widget,
#          continuous_update=False,
#          font_size=4)
miRNA_widget.layout.width="100%"
file_widget.layout.width="100%"
def update_filelist(*args):
    if os.path.isdir(w_default_folder.value) and w_default_folder.value[-1] == "/" :
        w_default_folder_valid.value=True
        print w_default_folder.value
        track_folder = w_default_folder.value
        all_files = os.listdir(track_folder)
        file_names = []
        file_types = ["bam","bw"]
        for f in all_files:
            if f.split(".")[-1] in file_types:
                file_names.append(f)
        file_widget.options = file_names
    else:
        w_default_folder_valid.value=False
        file_names = []
        file_widget.options =[]
w_default_folder.observe(update_filelist,'value')

# Display #
display(widgets.HTML(value="Alignments to Use"))
display(file_widget)
display(w_as_selectors)
display(widgets.HTML(value="<h3>Formatting</h3>"))
display(selectors1)
display(widgets.HTML(value="<h4>Color Picker</h4>"))
display(selectors_color)
display(widgets.HTML(value="<h4>Output Format</h4>"))
display(selectors2)
display(hboxoutputfolder)
display(widgets.HTML(value="<br><br>"))

accord.selected_index=1 #starts the accordian closed.


###### LAUNCH BUTTON #####
button = widgets.Button(description="Graph!")
display(button)
def on_button_clicked(b):
    clear_output()

    ## SANITY CHECKS ###
    if not len(file_widget.value)>0:
        print "ERROR: It's required to pick a .bam alignment!"
        return
    #####################

    if lookuptype_widget.value=="location":
        chrom,start,stop = ct.easylocation(location_widget.value)
        strand = strand_widget.value
    elif lookuptype_widget.value=="geneid":
        chrom,start,stop,value,strand = df_refseq_3utr.loc[refseqid_widget.value]
    if bedtracks_widget.value == "None":
        bedtrack=False
        bedfile=None
        bedtype=None
        name=None
    elif bedtracks_widget.value == "Peaks":
        bedtrack=True
        bedfile = bedfiles_allowed[bedtracks_widget.value]["bedfile"]
        bedtype = "bed"
        name = "Peaks"
    elif bedtracks_widget.value == "Other":
        bedtrack=True
        bedfile = other_bedtracks_widget.value
        bedtype = "bed"
        name = "Bedtrack"       
    elif bedtracks_widget.value == "Targetscan":
        bedtrack=True
        bedfile = bedfiles_allowed[bedtracks_widget.value]["bedfile"]
        if miRNA_widget.value == "ALL":
            bedtype = bedfiles_allowed[bedtracks_widget.value]["bedtype"]
            name = bedfiles_allowed[bedtracks_widget.value]["name"]
        else:
            bedtype = "targetscan"
            name = miRNA_widget.value
    elif bedtracks_widget.value == "Custom":
        bedtrack=True
        bedfile = w_default_folder.value+miRNA_widget.value
        bedtype = "bed"
        name = miRNA_widget.value
    track_type=[]
    for t in w_antisense_check.options:
        if t in w_antisense_check.value:
            track_type.append("as")
        else:
            track_type.append("s")
    geneid= geneid_widget.value
    refseqid = refseqid_widget.value
    track_names = [f for f in w_antisense_check.options if f.split(".")[-1]=="bam"]
    bigwignames = [f for f in w_antisense_check.options if f.split(".")[-1]=="bw"]
    track_files = [w_default_folder.value + f for f in track_names]
    bigwigfiles = [w_default_folder.value + f for f in bigwignames]
    depths = get_depth_data(track_files,track_names,chrom,start,stop,strand,track_type)
    wig_df_list = get_wig_data(bigwigfiles,bigwignames,chrom,start,stop)
    
    outputformat = w_fileformat.value
    figwidth = w_xscale.value
    dpi = w_dpi.value
    LeftToRight = w_invert.value
    annotate_bed = w_labels.value
    staggerbed = w_stagger.value
    refseqtrack = w_refseq.value
    shade_by_bed = w_shadeBed.value
    outputsuffix = w_filesuffix.value
    staticaxes = w_staticaxes.value
    axis_off= not w_boundingbox.value
    fontsize = w_fontsize.value
    legend = w_legend.value
    figheight = 2.5*len(w_antisense_check.options)
    output_folder = w_outputfolder.value

    color_values = [w_cp1.value,w_cp2.value,w_cp3.value]
    shade = itertools.cycle(color_values)
    colors = itertools.cycle([spectra.html(i).darken(20).hexcode for i in color_values])
    plot(figwidth,figheight,refseqtrack,LeftToRight,strand,depths,
       colors,shade,limits,bedtrack,start,stop,staggerbed,bigwignames,
        wig_df_list,shade_by_bed,output_folder,geneid,outputsuffix,outputformat,dpi,track_names,axis_off,
       legend,staticaxes,bedfile,bedtype,name,chrom,refseqid,annotate_bed,fontsize)

button.on_click(on_button_clicked)