Add ase track

docs/content/describe_figure.rst

@@ -424,6 +424,32 @@ Parameters:
 
 * ``grid_cn``: whether or not to display horizontal lines for each integer copy number.
 
+ase
+^^^^^^^^
+
+Allele specific expression: track showing the variant allele frequency of SNPs in RNA-seq and DNA-seq data. This can be useful to show when only one allele is expressed, for example for imprinted genes or genes activated by enhancer hijacking.
+The input data required for this track is a tsv file which can be generated by `fast_ase <https://github.com/e-sollier/fast_ase>`_ and which has the following columns: contig, position, variantID, refAllele, altAllele, refCount, altCount, refCount_DNA, and altCount_DNA (where refCount and altCount are the counts of reads supporting the reference and alternative alleles in the RNA-seq data).
+
+.. image:: images/figure_ase.png 
+  :width: 500
+
+Parameters:
+
+* ``file``: Path to the tsv file generated by `fast_ase <https://github.com/e-sollier/fast_ase>`_. 
+
+* ``vcf_DNA``: Path to a vcf file containing the read counts in the DNA-seq data. This is only required if, instead of using fast_ase, you used GATK HaplotypeCaller and GATK ASEReadCounter for preprocessing the bam files.
+
+* ``color1``, ``color2``: Colors for the minor and major allele frequencies.
+
+* ``min_depth``: Minimum number of reads covering a variant in the RNA-seq data to show it.
+
+* ``max_bar_width``: Maximum width of the bars, in mm. If too many variants are shown, the actual width might be narrower, to avoid overlaps.
+
+* ``lw``: Line width for the line connecting each bar to the position of the corresponding SNP.
+
+* ``only_exonic``: If true, will only show variants located in exons (default: false).
+
+* ``grid``: if true, will display horizontal lines at VAFs of 0.25, 0.50 and 0.75 (default: false).
 
 
 

docs/content/examples.rst

@@ -1143,4 +1143,88 @@ Here is an example of nanopore reads spanning a foldback inversion (resulting fr
 				"chr_prefix": "chr"
 			}
 		]
+	}
+
+Allele-specific expression
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ase track can be used to visualize allele-specific expression. For each variant, the minor allele frequency in the DNA is shown at the top (showing that the variants are heterozygous), and the minor allele frequency in the RNA-seq data is shown at the bottom.
+Here, we see that only one allele of L3MBTL1 is expressed, because this gene is imprinted.
+
+.. image:: images/figure_ase.png 
+	:width: 500
+
+.. toggle:: 
+
+  .. code:: json
+	
+	{
+		"general": {
+			"layout": "horizontal",
+			"reference": "hg19"
+		},
+		"output": {
+			"file": "/home/e840r/Documents/Scripts/figeno/figeno/gui/figure_ase.png",
+			"dpi": 400,
+			"width": 100
+		},
+		"regions": [
+			{
+				"chr": "20",
+				"start": 42134174,
+				"end": 42181756
+			}
+		],
+		"highlights": [],
+		"tracks": [
+			{
+				"type": "ase",
+				"height": 50,
+				"margin_above": 1.5,
+				"bounding_box": false,
+				"fontscale": 1,
+				"label": "RNA,DNA",
+				"label_rotate": true,
+				"file": "/path/to/sample.tsv",
+				"vcf_DNA": "",
+				"min_depth": "6",
+				"color1": "#e55039",
+				"color2": "#4a69bd",
+				"max_bar_width": "10.0",
+				"lw": "0.1",
+				"only_exonic": false,
+				"grid": false
+			},
+			{
+				"type": "genes",
+				"height": 10,
+				"margin_above": 1.5,
+				"bounding_box": false,
+				"fontscale": 1,
+				"label": "",
+				"label_rotate": false,
+				"style": "default",
+				"collapsed": true,
+				"only_protein_coding": true,
+				"exon_color": "#2980b9",
+				"genes": "auto",
+				"show_gene_names": true
+			},
+			{
+				"type": "chr_axis",
+				"height": 10,
+				"margin_above": 1.5,
+				"bounding_box": false,
+				"fontscale": 1,
+				"label": "",
+				"label_rotate": false,
+				"style": "default",
+				"lw_scale": "1.0",
+				"ticklabels_pos": "below",
+				"unit": "kb",
+				"ticks_interval": "auto",
+				"ticks_angle": 0,
+				"chr_prefix": "chr"
+			}
+		]
 	}

figeno/ase.py

@@ -1,12 +1,12 @@
 import numpy as np
 import pandas as pd
 import vcfpy
-from figeno.genes import Gene
+from figeno.utils import KnownException
 
 
 def read_SNPs_RNA(ase_file,gene=None,chr=None,start=None,end=None,exons=None,min_depth=0):
     """
-    Reads a tsv file generated by ASEReadCounter.
+    Reads a tsv file generated by fast_ase or ASEReadCounter.
     Return a dataframe whose rows are SNPs, indicating the read counts of each allele in the RNAseq data.
     """
     if gene is None and (chr is None or start is None or end is None):
@@ -15,7 +15,15 @@ def read_SNPs_RNA(ase_file,gene=None,chr=None,start=None,end=None,exons=None,min
         chr = gene.chr
         start = gene.start
         end = gene.end
-    df = pd.read_csv(ase_file,sep="\t",dtype={"contig":str})
+    try:
+        df = pd.read_csv(ase_file,sep="\t",dtype={"contig":str})
+    except:
+        raise KnownException("Failed to open the ase file: "+str(ase_file))
+    if not "contig" in df.columns: raise KnownException("The input file for the ase track needs a contig column.")
+    if not "position" in df.columns: raise KnownException("The input file for the ase track needs a position column.")
+    if not "refCount" in df.columns: raise KnownException("The input file for the ase track needs a refCount column.")
+    if not "altCount" in df.columns: raise KnownException("The input file for the ase track needs a altCount column.")
+    if not "variantID" in df.columns: raise KnownException("The input file for the ase track needs a variantID column.")
     df["contig"] = [x.lstrip("chr") for x in df["contig"]]
     df = df.loc[df["contig"]==chr]
     df = df.loc[(df["position"]>=start) & (df["position"]<=end)]

figeno/cli/cli.py

@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.5.1"
+__version__ = "1.6.0"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)

figeno/gui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.5.1",
+  "version": "1.6.0",
   "private": true,
   "homepage": "./",
   "dependencies": {

figeno/gui/src/Track.jsx

@@ -42,6 +42,9 @@ export function Track({track, set_value, change_track_type, copy_track, delete_t
         if (track.type=="copynumber"){
             return CopynumberTrack({"track":track,"set_value":set_value,"openColorPanel":openColorPanel,"setFileDialogData":setFileDialogData,"setFileDialogActive":setFileDialogActive});
         }
+        if (track.type=="ase"){
+            return AseTrack({"track":track,"set_value":set_value,"openColorPanel":openColorPanel,"setFileDialogData":setFileDialogData,"setFileDialogActive":setFileDialogActive});
+        }
     }
     function handleTrackIcon(){
         openTrackTypePanel((t)=>{set_value("type",t)})
@@ -784,6 +787,49 @@ function CopynumberTrack({track,set_value,openColorPanel, setFileDialogData,setF
     )
 }
 
+function AseTrack({track,set_value,openColorPanel, setFileDialogData,setFileDialogActive}){
+    const fileClass= (track.file.endsWith(".tsv"))? "":"unsetPath"; 
+    return (
+        <>
+            <div className="optionGroup">
+                <PathEntry id={"file"+track.id} label="File:" value={track.file} set_value={(val) => set_value("file",val)} className={fileClass}  setFileDialogData={setFileDialogData} setFileDialogActive={setFileDialogActive}/>
+                <PathEntry id={"vcf_DNA"+track.id} label="VCF DNA:" value={track.vcf_DNA} set_value={(val) => set_value("vcf_DNA",val)} setFileDialogData={setFileDialogData} setFileDialogActive={setFileDialogActive}/>
+                <div className='formItem' >
+                    <label htmlFor={"color1"+track.id}>Color 1: </label>
+                    <ColorButton id={"color1"+track.id} color={track.color1} setColor={(c)=>set_value("color1",c)} openColorPanel={openColorPanel}></ColorButton>
+                </div>
+                <div className='formItem' >
+                    <label htmlFor={"color2"+track.id}>Color 2: </label>
+                    <ColorButton id={"color2"+track.id} color={track.color2} setColor={(c)=>set_value("color2",c)} openColorPanel={openColorPanel}></ColorButton>
+                </div>
+            </div>
+            <div className="optionGroup">
+                <div className='formItem'>
+                    <label htmlFor={"min_depth"+track.id}>Min depth:</label>
+                    <input id={"min_depth"+track.id} style={{width:"3em"}} value={track.min_depth} onChange={(e) => set_value("min_depth",e.target.value)} ></input>
+                </div>
+                <div className='formItem'>
+                    <label htmlFor={"max_bar_width"+track.id}>Max bar width:</label>
+                    <input id={"max_bar_width"+track.id} style={{width:"3em"}} value={track.max_bar_width} onChange={(e) => set_value("max_bar_width",e.target.value)} ></input>
+                </div>
+                <div className='formItem'>
+                    <label htmlFor={"lw"+track.id}>lw:</label>
+                    <input id={"lw"+track.id} style={{width:"3em"}} value={track.lw} onChange={(e) => set_value("lw",e.target.value)} ></input>
+                </div>
+                <div className='formItem'>
+                    <label htmlFor={"only_exonic"+track.id}>Only exonic:</label>
+                    <input type="checkbox" id={"only_exonic"+track.id} checked={track.only_exonic} onChange={() => set_value("only_exonic",!track.only_exonic)} />
+                </div>
+                <div className='formItem'>
+                    <label htmlFor={"grid"+track.id}>Grid:</label>
+                    <input type="checkbox" id={"grid"+track.id} checked={track.grid} onChange={() => set_value("grid",!track.grid)} />
+                </div>
+
+            </div>
+
+        </>
+    )
+}
 
 export function TrackIcon({track_type, onClick}){
     return(
@@ -887,6 +933,19 @@ export function TrackIcon({track_type, onClick}){
             </g>
            </svg>
         ):""}
+
+        {(track_type=="ase")?(
+            <svg width="15mm" height="15mm" version="1.1" viewBox="0 0 10 10" xmlns="http://www.w3.org/2000/svg">
+            <g stroke-linejoin="round" strokeLinecap="round">
+            <rect x="2.8333" y="3" width="1.6667" height="1.6667" fill="#e55039" opacity=".97208" stroke-width=".1093"/>
+            <rect x="2.8333" y="1.3333" width="1.6667" height="1.6667" fill="#4a69bd" opacity=".97208" stroke-width=".1093"/>
+            <rect x="2.8333" y="5.3333" width="1.6667" height="3.3333" fill="#4a69bd" opacity=".97208" stroke-width=".15458"/>
+            <rect x="5.5" y="3.2029" width="1.6667" height="1.4637" fill="#e55039" opacity=".97208" stroke-width=".10243"/>
+            <rect x="5.5" y="1.3333" width="1.6667" height="1.8887" fill="#4a69bd" opacity=".97208" stroke-width=".11635"/>
+            <rect x="5.5" y="5.3333" width="1.6667" height="3.3333" fill="#4a69bd" opacity=".97208" stroke-width=".15458"/>
+            </g>
+           </svg>
+        ):""}
         </div>
 
 

figeno/gui/src/TrackTypePanel.jsx

@@ -5,7 +5,7 @@ import { TrackIcon } from './Track';
 
 
 export function TrackTypePanel({setTrackType,close}){
-    const track_types = ["chr_axis", "genes", "bed", "bigwig", "coverage", "alignments", "basemod_freq", "hic", "sv", "copynumber"];
+    const track_types = ["chr_axis", "genes", "bed", "bigwig", "coverage", "alignments", "basemod_freq", "hic", "sv", "copynumber", "ase"];
     const popover = useRef();
     useClickOutside(popover, close);
 

figeno/gui/src/TracksContainer.jsx

@@ -187,6 +187,23 @@ export const defaultTrackValues={
         color_gain:"#e55039",
         color_cnloh:"#f6b93b"
     },
+    "ase":{
+        height:"50",
+        margin_above:"1.5",
+        bounding_box:false,
+        fontscale:1.0,
+        label:"RNA,DNA",
+        label_rotate:true,
+        file:"",
+        vcf_DNA:"",
+        min_depth:"6",
+        color1:"#e55039",
+        color2:"#4a69bd",
+        max_bar_width:"10.0",
+        lw: "0.1",
+        only_exonic: false,
+        grid:false
+    },
     "other":{
         height:"8",
         margin_above:"1.5",
@@ -227,7 +244,7 @@ export function TracksContainer({tracksList,setTracksList,openColorPanel, openTr
 
     function create_track({id,type,track={}}){
         let new_track = {id:id, type:type};
-        if (["chr_axis","genes","bed","bigwig","coverage","alignments", "basemod_freq","hic","sv","copynumber"].includes(new_track.type)){
+        if (["chr_axis","genes","bed","bigwig","coverage","alignments", "basemod_freq","hic","sv","copynumber","ase"].includes(new_track.type)){
             for (const attribute in defaultTrackValues[new_track.type]){
                 new_track[attribute] = track.hasOwnProperty(attribute) ? track[attribute] : defaultTrackValues[new_track.type][attribute]
             }

figeno/gui/src/style.css

@@ -114,6 +114,7 @@ input{
   display: grid;
   grid-template-columns: 1fr 1fr 1fr;
   gap:10px;
+  margin:5px;
 }
 
 .TemplatePanel{