shoebox support - round 2

igvteam · Oct 12, 2024 · 78aec24 · 78aec24
1 parent b962c35
commit 78aec24
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Showing 11 changed files with 404 additions and 4 deletions.
diff --git a/dev/shoebox/bedToSampleInfo.cjs → dev/shoebox/old/bedToSampleInfo.cjs b/dev/shoebox/bedToSampleInfo.cjs → dev/shoebox/old/bedToSampleInfo.cjs
diff --git a/dev/shoebox/celltypeAnnotation.bed → dev/shoebox/old/celltypeAnnotation.bed b/dev/shoebox/celltypeAnnotation.bed → dev/shoebox/old/celltypeAnnotation.bed
diff --git a/dev/shoebox/sampleInfo.txt → dev/shoebox/old/sampleInfo.txt b/dev/shoebox/sampleInfo.txt → dev/shoebox/old/sampleInfo.txt
diff --git a/dev/shoebox/session.json → dev/shoebox/old/session.json b/dev/shoebox/session.json → dev/shoebox/old/session.json
diff --git a/dev/shoebox/old/shoebox.html b/dev/shoebox/old/shoebox.html
@@ -0,0 +1,44 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>Seg Big</title>
+
+</head>
+
+<body>
+
+<h1>Shoebox</h1>
+
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js"
+
+    var options =
+        {
+            genome: "hg38"
+        }
+
+    var igvDiv = document.getElementById("igvDiv")
+
+    igv.createBrowser(igvDiv, options)
+        .then(function (browser) {
+            console.log("Created IGV browser")
+            browser.loadSession({url: "session.json"})
+        })
+
+
+</script>
+
+</body>
+
+</html>
+</title>
+</head>
+<body>
+
+</body>
+</html>
diff --git a/dev/shoebox/shoebox.html b/dev/shoebox/shoebox.html
@@ -19,15 +19,62 @@ <h1>Shoebox</h1>
 
     var options =
         {
-            genome: "hg38"
+            sampleNameViewportWidth: 6,
+            genome: "hg38",
+            locus: "chr1:1,001,575-1,002,408",
+            tracks: [
+                {
+                    "url": "https://www.dropbox.com/scl/fi/2tv6vnqqlfy6kxzahshwc/pseudobulk_14.bed?rlkey=ytrotr3v197k26pe2dettfgsr&dl=0",
+                    "name": "pseudobulk 14",
+                    "type": "shoebox",
+                    "format": "shoebox"
+                },
+                {
+                    "name": "Homo sapiens HepG2 H3K4me3 ",
+                    "url": "https://www.encodeproject.org/files/ENCFF752OCZ/@@download/ENCFF752OCZ.bigWig",
+                    "color": "rgb(0,150,0)",
+                    "metadata": {
+                        "Biosample": "Homo sapiens HepG2",
+                        "AssayType": "ChIP-seq",
+                        "Target": "H3K4me3 ",
+                        "BioRep": "1",
+                        "TechRep": "1_1",
+                        "OutputType": "signal p-value",
+                        "Format": "bigWig",
+                        "Lab": "John Stamatoyannopoulos, UW",
+                        "Accession": "ENCFF752OCZ",
+                        "Experiment": "ENCSR000DUF"
+                    },
+                    "format": "bigwig",
+                    "type": "wig"
+                },
+                {
+                    "name": "Homo sapiens HepG2 CTCF ",
+                    "url": "https://www.encodeproject.org/files/ENCFF160QOX/@@download/ENCFF160QOX.bigWig",
+                    "metadata": {
+                        "Biosample": "Homo sapiens HepG2",
+                        "AssayType": "ChIP-seq",
+                        "Target": "CTCF ",
+                        "BioRep": "1",
+                        "TechRep": "1_1",
+                        "OutputType": "fold change over control",
+                        "Format": "bigWig",
+                        "Lab": "Richard Myers, HAIB",
+                        "Accession": "ENCFF160QOX",
+                        "Experiment": "ENCSR000BIE"
+                    },
+                    "format": "bigwig",
+                    "type": "wig"
+                }
+            ]
         }
 
+
     var igvDiv = document.getElementById("igvDiv")
 
     igv.createBrowser(igvDiv, options)
         .then(function (browser) {
             console.log("Created IGV browser")
-            browser.loadSession({url: "session.json"})
         })
 
 

diff --git a/js/feature/decode/ucsc.js b/js/feature/decode/ucsc.js
@@ -538,6 +538,29 @@ function decodeSNP(tokens, header) {
 
 }
 
+function decodeShoebox(tokens, header, maxColumnCount = Number.MAX_SAFE_INTEGER) {
+
+    if (tokens.length < 4) return undefined
+
+    const chr = tokens[0]
+    const start = parseInt(tokens[1])
+    const end = tokens.length > 2 ? parseInt(tokens[2]) : start + 1
+    if (isNaN(start) || isNaN(end)) {
+        return new DecodeError(`Unparsable bed record.`)
+    }
+    const feature = new UCSCBedFeature({chr: chr, start: start, end: end, score: 1000})
+
+    const values = []
+    for(let i = 3; i< tokens.length; i++) {
+        values.push(Number.parseInt(tokens[i]))
+    }
+    feature.values = values;
+
+
+    return feature
+}
+
+
 class UCSCBedFeature {
 
     constructor(properties) {
@@ -650,6 +673,6 @@ class PSLFeature {
 
 export {
     decodeBed, decodeBedGraph, decodeGenePred, decodeGenePredExt, decodePeak, decodeReflat, decodeRepeatMasker,
-    decodeSNP, decodeWig, decodePSL, decodeBedmethyl, decodeGappedPeak, decodeNarrowPeak
+    decodeSNP, decodeWig, decodePSL, decodeBedmethyl, decodeGappedPeak, decodeNarrowPeak, decodeShoebox
 }
 
diff --git a/js/feature/featureParser.js b/js/feature/featureParser.js
@@ -36,6 +36,7 @@ import {
     decodePeak,
     decodeReflat,
     decodeRepeatMasker,
+    decodeShoebox,
     decodeSNP,
     decodeWig
 } from "./decode/ucsc.js"
@@ -319,6 +320,10 @@ class FeatureParser {
                 this.decode = decodeGcnv
                 this.delimiter = "\t"
                 break
+            case "shoebox":
+                this.decode = decodeShoebox
+                this.delimiter = "\t"
+                break
             default:
                 const customFormat = getFormat(format)
                 if (customFormat !== undefined) {