cnvpytor bug fix -- undefined bin_size and genome_size

igvteam · Aug 30, 2023 · 234e575 · 234e575
1 parent 78722b8
commit 234e575
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Showing 5 changed files with 145 additions and 6 deletions.
diff --git a/dev/cnvpytor/cnvpytorTrackVCF.html b/dev/cnvpytor/cnvpytorTrackVCF.html
@@ -0,0 +1,41 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <link href=https://igv.org/web/img/favicon.ico rel="shortcut icon">
+    <title>igv</title>
+
+</head>
+
+<body>
+
+<h2>CNVpytor Track</h2>
+
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../dist/igv.esm.js"
+    const options =
+        {
+            genome: "hg19",
+            locus: "chr16",
+            tracks: [
+                {
+                    type: "cnvpytor",
+                    name: "HepG2 VCF",
+                    url: "https://www.dropbox.com/scl/fi/gbnfsvkf44oe6ibod87t2/HepG2.sample.vcf.gz?rlkey=bu787lu1aq0j4fvryal213e69&dl=0",
+                    indexed: false
+
+                }
+            ]
+        }
+
+    igv.createBrowser(document.getElementById('igvDiv'), options)
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/dev/cnvpytor/cnvpytorTrackVCF_large.html b/dev/cnvpytor/cnvpytorTrackVCF_large.html
@@ -0,0 +1,56 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <link href=https://igv.org/web/img/favicon.ico rel="shortcut icon">
+    <title>igv</title>
+
+</head>
+
+<body>
+
+<h2>CNVpytor Track</h2>
+
+<button id="log-state">Log Session Json</button>
+<button id="pytor">Change to Pytor</button>
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js"
+
+    const options =
+        {
+            genome: "hg19",
+            locus: "chr16",
+            tracks: [
+                // {
+                //     type: "cnvpytor",
+                //     name: "HepG2 VCF",
+                //     url: "https://igv-genepattern-org.s3.amazonaws.com/test/pytor/HepG2.sample.vcf.gz"
+                //
+                // },
+                {
+                    type: "variant",
+                    name: "HepG2 VCF",
+                    //url: "https://storage.googleapis.com/cnvpytor_data/HepG2.vcf.gz",
+                    url: "https://igv-genepattern-org.s3.amazonaws.com/test/pytor/HepG2.sample.vcf.gz"
+                }
+            ]
+        }
+
+    igv.createBrowser(document.getElementById('igvDiv'), options)
+        .then(browser => {
+            const track = browser.findTracks("type", "variant")[0];
+            document.getElementById("log-state").addEventListener("click", () => console.log(browser.toJSON()))
+            document.getElementById("pytor").addEventListener("click", () => {
+               track.convertToPytor()
+            })
+        })
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/examples/cnvpytor/cnvpytorTrackVCF_small.html b/examples/cnvpytor/cnvpytorTrackVCF_small.html
@@ -0,0 +1,40 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <link href=https://igv.org/web/img/favicon.ico rel="shortcut icon">
+    <title>igv</title>
+
+</head>
+
+<body>
+
+<h2>CNVpytor Track</h2>
+
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../dist/igv.esm.js"
+    const options =
+        {
+            genome: "hg19",
+            locus: "chr16",
+            tracks: [
+                {
+                    type: "cnvpytor",
+                    name: "HepG2 VCF",
+                    url: "https://storage.googleapis.com/cnvpytor_data/HepG2.vcf.gz",
+
+                }
+            ]
+        }
+
+    igv.createBrowser(document.getElementById('igvDiv'), options)
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/js/cnvpytor/MeanShiftUtil.js b/js/cnvpytor/MeanShiftUtil.js
@@ -2,6 +2,8 @@
 import g_utils from './GeneralUtil.js'
 import t_dist from './t_dist.js'
 
+// TODO -- remove this hardcoded value
+const genome_size = 2871000000;
 
 function erf(x) {
     var m = 1.0, s = 1.0, sum = x * 1.0;
@@ -122,7 +124,8 @@ export class Partition {
         return new_array
     }
 
-    meanShiftCaller(repeats = 3) {
+    meanShiftCaller(bins_size, repeats = 3) {
+
         var ChrLevels = {}
 
         Object.entries(this.rd).forEach(([chr, chr_rd]) => {
@@ -274,7 +277,6 @@ export class Partition {
     call_mean_shift(repeats = 3) {
         const bin_size = 1000;
         // const genome_size = bin_size * this.rd.length;
-        const genome_size = 2871000000;
         var masked = new Array(this.rd.length).fill(false);
 
         // set the level
@@ -468,16 +470,16 @@ export class Partition {
     }
 
     cnv_calling(bin_size = 100000) {
-        var delta = 0.25
-        var delta = delta * this.mean
+
+        var delta = 0.25 * this.mean
 
         var min = this.mean - delta, max = this.mean + delta;
         // console.log('min: ', min, ', Max: ', max)
 
         // console.log('delta', delta)
         var normal_genome_size = 2971000000
 
-        var levels = this.meanShiftCaller()
+        var levels = this.meanShiftCaller(bin_size)
 
 
         var merged_level = {}

diff --git a/js/cnvpytor/cnvpytorVCF.js b/js/cnvpytor/cnvpytorVCF.js
@@ -139,7 +139,7 @@ class CNVpytorVCF {
 
         // Apply partition method
         var partition = new read_depth_caller.Partition(wigFeatures, globamMean, globalStd);
-        var partition_array = partition.meanShiftCaller()
+        var partition_array = partition.meanShiftCaller(this.binSize)
         var caller_array = partition.cnv_calling()
 
         // Assign the partition values to each bin