igv example uses positions instead of gene names

anders-biostat · Aug 7, 2023 · f6187a6 · f6187a6
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diff --git a/docs/rlc/tutorials/igv/localBam.html b/docs/rlc/tutorials/igv/localBam.html
@@ -0,0 +1,101 @@
+<!--Based on the example from https://igv.org/web/release/2.2.2/examples/localBam.html -->
+<head>
+    <title>IGV - Local Bam</title>
+    <script src="https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/igv.min.js"></script>
+</head>
+
+<body>
+<div id="linked-charts">
+    <table><tr>
+        <td id="A1"></td>
+        <td id="A2"></td>
+    </tr></table>
+</div>
+<div>
+    <p>
+        <label>BAM file and index
+            <input id="fileWidget" type="file" multiple="true" accept=".bam,.bai" onchange="load()"/>
+        </label>
+    </p>
+</div>
+
+<script type="text/javascript">
+
+    var igvBrowser;
+
+    document.addEventListener("DOMContentLoaded", function () {
+
+        var div = document.getElementById("A2");
+        var options = {
+            locus: "TSPAN6",       // OPTIONAL, open at a specific location
+            genome: "hg38"
+        };
+        igv.createBrowser(div, options)
+            .then(function (b) {
+                igvBrowser = b;
+            })
+    })
+
+    function load() {
+
+        var fileWidget = document.getElementById("fileWidget");
+        var files = fileWidget.files;
+
+        // Find BAM files and cache index files.  Note there are 2 index naming conventions, .bam.bai and .bai
+        // This scheme catches both.
+        var bamFiles = [];
+        var indexFiles = {};
+
+        for (let file of files) {
+            if (file.name.endsWith(".bam")) {
+                bamFiles.push(file);
+            }
+            else if (file.name.endsWith(".bai")) {
+                var key = getKey(file.name);
+                indexFiles[key] = file;
+            }
+            else {
+                alert("Unsupported file type: " + file.name);
+            }
+        }
+
+        // Create track objects
+        var trackConfigs = [];
+
+        for (let file of bamFiles) {
+
+            var key = getKey(file.name);
+            var indexFile = indexFiles[key];
+            if (indexFile) {
+                trackConfigs.push({
+                    name: file.name,
+                    type: "alignment",
+                    format: "bam",
+                    height: 150,
+                    url: file,
+                    indexURL: indexFile
+                })
+            }
+            else {
+                alert("No index file for: " + file.name);
+            }
+        }
+
+        if (trackConfigs.length > 0) {
+            igvBrowser.loadTrackList(trackConfigs);
+        }
+
+
+        function getKey(filename) {
+            var idx = filename.indexOf(".");
+            if (idx < 0) {
+                console.error("File with no extension: " + filename);
+            }
+            else {
+                return filename.substring(0, idx);
+            }
+
+        }
+    }
+</script>
+</body>
diff --git a/example/igv_browser/localBam.html b/example/igv_browser/localBam.html
@@ -19,17 +19,13 @@
     </p>
 </div>
 
-<div id="myDiv" style="padding-top: 50px;padding-bottom: 20px; border-style: inset; height: auto">
-</div>
-
-
 <script type="text/javascript">
 
     var igvBrowser;
 
     document.addEventListener("DOMContentLoaded", function () {
 
-        var div = document.getElementById("myDiv");
+        var div = document.getElementById("A2");
         var options = {
             locus: "TSPAN6",       // OPTIONAL, open at a specific location
             genome: "hg38"

diff --git a/example/igv_browser/run_browser.R b/example/igv_browser/run_browser.R
@@ -4,7 +4,7 @@ load("src/oscc.rda")
 
 app <- openPage(useViewer = FALSE, startPage = "localBam.html")
 
-gene <- 1
+gene <- "TSPAN6"
 
 lc_scatter(dat(
   x = voomResult$AveExpr,
@@ -14,20 +14,10 @@ lc_scatter(dat(
   size = 1.3,
   on_click = function(k) {
     geneName <- rownames(voomResult)[k]
+    position <- paste0("chr", gene_positions[geneName, "chr"], ":", 
+                       gene_positions[geneName, "start"], "-", 
+                       gene_positions[geneName, "end"])
     com <- paste0("igvBrowser.search('", geneName, "')")
     app$getSession(.id)$sendCommand(com)
-    gene <<- k; updateCharts("A2")
     } ),
-  "A1")
-
-countsums <- colSums(countMatrix)
-
-lc_scatter(dat(
-  x = sampleTable$patient,
-  y = countMatrix[gene,] / countsums * 1e6 + .1,
-  logScaleY = 10,
-  colorValue = sampleTable$tissue,
-  title = rownames(countMatrix)[gene],
-  axisTitleY = "counts per million (CPM)",
-  ticksRotateX = 45),
-  "A2")
+  "A1")