Enable use of annotations include list

eweitz · Sep 28, 2020 · 3b561bc · 3b561bc
1 parent ebf381d
commit 3b561bc
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Showing 3 changed files with 28 additions and 4 deletions.
diff --git a/examples/vanilla/related-genes.html b/examples/vanilla/related-genes.html
@@ -217,6 +217,9 @@ <h1>Related genes | Ideogram</h1>
       showTools: true
     }
 
+    // annotsInList = ['CDK9', 'CDK19', 'CDK1'];
+    // let ideogram = Ideogram.initRelatedGenes(config, annotsInList)
+
     let ideogram = Ideogram.initRelatedGenes(config)
   </script>
 </body>

diff --git a/src/js/ideogram.js b/src/js/ideogram.js
@@ -293,7 +293,7 @@ export default class Ideogram {
    *
    * @param {Object} config Ideogram configuration object
    */
-  static initRelatedGenes(config) {
-    return _initRelatedGenes(config);
+  static initRelatedGenes(config, annotsInList='all') {
+    return _initRelatedGenes(config, annotsInList);
   }
 }
diff --git a/src/js/kit/related-genes.js b/src/js/kit/related-genes.js
@@ -272,6 +272,20 @@ function parseAnnotFromMgiGene(gene, ideo, color='red') {
   return annot;
 }
 
+/** Filter annotations to only include those in configured list */
+function applyAnnotsIncludeList(annots, ideo) {
+
+  if (ideo.config.annotsInList === 'all') return annots;
+
+  const includedAnnots = [];
+  annots.forEach(annot => {
+    if (ideo.config.annotsInList.includes(annot.name.toLowerCase())) {
+      includedAnnots.push(annot);
+    }
+  });
+  return includedAnnots;
+}
+
 /**
  * For given gene, finds and draws interacting genes and paralogs
  *
@@ -345,13 +359,15 @@ async function plotRelatedGenes(geneSymbol) {
     width: 140px;`;
 
   // Draw interacting genes immediately
+  annots = applyAnnotsIncludeList(annots, ideo);
   annots.sort((a, b) => {return b.name.length - a.name.length;});
   ideo.drawAnnots(annots);
   document.querySelector('#_ideogramLegend').style = legendStyle;
 
   await fetchParalogPositions(annot, annots, ideo);
 
   // Add paralogs to related genes, and draw all related genes
+  annots = applyAnnotsIncludeList(annots, ideo);
   annots.sort((a, b) => {return b.name.length - a.name.length;});
   ideo.drawAnnots(annots);
   document.querySelector('#_ideogramLegend').style = legendStyle;
@@ -410,13 +426,18 @@ const legend = [{
  *
  * @param {Object} config Ideogram configuration object
  */
-function _initRelatedGenes(config) {
+function _initRelatedGenes(config, annotsInList) {
+
+  if (annotsInList !== 'all') {
+    annotsInList = annotsInList.map(name => name.toLowerCase());
+  }
 
   Object.assign(config, {
     showFullyBanded: false,
     rotatable: false,
     legend: legend,
-    onWillShowAnnotTooltip: decorateGene
+    onWillShowAnnotTooltip: decorateGene,
+    annotsInList: annotsInList
   });
 
   const ideogram = new Ideogram(config);