Merge from upstream

eweitz · Dec 7, 2024 · 77247f0 · 77247f0
2 parents 669eda2 + 36ca987
commit 77247f0
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Showing 18 changed files with 1,920 additions and 44 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,7 +3,7 @@ name: CI
 on:
   push:
     branches:
-      - github-actions
+      - '*'
   pull_request:
     branches:
       - main

diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ A [broader overview](https://speakerdeck.com/eweitz/ideogramjs-chromosome-visual
 
 To link directly to the latest release, copy this snippet:
 ```
-<script src="https://cdn.jsdelivr.net/npm/ideogram@1.48.0/dist/js/ideogram.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/ideogram@1.49.0/dist/js/ideogram.min.js"></script>
 ```
 
 You can also easily use the library locally:
@@ -43,7 +43,7 @@ import Ideogram from 'ideogram';
 # Usage
 ```html
 <head>
-  <script src="https://cdn.jsdelivr.net/npm/ideogram@1.48.0/dist/js/ideogram.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/ideogram@1.49.0/dist/js/ideogram.min.js"></script>
 </head>
 <body>
 <script>

diff --git a/dist/js/ideogram.min.js b/dist/js/ideogram.min.js
diff --git a/dist/js/ideogram.min.js.LICENSE.txt b/dist/js/ideogram.min.js.LICENSE.txt
@@ -1 +1 @@
-/*! Ideogram.js, version 1.48.0.  Developed by Eric Weitz.  https://github.com/eweitz/ideogram.  Public domain (CC0 1.0). */
+/*! Ideogram.js, version 1.49.0.  Developed by Eric Weitz.  https://github.com/eweitz/ideogram.  Public domain (CC0 1.0). */
diff --git a/dist/js/ideogram.min.js.map b/dist/js/ideogram.min.js.map
diff --git a/examples/vanilla/img/gene_leads_ideogram.png b/examples/vanilla/img/gene_leads_ideogram.png
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "ideogram",
-  "version": "1.48.0",
+  "version": "1.49.0",
   "description": "Chromosome visualization for the web",
   "main": "src/js/index.js",
   "preferGlobal": true,

diff --git a/src/js/annotations/events.js b/src/js/annotations/events.js
@@ -105,8 +105,8 @@ function getContentAndYOffset(annot, includeLength=false) {
 /**
  * Optional callback, invoked before showing annotation tooltip
  */
-function onWillShowAnnotTooltip(annot) {
-  call(this.onWillShowAnnotTooltipCallback, annot);
+function onWillShowAnnotTooltip(event, context) {
+  call(this.onWillShowAnnotTooltipCallback, event, context);
 }
 
 function onDidShowAnnotTooltip() {
@@ -118,6 +118,7 @@ function onDidShowAnnotTooltip() {
  */
 function onClickAnnot(annot) {
   this.prevClickedAnnot = annot;
+  this.hasShownAnnotSinceClick = false;
   this.onClickAnnotCallback(annot);
 }
 
@@ -145,7 +146,7 @@ function showAnnotTooltip(annot, context) {
   clearTimeout(ideo.hideAnnotTooltipTimeout);
 
   if (ideo.onWillShowAnnotTooltipCallback) {
-    annot = ideo.onWillShowAnnotTooltipCallback(annot);
+    annot = ideo.onWillShowAnnotTooltipCallback(annot, context);
   }
 
   // Enable onWillShowAnnotTooltipCallback to cancel showing tooltip

diff --git a/src/js/annotations/labels.js b/src/js/annotations/labels.js
@@ -14,17 +14,17 @@ const allLabelStyle = `
       stroke-linejoin: bevel;
     }
 
-    #_ideogram ._ideogramLabel._ideoActive {
+    #_ideogram .annot ._ideogramLabel._ideoActive {
       fill: #77F !important;
       stroke: #F0F0FF !important;
     }
 
-    #_ideogram .annot > ._ideoActive {
+    #_ideogram .annot > path._ideoActive {
       stroke: #D0D0DD !important;
       stroke-width: 1.5px;
     }
 
-    #_ideogram ._ideogramLabel {
+    #_ideogram .annot ._ideogramLabel {
       stroke: white;
       stroke-width: 5px;
       stroke-linejoin: round;
@@ -59,6 +59,10 @@ function triggerAnnotEvent(event, ideo) {
     const annotElement = target.parentElement;
     labelId = 'ideogramLabel_' + annotElement.id;
     annotId = annotElement.id;
+
+    if (targetClasses.includes('_ideogramLabelRect')) {
+      d3.select('#' + annotId + ' path').dispatch(type);
+    }
   }
 
   if (type === 'mouseout') {
@@ -96,15 +100,26 @@ function renderLabel(annot, style, ideo) {
 
   fill = ensureContrast(fill);
 
-  d3.select('#_ideogram').append('text')
+  const translate = `translate(-${style.width + 9},${style.height/2 - 1.5})`;
+  d3.select('#' + annot.domId).append('text')
     .attr('id', id)
     .attr('class', '_ideogramLabel')
-    .attr('x', style.left)
-    .attr('y', style.top)
+    .attr('transform', `rotate(-90) ${translate}`)
     .style('font', font)
     .style('fill', fill)
     .style('pointer-events', null) // Prevent bug in clicking chromosome
     .html(annot.name);
+
+  const paralogNeighborhoodMargin = 10;
+  const rectWidth = style.width + paralogNeighborhoodMargin;
+  const rectTranslate = `translate(-${rectWidth}, -${style.height/2})`;
+
+  d3.select('#' + annot.domId).append('rect')
+    .attr('class', '_ideogramLabelRect')
+    .attr('transform', `rotate(-90) ${rectTranslate}`)
+    .attr('width', style.width + 10)
+    .attr('height', style.height)
+    .attr('style', 'opacity: 0');
 }
 
 /** Get annotation object by name, e.g. "BRCA1" */
@@ -445,7 +460,7 @@ function fillAnnotLabels(sortedAnnots=[], numLabels=10) {
     ideo.addAnnotLabel(annot.name);
   });
 
-  d3.selectAll('._ideogramLabel, .annot')
+  d3.selectAll('.annot')
     .on('mouseover', (event) => triggerAnnotEvent(event))
     .on('mouseout', (event) => triggerAnnotEvent(event, ideo))
     .on('click', (event) => triggerAnnotEvent(event));

diff --git a/src/js/kit/related-genes.js b/src/js/kit/related-genes.js
@@ -473,36 +473,48 @@ function fetchGenesFromCache(names, type, ideo) {
   const locusMap = isSymbol ? cache.lociByName : cache.lociById;
   const nameMap = isSymbol ? cache.idsByName : cache.namesById;
 
+  const ensemblGeneIdRegex = /ENS[A-Z]{0,3}G\d{11}/;
+
   const hits = names.map(name => {
 
-    const nameLc = name.toLowerCase();
+    let isSynonym = false;
+    let synonym = null;
 
-    if (
-      !locusMap[name] &&
-      !cache.nameCaseMap[nameLc] &&
-      !getGeneBySynonym(name, ideo)
-    ) {
-      if (isSymbol) {
-        throwGeneNotFound(name, ideo);
-      } else {
-        return;
-      }
+    if (ensemblGeneIdRegex.test(name)) {
+      // Omit version if given Ensembl gene ID + version, e.g.
+      // ENSG00000010404.11 -> ENSG00000010404
+      name = name.split('.')[0];
     }
+    const isIdentifier = name in cache.namesById;
+    if (isIdentifier && isSymbol) {
+      name = cache.namesById[name];
+    } else {
+      const nameLc = name.toLowerCase();
 
-    let isSynonym = false;
-    let synonym = null;
+      if (
+        !locusMap[name] &&
+        !cache.nameCaseMap[nameLc] &&
+        !getGeneBySynonym(name, ideo)
+      ) {
+        if (isSymbol) {
+          throwGeneNotFound(name, ideo);
+        } else {
+          return;
+        }
+      }
 
-    // Canonicalize name if it is mistaken in upstream data source.
-    // This can sometimes happen in WikiPathways, e.g. when searching
-    // interactions for rat Pten, it includes a result for "PIK3CA".
-    // In that case, this would correct PIK3CA to be Pik3ca.
-    if (isSymbol && !locusMap[name]) {
-      if (cache.nameCaseMap[nameLc]) {
-        name = cache.nameCaseMap[nameLc];
-      } else {
-        synonym = name;
-        name = getGeneBySynonym(synonym, ideo);
-        isSynonym = true;
+      // Canonicalize name if it is mistaken in upstream data source.
+      // This can sometimes happen in WikiPathways, e.g. when searching
+      // interactions for rat Pten, it includes a result for "PIK3CA".
+      // In that case, this would correct PIK3CA to be Pik3ca.
+      if (isSymbol && !locusMap[name]) {
+        if (cache.nameCaseMap[nameLc]) {
+          name = cache.nameCaseMap[nameLc];
+        } else {
+          synonym = name;
+          name = getGeneBySynonym(synonym, ideo);
+          isSynonym = true;
+        }
       }
     }
 
@@ -522,6 +534,7 @@ function fetchGenesFromCache(names, type, ideo) {
         ensemblgene: ensemblId
       },
       isSynonym,
+      isIdentifier,
       synonym
     };
 
@@ -1792,12 +1805,18 @@ function decorateAnnot(annot) {
   const ideo = this;
   if (
     annot.name === ideo.prevClickedAnnot?.name &&
+    annot.name === ideo.prevShownAnnot?.name &&
+    !ideo.hasShownAnnotSinceClick &&
     ideo.isTooltipCooling
   ) {
+    ideo.prevShownAnnot = annot;
     // Cancels showing tooltip immediately after clicking gene
     return null;
   }
 
+  ideo.prevShownAnnot = annot;
+  ideo.hasShownAnnotSinceClick = true;
+
   let descObj = ideo.annotDescriptions.annots[annot.name];
 
   if (ideo.config.relatedGenesMode === 'related') {

diff --git a/src/js/version.js b/src/js/version.js
@@ -1,2 +1,2 @@
-var version = '1.48.0';
+var version = '1.49.0';
 export default version;
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		/! Ideogram.js, version 1.48.0. Developed by Eric Weitz. https://github.com/eweitz/ideogram. Public domain (CC0 1.0). /
		/! Ideogram.js, version 1.49.0. Developed by Eric Weitz. https://github.com/eweitz/ideogram. Public domain (CC0 1.0). /