Undefined percentage iVis-at-Bilkent#288

gorkemsolun · Aug 25, 2023 · 6043de9 · 6043de9
1 parent add9492
commit 6043de9
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Showing 6 changed files with 24 additions and 44 deletions.
diff --git a/packages/pathway-mapper/dist/index.es5.js b/packages/pathway-mapper/dist/index.es5.js
diff --git a/packages/pathway-mapper/dist/index.es5.js.map b/packages/pathway-mapper/dist/index.es5.js.map
diff --git a/packages/pathway-mapper/dist/managers/GenomicDataOverlayManager.d.ts b/packages/pathway-mapper/dist/managers/GenomicDataOverlayManager.d.ts
@@ -33,7 +33,7 @@ export default class GenomicDataOverlayManager {
     showGenomicData(resizeNodeCallback?: (node: any) => void): void;
     generateHTMLContentForComparisonNodeTooltip(ele: any, groupsToBeRendered: any): JQuery<HTMLElement>;
     showGroupComparisonData(groupsToBeRendered: any[], resizeNodeCallback?: (node: any) => void): void;
-    parseGenomicData: (genomicData: any, groupID: any, isCollaborative: boolean, isFromPortal: boolean) => {
+    prepareGenomicData: (genomicData: any, groupID: any, isCollaborative: boolean, isFromPortal: boolean) => {
         genomicDataMap: any;
         visibilityMap: any;
     };

diff --git a/packages/pathway-mapper/package.json b/packages/pathway-mapper/package.json
@@ -42,7 +42,7 @@
     "cytoscape-layout-utilities": "github:iVis-at-Bilkent/cytoscape.js-layout-utilities#unstable",
     "cytoscape-navigator": "^1.3.3",
     "cytoscape-node-editing": "github:iVis-at-Bilkent/cytoscape.js-node-editing#unstable",
-    "cytoscape-panzoom": "~2.5.3",
+    "cytoscape-panzoom": "~2.5.2",
     "cytoscape-popper": "^2.0.0",
     "cytoscape-undo-redo": "github:iVis-at-Bilkent/cytoscape.js-undo-redo#unstable",
     "cytoscape-view-utilities": "github:iVis-at-Bilkent/cytoscape.js-view-utilities#unstable",

diff --git a/packages/pathway-mapper/src/managers/GenomicDataOverlayManager.ts b/packages/pathway-mapper/src/managers/GenomicDataOverlayManager.ts
@@ -366,37 +366,34 @@ export default class GenomicDataOverlayManager {
       y: eleBBox.h / 2 + overlayRecBoxH / 2 - 18,
     };
 
-    const genomicFrequencyData = this.genomicDataMap[nodeLabel];
-
     let maxGenomicDataBoxCount = /*(genomicDataBoxCount > 3) ? 3:*/ genomicDataBoxCount;
     let genomicBoxCounter = 0;
 
     for (let i in this.groupedGenomicDataMap) {
       for (let j in this.groupedGenomicDataMap[i]) {
-        const cancerType = this.groupedGenomicDataMap[i][j];
-        if (!this.visibleGenomicDataMapByType[cancerType]) {
+        if (!this.visibleGenomicDataMapByType[this.groupedGenomicDataMap[i][j]]) {
           continue;
         }
-
-          genomicDataRectangleGenerator(
-            overLayRectBBox.x +
-              (genomicBoxCounter * overLayRectBBox.w) / maxGenomicDataBoxCount,
-            overLayRectBBox.y,
-            overLayRectBBox.w / maxGenomicDataBoxCount,
-            overLayRectBBox.h,
-            genomicFrequencyData[cancerType] !== undefined ? genomicFrequencyData[cancerType] : null,
-            svg,
-            this.colorScheme
-          );
+        if (!this.genomicDataMap[nodeLabel][this.groupedGenomicDataMap[i][j]]) {
+          this.genomicDataMap[nodeLabel][this.groupedGenomicDataMap[i][j]] = "0.00";
+        }
+        genomicDataRectangleGenerator(
+          overLayRectBBox.x +
+            (genomicBoxCounter * overLayRectBBox.w) / maxGenomicDataBoxCount,
+          overLayRectBBox.y,
+          overLayRectBBox.w / maxGenomicDataBoxCount,
+          overLayRectBBox.h,
+          this.genomicDataMap[nodeLabel][this.groupedGenomicDataMap[i][j]],
+          svg,
+          this.colorScheme
+        );
 
         genomicBoxCounter++;
       }
     }    
     return svg;
   }
   generateSVGForGroupComparisonNode(ele, groupsToBeRendered? ) {
-    const genomicDataBoxCount = 0;
-
     // Experimental data overlay part !
     const dataURI = "data:image/svg+xml;utf8,";
     const svgNameSpace = "http://www.w3.org/2000/svg";
@@ -431,42 +428,25 @@ export default class GenomicDataOverlayManager {
     let maxGenomicDataBoxCount = groupsToBeRendered.length;
     let genomicBoxCounter = 0;
 
-  /*  for (let i in this.groupComparisonData) {
-         if( i !== nodeLabel)
-             continue;*/
       let i = nodeLabel;
       for (let j in this.groupComparisonData[i]) {
-        const percentageInGroup = this.groupComparisonData[i][j];
-        if (percentageInGroup !== undefined && i === nodeLabel) {
+        if (!this.groupComparisonData[i][j]) {
+          this.groupComparisonData[i][j] = 0;
+        }
+        if (i === nodeLabel) {
           genomicDataRectangleGenerator(
             overLayRectBBox.x +
               (genomicBoxCounter * overLayRectBBox.w) / maxGenomicDataBoxCount,
             overLayRectBBox.y,
             (overLayRectBBox.w  ) / maxGenomicDataBoxCount - 2,
             overLayRectBBox.h,
-            percentageInGroup,
+            this.groupComparisonData[i][j],
             svg,
             this.colorScheme,
             groupsToBeRendered[genomicBoxCounter].color
           );
           genomicBoxCounter++;
-        } else if( i === nodeLabel ){
-          genomicDataRectangleGenerator(
-            overLayRectBBox.x +
-            (genomicBoxCounter * overLayRectBBox.w) / maxGenomicDataBoxCount,
-          overLayRectBBox.y,
-          (overLayRectBBox.w  ) / maxGenomicDataBoxCount - 4,
-          overLayRectBBox.h,
-          0,
-          svg,
-          this.colorScheme,
-          groupsToBeRendered[genomicBoxCounter].color
-          );
-          genomicBoxCounter++;
         }
-
-
-
       }
     return svg;
   }

diff --git a/yarn.lock b/yarn.lock
@@ -5447,7 +5447,7 @@ cytoscape-navigator@^1.3.3:
   version "3.2.1"
   resolved "https://codeload.github.com/iVis-at-Bilkent/cytoscape.js-node-editing/tar.gz/2ea4f63a0da8f13b5e7462d2380e48964d9c042f"
 
-cytoscape-panzoom@~2.5.3:
+cytoscape-panzoom@~2.5.2:
   version "2.5.3"
   resolved "https://registry.yarnpkg.com/cytoscape-panzoom/-/cytoscape-panzoom-2.5.3.tgz#edf041b5aa8be1cbe3c001f16a8b2193b46127a7"
   integrity sha512-//qLOqbbFUCGddarNKHDZArItOJHgnkQ1TvxI9nV2/8aOOl/5wuEOHmra3fL/aWSjB4AYpYTG4LX7w96uWfRTQ==