Merge pull request #1134 from dondi/maika-1068

#1068 Allow node coloring for PPI by matching the gene name (MERGE #1080 first)
dondi · Nov 4, 2024 · f978dbb · f978dbb
2 parents 9b24710 + 5f1ab4e
commit f978dbb
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Showing 3 changed files with 23 additions and 7 deletions.
diff --git a/server/dals/expression-dal.js b/server/dals/expression-dal.js
@@ -20,7 +20,7 @@ var sequelize = new Sequelize(
 const buildExpressionGenesQuery = function (geneString) {
     let genes = "";
     let geneList = geneString.split(",");
-    geneList.forEach(x => genes += ( `(gene_expression.gene.display_gene_id =\'${x}\') OR `));
+    geneList.forEach(x => genes += ( `(LOWER(gene_expression.gene.display_gene_id) = LOWER(\'${x}\')) OR `));
     return genes.substring(0, genes.length - 4);
 };
 
@@ -62,7 +62,7 @@ const buildExpressionQuery = function (query) {
 const listExpressionGeneData = function (gene, totalOutput) {
     let listOfData = [];
     totalOutput.forEach(function (x) {
-        if (x.display_gene_id === gene) {
+        if (x.display_gene_id.toLowerCase() === gene.toLowerCase()) {
             listOfData.push(Number(x.expression));
         }
     });

diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js
@@ -1,6 +1,11 @@
 import Grid from "d3-v4-grid";
 import { grnState } from "./grnstate";
-import { modifyChargeParameter, modifyLinkDistanceParameter, valueValidator } from "./update-app";
+import {
+    modifyChargeParameter,
+    modifyLinkDistanceParameter,
+    valueValidator,
+    adjustGeneNameForExpression,
+} from "./update-app";
 import {
     ENDS_IN_EXPRESSION_REGEXP,
     VIEWPORT_FIT,
@@ -1086,11 +1091,12 @@ export var drawGraph = function (workbook) {
                 .selectAll(".coloring")
                 .data(function () {
                     if (grnState.workbook.expression[dataset]) {
+                        const geneName = adjustGeneNameForExpression(p);
                         if (
-                            grnState.workbook.expression[dataset].data[p.name]
+                            grnState.workbook.expression[dataset].data[geneName]
                         ) {
                             const result = getExpressionData(
-                                p.name,
+                                geneName,
                                 dataset,
                                 average
                             );

diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js
@@ -384,6 +384,14 @@ const enableNodeColoringUI = function () {
     $(LOG_FOLD_CHANGE_MAX_VALUE_HEADER).removeClass("hidden");
 };
 
+const adjustGeneNameForExpression = function (gene) {
+    const geneName = gene.name;
+    return grnState.workbook.meta.data.workbookType === NETWORK_PPI_MODE &&
+        geneName.endsWith("p")
+        ? geneName.slice(0, -1)
+        : geneName;
+};
+
 const loadExpressionDatabase = function (isTopDataset) {
     const dataset = isTopDataset ? grnState.nodeColoring.topDataset : grnState.nodeColoring.bottomDataset;
     startLoadingIcon();
@@ -394,7 +402,9 @@ const loadExpressionDatabase = function (isTopDataset) {
         queryExpressionDatabase({
             type:"ExpressionData",
             dataset,
-            genes : grnState.workbook.genes.map(gene => {return gene.name;}).join(","),
+            genes: grnState.workbook.genes
+                    .map(adjustGeneNameForExpression)
+                    .join(","),
             timepoints: timepointsResponse[dataset]
         }).then(function (response) {
             if (isTopDataset) {
@@ -1027,4 +1037,4 @@ export const updateApp = grnState => {
 };
 
 
-export { stopLoadingIcon, startLoadingIcon};
+export { stopLoadingIcon, startLoadingIcon, adjustGeneNameForExpression};