Merge pull request #1459 from adamabeshouse/profiled-in

fix bug where profiled in tracks were appearing when they shouldnt
cBioPortal · Sep 18, 2018 · a5bf7b1 · a5bf7b1
2 parents 78126de + 4c731d1
commit a5bf7b1
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Showing 3 changed files with 44 additions and 4 deletions.
diff --git a/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/src/shared/components/oncoprint/ResultsViewOncoprintUtils.spec.ts b/src/shared/components/oncoprint/ResultsViewOncoprintUtils.spec.ts
@@ -34,6 +34,27 @@ describe("ResultsViewOncoprintUtils",()=>{
                 "multiple study"
             );
         });
+        it("does not create any if all samples profiled in every selected alteration type, special case sample is not profiled for one gene but profiled for another", ()=>{
+            const coverageInformation = {
+                "sample1":{
+                    byGene:{"BRCA1":[{ molecularProfileId: "mutations" } as GenePanelData]},
+                    allGenes: [],
+                    notProfiledByGene: {"KRAS":[{ molecularProfileId: "mutations" } as GenePanelData]},
+                    notProfiledAllGenes:[]
+                }
+            };
+            const selectedMolecularProfiles = [molecularProfileIdToMolecularProfile.mutations];
+            assert.deepEqual(
+                makeProfiledInClinicalAttributes(coverageInformation, molecularProfileIdToMolecularProfile, selectedMolecularProfiles, 1, true),
+                [],
+                "single study"
+            );
+            assert.deepEqual(
+                makeProfiledInClinicalAttributes(coverageInformation, molecularProfileIdToMolecularProfile, selectedMolecularProfiles, 1, false),
+                [],
+                "multiple study"
+            );
+        });
         it("creates an attribute for one selected alteration type in which not all samples profiled", ()=>{
             const coverageInformation = {
                 "sample1":{

diff --git a/src/shared/components/oncoprint/ResultsViewOncoprintUtils.ts b/src/shared/components/oncoprint/ResultsViewOncoprintUtils.ts
@@ -34,6 +34,8 @@ export function makeProfiledInClinicalAttributes(
 
     const existsUnprofiledCount:{[alterationType:string]:number} = _.reduce(coverageInformation, (map, sampleCoverage)=>{
         const isUnprofiled:{[alterationType:string]:boolean} = {};
+
+        // if a sample is not profiled in all genes, its certainly unprofiled for this profile
         for (const gpData of sampleCoverage.notProfiledAllGenes) {
             if (gpData.molecularProfileId in selectedMolecularProfilesMap) {
                 // mark isUnprofiled for this type because this is a selected profile
@@ -42,6 +44,8 @@ export function makeProfiledInClinicalAttributes(
                 ] = true;
             }
         }
+
+        // if a sample is not profiled in some gene, then it is maybe unprofiled
         _.forEach(sampleCoverage.notProfiledByGene, (geneInfo)=>{
             for (const gpData of geneInfo) {
                 if (gpData.molecularProfileId in selectedMolecularProfilesMap) {
@@ -52,11 +56,26 @@ export function makeProfiledInClinicalAttributes(
                 }
             }
         });
+
+        // if a sample is profiled in some gene, then it is not unprofiled
+        _.forEach(sampleCoverage.byGene, geneInfo=>{
+            for (const gpData of geneInfo) {
+                if (gpData.molecularProfileId in selectedMolecularProfilesMap) {
+                    // unmark isUnprofiled
+                    isUnprofiled[
+                        molecularProfileIdToMolecularProfile[gpData.molecularProfileId].molecularAlterationType
+                    ] = false;
+                }
+            }
+        });
+
         // increment counts
-        for (const alterationType of Object.keys(isUnprofiled)) {
-            map[alterationType] = map[alterationType] || 0;
-            map[alterationType] += 1;
-        }
+        _.forEach(isUnprofiled, (_isUnprofiled, alterationType)=>{
+            if (_isUnprofiled) {
+                map[alterationType] = map[alterationType] || 0;
+                map[alterationType] += 1;
+            }
+        });
         return map;
     }, {} as {[alterationType:string]:number});