Merge pull request #1377 from adamabeshouse/expr-cna

Cna and putative driver coloring in expression tab

Former-commit-id: 40d1713

src/pages/resultsView/ResultsViewPage.tsx

@@ -260,13 +260,14 @@ export default class ResultsViewPage extends React.Component<IResultsViewPagePro
 
                             const store = this.resultsViewPageStore;
 
-                            if (store.rnaSeqMolecularData.isComplete && store.studyIdToStudy.isComplete
-                                && store.mutations.isComplete && store.genes.isComplete && store.coverageInformation.isComplete) {
+                            if (store.studyIdToStudy.isComplete
+                                && store.putativeDriverAnnotatedMutations.isComplete && store.genes.isComplete && store.coverageInformation.isComplete) {
                                 return <ExpressionWrapper store={store}
                                                         studyMap={store.studyIdToStudy.result}
                                                           genes={store.genes.result}
-                                                          data={store.rnaSeqMolecularData.result}
-                                                          mutations={store.mutations.result}
+                                                          expressionProfiles={store.expressionProfiles}
+                                                          numericGeneMolecularDataCache={store.numericGeneMolecularDataCache}
+                                                          mutations={store.putativeDriverAnnotatedMutations.result}
                                                           RNASeqVersion={store.expressionTabSeqVersion}
                                                           coverageInformation={store.coverageInformation.result}
                                                           onRNASeqVersionChange={(version:number)=>store.expressionTabSeqVersion=version}

src/pages/resultsView/ResultsViewPageStore.ts

@@ -1768,6 +1768,39 @@ export class ResultsViewPageStore {
         }
     });
 
+    public annotatedCnaCache =
+        new MobxPromiseCache<{entrezGeneId:number}, AnnotatedNumericGeneMolecularData[]>(
+            q=>({
+                await: ()=>this.numericGeneMolecularDataCache.await(
+                    [this.studyToMolecularProfileDiscrete, this.entrezGeneIdToGene, this.getOncoKbCnaAnnotationForOncoprint, this.molecularProfileIdToMolecularProfile],
+                    (studyToMolecularProfileDiscrete)=>{
+                        return _.values(studyToMolecularProfileDiscrete).map(p=>({entrezGeneId: q.entrezGeneId, molecularProfileId: p.molecularProfileId}));
+                    }),
+                invoke:()=>{
+                    const results = _.flatten(this.numericGeneMolecularDataCache.getAll(
+                        _.values(this.studyToMolecularProfileDiscrete.result!).map(p=>({entrezGeneId: q.entrezGeneId, molecularProfileId: p.molecularProfileId}))
+                    ).map(p=>p.result!));
+                    const entrezGeneIdToGene = this.entrezGeneIdToGene.result!;
+                    let getOncoKbAnnotation:(datum:NumericGeneMolecularData)=>IndicatorQueryResp|undefined;
+                    if (this.getOncoKbCnaAnnotationForOncoprint.result! instanceof Error) {
+                        getOncoKbAnnotation = ()=>undefined;
+                    } else {
+                        getOncoKbAnnotation = this.getOncoKbCnaAnnotationForOncoprint.result! as typeof getOncoKbAnnotation;
+                    }
+                    const profileIdToProfile = this.molecularProfileIdToMolecularProfile.result!;
+                    return Promise.resolve(results.map(d=>{
+                            return annotateMolecularDatum(
+                                d,
+                                getOncoKbAnnotation,
+                                profileIdToProfile,
+                                entrezGeneIdToGene
+                            );
+                        })
+                    );
+                }
+            })
+        );
+
     readonly getPutativeDriverInfo = remoteData({
         await:()=>{
             const toAwait = [];

src/pages/resultsView/expression/ExpressionWrapper.spec.tsx

@@ -18,37 +18,15 @@ describe('Expression Wrapper',()=>{
         instance = wrapper.instance() as ExpressionWrapper;
     });
 
-
-   it('data transformer returns correct value based on logScale state',()=>{
-
-       instance.logScale = true;
-       assert.equal(instance.dataTransformer({value: 100} as NumericGeneMolecularData), 6.643856189774724);
-
-       instance.logScale = false;
-       assert.equal(instance.dataTransformer({value: 100} as NumericGeneMolecularData), 100);
-
-   });
-
-    it('data transformer caps expression value >= constant',()=>{
-
-        instance.logScale = true;
-        assert.equal(instance.dataTransformer({value: 0.0001} as NumericGeneMolecularData), -6.643856189774724, 'value less than cap');
-        assert.equal(instance.dataTransformer({value: 0} as NumericGeneMolecularData), -6.643856189774724, 'zero value');
-
-        instance.logScale = false;
-        assert.equal(instance.dataTransformer({value: 0.0001} as NumericGeneMolecularData), .0001, 'non log');
-        assert.equal(instance.dataTransformer({value: 0} as NumericGeneMolecularData), 0, 'non log zero');
-    });
-
     // this is failing. we need new data to debug
-    it.skip('studies are sorted properly depending on sortBy setting',()=>{
+    /*it.skip('studies are sorted properly depending on sortBy setting',()=>{
 
         instance.sortBy = "alphabetic";
         assert.equal(instance.sortedData[2][0].studyId,  'chol_tcga', 'sorting is alphabetical');
 
         instance.sortBy = "median";
         assert.equal(instance.sortedData[2][0].studyId,  'laml_tcga', 'sort according to median values');
 
-    });
+    });*/
 
 });