Merge pull request #2802 from adamabeshouse/plots-coexp-mrna-profiles

Dont filter out profiles without data for selection in coexpression and plots Former-commit-id: d715725ed41a94dff8e59a9885dd23d878046576
cBioPortal · Oct 22, 2019 · fac863e · fac863e
2 parents cee9b0f + 812c14f
commit fac863e
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Showing 6 changed files with 30 additions and 16 deletions.
diff --git a/end-to-end-test/local/specs/gsva.spec.js b/end-to-end-test/local/specs/gsva.spec.js
@@ -405,6 +405,7 @@ describe('gsva feature', function() {
             it('shows gene sets in table when GSVA scores selected in subject profile select box', () => {
                 selectReactSelectOption($('.coexpression-select-query-profile'), 'GSVA scores on oncogenic signatures gene sets (5 samples)');
                 $('//*[@id="coexpressionTabGeneTabs"]').waitForExist();
+                $('span*=GO_').waitForExist();
                 assert.equal($$('span*=GO_').length, 7);
             });
 

diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -1243,15 +1243,15 @@ export class ResultsViewPageStore {
     });
 
     readonly coexpressionTabMolecularProfiles = remoteData<MolecularProfile[]>({
-        await: () => [this.molecularProfilesWithData],
+        await: () => [this.molecularProfilesInStudies],
         invoke: () =>
             Promise.resolve(
                 sortRnaSeqProfilesToTop(
                     filterAndSortProfiles(
-                        this.molecularProfilesWithData.result!
+                        this.molecularProfilesInStudies.result!
                     ).concat(
                         getGenesetProfiles(
-                            this.molecularProfilesWithData.result!
+                            this.molecularProfilesInStudies.result!
                         )
                     )
                 )

diff --git a/src/pages/resultsView/coExpression/CoExpressionTab.tsx b/src/pages/resultsView/coExpression/CoExpressionTab.tsx
@@ -279,6 +279,7 @@ export default class CoExpressionTab extends React.Component<ICoExpressionTabPro
 
     @bind
     private geneTabs() {
+        // we hack together MSKTabs this way because of some particular responsiveness needs and mobxpromise behavior that may or may not still be relevant
         if (this.selectedGeneticEntity.isComplete &&
             this.selectedProfileX.isComplete &&
             this.selectedProfileY.isComplete &&

diff --git a/src/pages/resultsView/coExpression/CoExpressionViz.tsx b/src/pages/resultsView/coExpression/CoExpressionViz.tsx
@@ -393,16 +393,27 @@ export default class CoExpressionViz extends React.Component<ICoExpressionVizPro
                 data-test="CoExpressionGeneTabContent"
             >
                 <div className="clearfix">
-                    <div style={{width:"40%", float:"left", marginTop:6}}>
-                        <Observer>
-                            {this.table}
-                        </Observer>
-                    </div>
-                    <div style={{width:"60%", float:"right", marginTop:6 /*align with table controls*/}}>
-                        <Observer>
-                            {this.plot}
-                        </Observer>
-                    </div>
+                    { this.dataStore.allData.length > 0 ? [
+                        <div style={{width:"40%", float:"left", marginTop:6}}>
+                            <Observer>
+                                {this.table}
+                            </Observer>
+                        </div>,
+                        <div style={{width:"60%", float:"right", marginTop:6 /*align with table controls*/}}>
+                            <Observer>
+                                {this.plot}
+                            </Observer>
+                        </div>
+                    ] : (
+                        <div style={{
+                            position:"absolute",
+                            top:200,
+                            left:"50%",
+                            transform:"translate(-50%, 0)"
+                        }}>
+                            There is no expression data for <strong>{this.props.geneticEntity.geneticEntityName}</strong> with the selected samples in <strong>{this.props.profileX.name}</strong>.
+                        </div>
+                    )}
                 </div>
             </div>
         );

diff --git a/src/pages/resultsView/plots/PlotsTab.tsx b/src/pages/resultsView/plots/PlotsTab.tsx
@@ -977,11 +977,11 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
 
     readonly dataTypeToDataSourceOptions = remoteData<{[dataType:string]:{value:string, label:string}[]}>({
         await:()=>[
-            this.props.store.molecularProfilesWithData,
+            this.props.store.molecularProfilesInStudies,
             this.clinicalAttributeOptions
         ],
         invoke:()=>{
-            const profiles = this.props.store.molecularProfilesWithData.result!;
+            const profiles = this.props.store.molecularProfilesInStudies.result!;
             const map = _.mapValues(
                 _.groupBy(profiles, profile=>profile.molecularAlterationType), // create a map from profile type to list of profiles of that type
                 profilesOfType=>(

diff --git a/src/shared/api/generated/CBioPortalAPIInternal-docs.json b/src/shared/api/generated/CBioPortalAPIInternal-docs.json
@@ -1808,7 +1808,8 @@
       "required": [
         "counts",
         "entrezGeneId",
-        "hugoGeneSymbol"
+        "hugoGeneSymbol",
+        "pValue"
       ],
       "properties": {
         "counts": {