Add mrna expression plots tab to patient page

src/pages/patientView/PatientViewPage.tsx

@@ -162,6 +162,7 @@ export class PatientViewPageInner extends React.Component<
 
         this.patientViewPageStore = new PatientViewPageStore(
             this.props.appStore,
+            this.urlWrapper,
             this.urlWrapper.query.studyId!,
             this.urlWrapper.query.caseId!,
             this.urlWrapper.query.sampleId,

src/pages/patientView/PatientViewPageTabs.tsx

@@ -37,6 +37,8 @@ import { HelpWidget } from 'shared/components/HelpWidget/HelpWidget';
 import MutationTableWrapper from './mutation/MutationTableWrapper';
 import { PatientViewPageInner } from 'pages/patientView/PatientViewPage';
 import { Else, If } from 'react-if';
+import PlotsTab from 'shared/components/plots/PlotsTab';
+import { PatientViewPlotsTabWrapper } from './PatientViewPlotsTabWrapper';
 
 export enum PatientViewPageTabs {
     Summary = 'summary',
@@ -49,6 +51,7 @@ export enum PatientViewPageTabs {
     TrialMatchTab = 'trialMatchTab',
     MutationalSignatures = 'mutationalSignatures',
     PathwayMapper = 'pathways',
+    Plots = 'plots',
 }
 
 export const PatientViewResourceTabPrefix = 'openResource_';
@@ -488,6 +491,15 @@ export function tabs(
             </MSKTab>
         );
 
+    tabs.push(
+        <MSKTab key={9} id={PatientViewPageTabs.Plots} linkText="Plots">
+            <PatientViewPlotsTabWrapper
+                store={pageComponent.patientViewPageStore}
+                urlWrapper={urlWrapper}
+            />
+        </MSKTab>
+    );
+
     tabs.push(
         <MSKTab
             key={8}

src/pages/patientView/PatientViewPlotsTabWrapper.tsx

@@ -0,0 +1,129 @@
+import * as React from 'react';
+import { PatientViewPageStore } from './clinicalInformation/PatientViewPageStore';
+import PatientViewUrlWrapper from './PatientViewUrlWrapper';
+import { observer } from 'mobx-react';
+import PlotsTab from 'shared/components/plots/PlotsTab';
+import CohortSelector from 'shared/components/plots/CohortSelector';
+import { SamplePointLabel } from 'shared/components/sampleLabel/SampleLabel';
+
+export enum CohortOptions {
+    WholeStudy = 'WholeStudy',
+    CancerType = 'CancerType',
+    CancerTypeDetailed = 'CancerTypeDetailed',
+}
+
+export const PatientViewPlotsTabWrapper: React.FunctionComponent<{
+    store: PatientViewPageStore;
+    urlWrapper: PatientViewUrlWrapper;
+}> = observer(function({ store, urlWrapper }) {
+    const cohortSelector = () => (
+        <CohortSelector
+            study={store.studies.result![0].name}
+            cancerTypes={
+                store.patientViewPlotsStore.highlightedCancerTypes.result
+            }
+            cancerTypesDetailed={
+                store.patientViewPlotsStore.highlightedDetailedCancerTypes
+                    .result
+            }
+            cohortSelection={store.patientViewPlotsStore.cohortSelection}
+            handleCohortChange={store.patientViewPlotsStore.handleCohortChange}
+        />
+    );
+
+    const customSamplePointComponent = (sampleId: string, mouseEvents: any) => (
+        <SamplePointLabel
+            label={(
+                store.sampleManager.result!.sampleIndex[sampleId] + 1
+            ).toString()}
+            events={mouseEvents}
+        />
+    );
+
+    return (
+        <PlotsTab
+            filteredSamplesByDetailedCancerType={
+                store.patientViewPlotsStore.filteredSamplesByDetailedCancerType
+            }
+            mutations={store.mutationData}
+            studies={store.studies}
+            molecularProfileIdSuffixToMolecularProfiles={
+                store.patientViewPlotsStore
+                    .molecularProfileIdSuffixToMolecularProfiles
+            }
+            entrezGeneIdToGene={
+                store.patientViewPlotsStore.entrezGeneIdToGeneAll
+            }
+            sampleKeyToSample={store.patientViewPlotsStore.sampleSetByKey}
+            genes={store.patientViewPlotsStore.allGenes}
+            clinicalAttributes={store.patientViewPlotsStore.clinicalAttributes}
+            genesets={store.patientViewPlotsStore.genesets}
+            genericAssayEntitiesGroupByMolecularProfileId={
+                store.patientViewPlotsStore
+                    .genericAssayEntitiesGroupedByProfileId
+            }
+            customAttributes={store.patientViewPlotsStore.customAttributes}
+            studyIds={store.patientViewPlotsStore.queriedPhysicalStudyIds}
+            molecularProfilesWithData={store.molecularProfilesInStudy}
+            molecularProfilesInStudies={store.molecularProfilesInStudy}
+            annotatedCnaCache={store.patientViewPlotsStore.annotatedCnaCache}
+            annotatedMutationCache={
+                store.patientViewPlotsStore.annotatedMutationCache
+            }
+            structuralVariantCache={
+                store.patientViewPlotsStore.structuralVariantCache
+            }
+            studyToMutationMolecularProfile={
+                store.patientViewPlotsStore.studyToMutationMolecularProfile
+            }
+            studyToMolecularProfileDiscreteCna={
+                store.patientViewPlotsStore.studyToMolecularProfileDiscreteCna
+            }
+            clinicalDataCache={store.patientViewPlotsStore.clinicalDataCache}
+            patientKeyToFilteredSamples={
+                store.patientViewPlotsStore.patientKeyToFilteredSamples
+            }
+            numericGeneMolecularDataCache={
+                store.patientViewPlotsStore.numericGeneMolecularDataCache
+            }
+            coverageInformation={
+                store.patientViewPlotsStore.coverageInformationForAllSamples
+            }
+            filteredSamples={store.patientViewPlotsStore.selectedCohortSamples}
+            genesetMolecularDataCache={
+                store.patientViewPlotsStore.genesetMolecularDataCache
+            }
+            genericAssayMolecularDataCache={
+                store.patientViewPlotsStore.genericAssayMolecularDataCache
+            }
+            studyToStructuralVariantMolecularProfile={
+                store.patientViewPlotsStore
+                    .studyToStructuralVariantMolecularProfile
+            }
+            driverAnnotationSettings={
+                store.patientViewPlotsStore.driverAnnotationSettings
+            }
+            studyIdToStudy={store.studyIdToStudy.result}
+            structuralVariants={store.structuralVariantData.result}
+            hugoGeneSymbols={
+                store.patientViewPlotsStore.allHugoGeneSymbols.result
+            }
+            selectedGenericAssayEntitiesGroupByMolecularProfileId={
+                store.patientViewPlotsStore
+                    .selectedGenericAssayEntitiesGroupByMolecularProfileId
+            }
+            molecularProfileIdToMolecularProfile={
+                store.molecularProfileIdToMolecularProfile
+            }
+            urlWrapper={urlWrapper}
+            hasNoQueriedGenes={true}
+            genePanelDataForAllProfiles={
+                store.patientViewPlotsStore.genePanelDataForAllProfiles.result
+            }
+            patients={store.patientViewPlotsStore.allPatientsInStudy}
+            highlightedSamples={store.sampleIds}
+            additionalControls={cohortSelector}
+            customSamplePointComponent={customSamplePointComponent}
+        />
+    );
+});

src/pages/patientView/PatientViewUrlWrapper.ts

@@ -22,6 +22,49 @@ export type PatientViewUrlQuery = {
 
         showOnlySelectedMutationsInTable?: string;
     };
+    plots_horz_selection: PlotsSelectionParam;
+    plots_vert_selection: PlotsSelectionParam;
+    plots_coloring_selection: PlotsColoringParam;
+    geneset_list: any;
+    generic_assay_groups: any;
+};
+
+export type PlotsSelectionParam = {
+    selectedGeneOption?: string;
+    selectedGenesetOption?: string;
+    selectedGenericAssayOption?: string;
+    dataType?: string;
+    selectedDataSourceOption?: string;
+    mutationCountBy?: string;
+    structuralVariantCountBy?: string;
+    logScale?: string;
+};
+
+const PlotsSelectionParamProps: Required<PlotsSelectionParam> = {
+    selectedGeneOption: '',
+    selectedGenesetOption: '',
+    selectedGenericAssayOption: '',
+    dataType: '',
+    selectedDataSourceOption: '',
+    mutationCountBy: '',
+    structuralVariantCountBy: '',
+    logScale: '',
+};
+
+export type PlotsColoringParam = {
+    selectedOption?: string;
+    logScale?: string;
+    colorByMutationType?: string;
+    colorByCopyNumber?: string;
+    colorBySv?: string;
+};
+
+const PlotsColoringParamProps: Required<PlotsColoringParam> = {
+    selectedOption: '',
+    logScale: '',
+    colorByMutationType: '',
+    colorByCopyNumber: '',
+    colorBySv: '',
 };
 
 export default class PatientViewUrlWrapper extends URLWrapper<
@@ -49,6 +92,20 @@ export default class PatientViewUrlWrapper extends URLWrapper<
                     showOnlySelectedMutationsInTable: '',
                 },
             },
+            plots_horz_selection: {
+                isSessionProp: false,
+                nestedObjectProps: PlotsSelectionParamProps,
+            },
+            plots_vert_selection: {
+                isSessionProp: false,
+                nestedObjectProps: PlotsSelectionParamProps,
+            },
+            plots_coloring_selection: {
+                isSessionProp: false,
+                nestedObjectProps: PlotsColoringParamProps,
+            },
+            geneset_list: { isSessionProp: true },
+            generic_assay_groups: { isSessionProp: false },
         });
         makeObservable(this);
     }

src/pages/patientView/clinicalInformation/PatientViewPageStore.spec.ts

@@ -7,12 +7,19 @@ import {
 } from './PatientViewPageStore';
 import { assert } from 'chai';
 import { AppStore } from '../../../AppStore';
+import PatientViewUrlWrapper from '../PatientViewUrlWrapper';
 
 describe('PatientViewPageStore', () => {
     let store: PatientViewPageStore;
+    let urlWrapper: PatientViewUrlWrapper;
 
     beforeAll(() => {
-        store = new PatientViewPageStore(new AppStore(), 'someId', '');
+        store = new PatientViewPageStore(
+            new AppStore(),
+            urlWrapper,
+            'someId',
+            ''
+        );
     });
 
     it('if there are pdf items in response and their name starts with a given patientId, return collection, otherwise returns empty array', () => {

src/pages/patientView/clinicalInformation/PatientViewPageStore.ts

@@ -107,10 +107,13 @@ import {
     tumorTypeResolver,
     evaluatePutativeDriverInfoWithHotspots,
     evaluatePutativeDriverInfo,
+    IDataQueryFilter,
+    generateDataQueryFilter,
 } from 'shared/lib/StoreUtils';
 import {
     computeGenePanelInformation,
     CoverageInformation,
+    getCoverageInformation,
 } from 'shared/lib/GenePanelUtils';
 import {
     fetchCivicGenes,
@@ -172,6 +175,7 @@ import {
     TMB_H_THRESHOLD,
     AlterationTypeConstants,
     DataTypeConstants,
+    REQUEST_ARG_ENUM,
 } from 'shared/constants';
 import {
     OTHER_BIOMARKER_HUGO_SYMBOL,
@@ -186,6 +190,7 @@ import {
 import {
     getGenericAssayMetaPropertyOrDefault,
     getGenericAssayCategoryFromName,
+    fetchGenericAssayMetaByMolecularProfileIdsGroupByMolecularProfileId,
 } from 'shared/lib/GenericAssayUtils/GenericAssayCommonUtils';
 import { GenericAssayTypeConstants } from 'shared/lib/GenericAssayUtils/GenericAssayConfig';
 
@@ -201,6 +206,8 @@ import { buildNamespaceColumnConfig } from 'shared/components/namespaceColumns/n
 import { SiteError } from 'shared/model/appMisc';
 import { AnnotatedExtendedAlteration } from 'shared/model/AnnotatedExtendedAlteration';
 import { CustomDriverNumericGeneMolecularData } from 'shared/model/CustomDriverNumericGeneMolecularData';
+import PatientViewUrlWrapper from '../PatientViewUrlWrapper';
+import { PatientViewPlotsStore } from './PatientViewPlotsStore';
 
 type PageMode = 'patient' | 'sample';
 type ResourceId = string;
@@ -323,6 +330,7 @@ function transformClinicalInformationToStoreShape(
 export class PatientViewPageStore {
     constructor(
         private appStore: AppStore,
+        private urlWrapper: PatientViewUrlWrapper,
         studyId: string,
         patientId: string,
         sampleId: string = '',
@@ -340,8 +348,16 @@ export class PatientViewPageStore {
         this._sampleId = sampleId;
 
         this.studyId = studyId;
+
+        this.patientViewPlotsStore = new PatientViewPlotsStore(
+            appStore,
+            urlWrapper,
+            this
+        );
     }
 
+    public patientViewPlotsStore: PatientViewPlotsStore;
+
     public internalClient: CBioPortalAPIInternal;
 
     @observable public activeLocus: string | undefined;