display gene panel id for mutated and not profiled samples

cBioPortal · Oct 22, 2019 · 4581762 · 4581762
1 parent f5ba1e6
commit 4581762
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Showing 6 changed files with 80 additions and 49 deletions.
diff --git a/src/pages/patientView/PatientViewPage.tsx b/src/pages/patientView/PatientViewPage.tsx
@@ -505,7 +505,7 @@ export default class PatientViewPage extends React.Component<IPatientViewPagePro
                                                     columnVisibilityProps={{
                                                         onColumnToggled: this.onMutationTableColumnVisibilityToggled
                                                     }}
-                                                    />
+                                                />
                                             </div>
                                         )
                                     }

diff --git a/src/pages/patientView/copyNumberAlterations/CopyNumberTableWrapper.tsx b/src/pages/patientView/copyNumberAlterations/CopyNumberTableWrapper.tsx
@@ -115,11 +115,18 @@ export default class CopyNumberTableWrapper extends React.Component<ICopyNumberT
             order: 30
         });
 
+        const GenePanelProps = (d:DiscreteCopyNumberData[]) => ({
+            data: d,
+            sampleToGenePanelId: this.props.sampleToGenePanelId,
+            sampleManager: this.props.sampleManager,
+            genePanelIdToGene: this.props.genePanelIdToEntrezGeneIds
+        });
+
         columns.push({
             name: "Gene panel",
-            render: (d:DiscreteCopyNumberData[]) => PanelColumnFormatter.renderFunction(d, this.props.sampleToMutationGenePanelId),
-            download: (d:DiscreteCopyNumberData[]) => PanelColumnFormatter.download(d, this.props.sampleToMutationGenePanelId),
-            sortBy: (d:DiscreteCopyNumberData[]) => PanelColumnFormatter.getGenePanelIds(d, this.props.sampleToMutationGenePanelId),
+            render: (d:DiscreteCopyNumberData[]) => PanelColumnFormatter.renderFunction(GenePanelProps(d)),
+            download: (d:DiscreteCopyNumberData[]) => PanelColumnFormatter.download(GenePanelProps(d)),
+            sortBy: (d:DiscreteCopyNumberData[]) => PanelColumnFormatter.getGenePanelIds(GenePanelProps(d)),
             visible: false,
             order: 35
         });

diff --git a/src/pages/patientView/mutation/PatientViewMutationTable.tsx b/src/pages/patientView/mutation/PatientViewMutationTable.tsx
@@ -101,12 +101,19 @@ export default class PatientViewMutationTable extends MutationTable<IPatientView
             download: (d:Mutation[])=>TumorColumnFormatter.getSample(d),
         };
 
+        const GenePanelProps = (d:Mutation[]) => ({
+            data: d,
+            sampleToGenePanelId: this.props.sampleToGenePanelId,
+            sampleManager: this.props.sampleManager,
+            genePanelIdToGene: this.props.genePanelIdToEntrezGeneIds
+        });
+
         this._columns[MutationTableColumnType.GENE_PANEL] = {
             name: "Gene panel",
-            render: (d:Mutation[]) => PanelColumnFormatter.renderFunction(d, this.props.sampleToMutationGenePanelId),
-            download: (d:Mutation[]) => PanelColumnFormatter.download(d, this.props.sampleToMutationGenePanelId),
+            render: (d:Mutation[]) => PanelColumnFormatter.renderFunction(GenePanelProps(d)),
+            download: (d:Mutation[]) => PanelColumnFormatter.download(GenePanelProps(d)),
             visible: false,
-            sortBy: (d:Mutation[]) => PanelColumnFormatter.getGenePanelIds(d, this.props.sampleToMutationGenePanelId)
+            sortBy: (d:Mutation[]) => PanelColumnFormatter.getGenePanelIds(GenePanelProps(d))
         }
 
         // customization for allele count columns

diff --git a/src/shared/components/mutationTable/MutationTable.tsx b/src/shared/components/mutationTable/MutationTable.tsx
@@ -95,7 +95,6 @@ export interface IMutationTableProps {
     showCountHeader?:boolean;
     columnVisibility?: {[columnId: string]: boolean};
     columnVisibilityProps?: IColumnVisibilityControlsProps;
-    sampleToMutationGenePanelId?: {[sampleId:string]: string};
 }
 
 export enum MutationTableColumnType {

diff --git a/src/shared/components/mutationTable/column/PanelColumnFormatter.spec.tsx b/src/shared/components/mutationTable/column/PanelColumnFormatter.spec.tsx
@@ -1,6 +1,7 @@
-import PanelColumnFormatter from "./PanelColumnFormatter";
-import { shallow } from "enzyme";
+import PanelColumnFormatter from './PanelColumnFormatter';
+import { shallow } from 'enzyme';
 import { assert } from 'chai';
+import SampleManager from 'pages/patientView/SampleManager';
 
 const mockData = [
   {
@@ -21,29 +22,39 @@ const mockData = [
   }
 ];
 
-const mockSampleToMutationGenePanelId = { 'sampleId': 'genePanelId' };
+const mockSamples = [
+  { id: 'sampleId', clinicalData: [] }
+]
 
-describe("PanelColumnFormatter", () => {
-  it('renders spinner icon if sampleToMutationGenePanelId object is empty', () => {
-    const PanelColumn = shallow(PanelColumnFormatter.renderFunction(mockData, {}));
+const mockSampleToGenePanelId = { 'sampleId': 'genePanelId' };
+const mockGenePanelIdToGene = { 'genePanelId': [1] };
+const mockSampleManager = new SampleManager(mockSamples);
+
+const mock = {
+  data: mockData,
+  sampleToGenePanelId: mockSampleToGenePanelId,
+  sampleManager: mockSampleManager,
+  genePanelIdToGene: mockGenePanelIdToGene
+}
+
+describe('PanelColumnFormatter', () => {
+  it('renders spinner icon if sampleToGenePanelId object is empty', () => {
+    const PanelColumn = shallow(PanelColumnFormatter.renderFunction({...mock, sampleToGenePanelId: {}}));
     assert.isTrue(PanelColumn.find('i.fa-spinner').exists());
   });
 
   it('renders gene panel information', () => {
-    const PanelColumn = shallow(PanelColumnFormatter.renderFunction(
-      mockData,
-      mockSampleToMutationGenePanelId
-    ));
+    const PanelColumn = shallow(PanelColumnFormatter.renderFunction(mock));
     assert.isTrue(PanelColumn.text().includes('genePanelId'));
   });
 
   it('returns a list of gene panel ids on download', () => {
-    const genePanelIds = PanelColumnFormatter.download(mockData, mockSampleToMutationGenePanelId);
+    const genePanelIds = PanelColumnFormatter.download(mock);
     assert.deepEqual(genePanelIds, ['genePanelId'])
   });
 
   it('returns a list of gene panel ids on getGenePanelIds', () => {
-    const genePanelIds = PanelColumnFormatter.getGenePanelIds(mockData, mockSampleToMutationGenePanelId);
+    const genePanelIds = PanelColumnFormatter.getGenePanelIds(mock);
     assert.deepEqual(genePanelIds, ['genePanelId'])
-  })
+  });
 })
diff --git a/src/shared/components/mutationTable/column/PanelColumnFormatter.tsx b/src/shared/components/mutationTable/column/PanelColumnFormatter.tsx
@@ -1,12 +1,14 @@
 import * as React from 'react';
-import {
-	Mutation,
-	DiscreteCopyNumberData
-} from 'shared/api/generated/CBioPortalAPI';
+import {map} from 'lodash';
+import SampleManager from 'pages/patientView/SampleManager';
+import { ClinicalDataBySampleId } from 'shared/api/api-types-extended';
+import TumorColumnFormatter from 'pages/patientView/mutation/column/TumorColumnFormatter';
 
 interface PanelColumnFormatterProps {
-	data: Mutation[] | DiscreteCopyNumberData[];
-	sampleToMutationGenePanelId: {[sampleId:string]: string} | undefined;
+	data: {sampleId:string, entrezGeneId:number}[];
+	sampleToGenePanelId: {[sampleId: string]: string|undefined};
+	sampleManager: SampleManager|null;
+	genePanelIdToGene: {[genePanelId: string]: number[]}
 }
 
 class PanelColumn extends React.Component<PanelColumnFormatterProps, {}> {
@@ -15,18 +17,14 @@ class PanelColumn extends React.Component<PanelColumnFormatterProps, {}> {
 	}
 
 	render() {
-    const { data, sampleToMutationGenePanelId } = this.props;
-
-    if (!sampleToMutationGenePanelId) return;
+		const { sampleToGenePanelId, sampleManager } = this.props;
+    if (!sampleToGenePanelId || !sampleManager) return;
 
-		if (sampleToMutationGenePanelId && !Object.keys(sampleToMutationGenePanelId).length) {
+		if (sampleToGenePanelId && !Object.keys(sampleToGenePanelId).length) {
 			return <i className='fa fa-spinner fa-pulse' />;
 		}
 
-		const genePanelIds: string[] = getGenePanelIds(
-			data,
-			sampleToMutationGenePanelId
-		);
+		const genePanelIds: string[] = getGenePanelIds(this.props);
 
 		return (
 			<div style={{ position: 'relative' }}>
@@ -38,30 +36,39 @@ class PanelColumn extends React.Component<PanelColumnFormatterProps, {}> {
 	}
 }
 
-const getGenePanelIds = (
-	data: any[],
-	sampleToMutationGenePanelId: {[sampleId:string]: string} | undefined
-) => {
-  if (sampleToMutationGenePanelId) {
-    const sampleIds = data.map((datum) => datum.sampleId);
-    return sampleIds.map((id) => sampleToMutationGenePanelId[id]);
+const getGenePanelIds = (props:PanelColumnFormatterProps) => {
+	const { data, sampleToGenePanelId, sampleManager, genePanelIdToGene } = props;
+  if (sampleToGenePanelId && sampleManager) {
+		const samples =  sampleManager.samples;
+		const sampleIds = map(samples, (sample:ClinicalDataBySampleId) => sample.id)
+		const entrezGeneId = data[0].entrezGeneId;
+		const mutatedSamples = TumorColumnFormatter.getPresentSamples(data);
+		const profiledSamples = TumorColumnFormatter.getProfiledSamplesForGene(entrezGeneId, sampleIds, sampleToGenePanelId, genePanelIdToGene);
+
+		const genePanelsIds = samples.map(sample => {
+			const isMutated = sample.id in mutatedSamples;
+			const isProfiled = sample.id in profiledSamples && profiledSamples[sample.id];
+			if (isProfiled && !isMutated) return "";
+			return sampleToGenePanelId[sample.id] || "N/A";
+		});
+
+		return genePanelsIds.filter(id => id);
   }
   return [];
 };
 
 export default {
 	renderFunction: (
-		data: Mutation[] | DiscreteCopyNumberData[],
-		sampleToMutationGenePanelId: {[sampleId:string]: string} | undefined
+		props:PanelColumnFormatterProps
 	) => (
 		<PanelColumn
-			data={data}
-			sampleToMutationGenePanelId={sampleToMutationGenePanelId}
+			data={props.data}
+			sampleToGenePanelId={props.sampleToGenePanelId}
+			sampleManager={props.sampleManager}
+			genePanelIdToGene={props.genePanelIdToGene}
 		/>
 	),
 	download: (
-		data: Mutation[] | DiscreteCopyNumberData[],
-		sampleToMutationGenePanelId: {[sampleId:string]: string} | undefined
-	) => getGenePanelIds(data, sampleToMutationGenePanelId),
+		props:PanelColumnFormatterProps) => getGenePanelIds(props),
 	getGenePanelIds
 };