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Add expression tab to patient page #5271

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0340c22
add expression tab to patient page
Oct 1, 2025
21191eb
fix undefined gene symbol error
Oct 1, 2025
0898520
set up profile selections
Oct 10, 2025
575490e
add support for other cna profiles
Oct 15, 2025
b599622
add expression value average when multiple samples
Oct 16, 2025
96e326d
add expression value average and edit mutation column display
Oct 22, 2025
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45 changes: 45 additions & 0 deletions src/pages/patientView/PatientViewPageTabs.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ 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 ExpressionTableWrapper from './expression/ExpressionTableWrapper';

export enum PatientViewPageTabs {
Summary = 'summary',
Expand All @@ -49,6 +50,7 @@ export enum PatientViewPageTabs {
TrialMatchTab = 'trialMatchTab',
MutationalSignatures = 'mutationalSignatures',
PathwayMapper = 'pathways',
Expression = 'expression',
}

export const PatientViewResourceTabPrefix = 'openResource_';
Expand Down Expand Up @@ -488,6 +490,49 @@ export function tabs(
</MSKTab>
);

pageComponent.patientViewPageStore.isExpressionProfiledForPatient
.isComplete &&
pageComponent.patientViewPageStore.isExpressionProfiledForPatient
.result &&
tabs.push(
<MSKTab
key={9}
id={PatientViewPageTabs.Expression}
linkText={'Expression'}
>
{pageComponent.patientViewPageStore
.mrnaExpressionDataByGeneThenProfile.isComplete &&
pageComponent.patientViewPageStore
.proteinExpressionDataByGeneThenProfile.isComplete &&
pageComponent.patientViewPageStore.mutationData.isComplete &&
pageComponent.patientViewPageStore.structuralVariantData
.isComplete &&
pageComponent.patientViewPageStore.cnaDataByGeneThenProfile
.isComplete &&
pageComponent.patientViewPageStore.allEntrezGeneIdsToGene
.isComplete &&
pageComponent.patientViewPageStore.allHugoGeneSymbolsToGene
.isComplete &&
pageComponent.patientViewPageStore
.analysisMrnaExpressionProfiles.isComplete &&
pageComponent.patientViewPageStore
.analysisProteinExpressionProfiles.isComplete ? (
<ExpressionTableWrapper
store={pageComponent.patientViewPageStore}
mergeOncoKbIcons={
pageComponent.mergeMutationTableOncoKbIcons
}
/>
) : (
<LoadingIndicator
isLoading={true}
size={'big'}
center={true}
/>
)}
</MSKTab>
);

tabs.push(
<MSKTab
key={8}
Expand Down
25 changes: 25 additions & 0 deletions src/pages/patientView/PatientViewPageUtils.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,14 @@ import {
MutationalSignatureLabelMap,
MutationalSignatureCount,
} from '/shared/model/MutationalSignature';
import {
CNA_COLOR_AMP,
CNA_COLOR_DEFAULT,
CNA_COLOR_GAIN,
CNA_COLOR_HETLOSS,
CNA_COLOR_HOMDEL,
} from 'cbioportal-frontend-commons';
import { DEFAULT_GREY } from 'shared/lib/Colors';

export function getMutationalSignaturesVersionFromProfileId(
inputProfileId: string
Expand Down Expand Up @@ -121,3 +129,20 @@ export function createMutationalCountsObjects(
}));
return result;
}

export function getCNAColorByAlteration(alteration: string): string {
switch (alteration) {
case 'HOMDEL':
return CNA_COLOR_HOMDEL;
case 'HETLOSS':
return '#2aced4';
case 'DIPLOID':
return DEFAULT_GREY;
case 'GAIN':
return '#ff8c9f';
case 'AMP':
return CNA_COLOR_AMP;
default:
return CNA_COLOR_DEFAULT;
}
}
266 changes: 265 additions & 1 deletion src/pages/patientView/clinicalInformation/PatientViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ import {
GenericAssayMeta,
GenericAssayDataMultipleStudyFilter,
GenericAssayMetaFilter,
MolecularDataFilter,
} from 'cbioportal-ts-api-client';
import { getClient } from '../../../shared/api/cbioportalClientInstance';
import internalClient from '../../../shared/api/cbioportalInternalClientInstance';
Expand Down Expand Up @@ -195,7 +196,10 @@ import {
} from 'shared/lib/GenericAssayUtils/MutationalSignaturesUtils';
import { getServerConfig } from 'config/config';
import { StructuralVariantFilter } from 'cbioportal-ts-api-client';
import { IGenePanelDataByProfileIdAndSample } from 'shared/lib/isSampleProfiled';
import {
IGenePanelDataByProfileIdAndSample,
isPatientProfiledInMultiple,
} from 'shared/lib/isSampleProfiled';
import { NamespaceColumnConfig } from 'shared/components/namespaceColumns/NamespaceColumnConfig';
import { buildNamespaceColumnConfig } from 'shared/components/namespaceColumns/namespaceColumnsUtils';
import { SiteError } from 'shared/model/appMisc';
Expand Down Expand Up @@ -470,6 +474,256 @@ export class PatientViewPageStore {
@observable
public patientIdsInCohort: string[] = [];

readonly allGenes = remoteData({
invoke: () => {
return getClient().getAllGenesUsingGET({
projection: 'SUMMARY',
});
},
});

readonly allEntrezGeneIdsToGene = remoteData<{
[entrezGeneId: number]: {
hugoGeneSymbol: string;
entrezGeneId: number;
};
}>({
await: () => [this.allGenes],
invoke: () =>
Promise.resolve(
_.keyBy(this.allGenes.result, gene => gene.entrezGeneId)
),
default: {},
});

readonly allHugoGeneSymbolsToGene = remoteData<{
[hugoGeneSymbol: string]: {
hugoGeneSymbol: string;
entrezGeneId: number;
};
}>({
await: () => [this.allGenes],
invoke: () =>
Promise.resolve(
_.keyBy(this.allGenes.result, gene => gene.hugoGeneSymbol)
),
default: {},
});

readonly cnaDataByGeneThenProfile = remoteData({
await: () => [this.cnaProfiles],
invoke: async () => {
const cnaMap: Record<
number,
Record<string, NumericGeneMolecularData[]>
> = {};
await Promise.all(
this.cnaProfiles.result.map(async p => {
let data = await getClient().fetchAllMolecularDataInMolecularProfileUsingPOST(
{
projection: 'DETAILED',
molecularProfileId: p.molecularProfileId,
molecularDataFilter: {
sampleIds: this.sampleIds,
} as MolecularDataFilter,
}
);
data.map(d => {
if (!cnaMap[d.entrezGeneId]) {
cnaMap[d.entrezGeneId] = {};
}
if (!cnaMap[d.entrezGeneId][d.molecularProfileId]) {
cnaMap[d.entrezGeneId][d.molecularProfileId] = [];
}
cnaMap[d.entrezGeneId][d.molecularProfileId].push(d);
});
})
);
return cnaMap;
},
default: {},
});

readonly cnaProfiles = remoteData(
{
await: () => [this.molecularProfilesInStudy],
invoke: () => {
return Promise.resolve(
this.molecularProfilesInStudy.result.filter(
p =>
p.molecularAlterationType ===
'COPY_NUMBER_ALTERATION'
)
);
},
},
[]
);

readonly mrnaExpressionDataByGeneThenProfile = remoteData({
await: () => [this.mrnaExpressionProfiles],
invoke: async () => {
const mrnaExpressionMap: Record<
number,
Record<string, NumericGeneMolecularData[]>
> = {};
await Promise.all(
this.mrnaExpressionProfiles.result.map(async p => {
let data = await getClient().fetchAllMolecularDataInMolecularProfileUsingPOST(
{
projection: 'DETAILED',
molecularProfileId: p.molecularProfileId,
molecularDataFilter: {
sampleIds: this.sampleIds,
} as MolecularDataFilter,
}
);
data.map(d => {
if (!mrnaExpressionMap[d.entrezGeneId]) {
mrnaExpressionMap[d.entrezGeneId] = {};
}
if (
!mrnaExpressionMap[d.entrezGeneId][
d.molecularProfileId
]
) {
mrnaExpressionMap[d.entrezGeneId][
d.molecularProfileId
] = [];
}
mrnaExpressionMap[d.entrezGeneId][
d.molecularProfileId
].push(d);
});
})
);
return mrnaExpressionMap;
},
default: {},
});

readonly mrnaExpressionProfiles = remoteData(
{
await: () => [this.molecularProfilesInStudy],
invoke: () => {
return Promise.resolve(
this.molecularProfilesInStudy.result.filter(
p => p.molecularAlterationType === 'MRNA_EXPRESSION'
)
);
},
},
[]
);

readonly analysisMrnaExpressionProfiles = remoteData(
{
await: () => [this.mrnaExpressionProfiles],
invoke: () => {
return Promise.resolve(
this.mrnaExpressionProfiles.result.filter(
p => p.showProfileInAnalysisTab
)
);
},
},
[]
);

readonly proteinExpressionDataByGeneThenProfile = remoteData({
await: () => [this.proteinExpressionProfiles],
invoke: async () => {
const proteinExpressionMap: Record<
number,
Record<string, NumericGeneMolecularData[]>
> = {};
await Promise.all(
this.proteinExpressionProfiles.result.map(async p => {
let data = await getClient().fetchAllMolecularDataInMolecularProfileUsingPOST(
{
projection: 'DETAILED',
molecularProfileId: p.molecularProfileId,
molecularDataFilter: {
sampleIds: this.sampleIds,
} as MolecularDataFilter,
}
);
data.map(d => {
if (!proteinExpressionMap[d.entrezGeneId]) {
proteinExpressionMap[d.entrezGeneId] = {};
}
if (
!proteinExpressionMap[d.entrezGeneId][
d.molecularProfileId
]
) {
proteinExpressionMap[d.entrezGeneId][
d.molecularProfileId
] = [];
}
proteinExpressionMap[d.entrezGeneId][
d.molecularProfileId
].push(d);
});
})
);
return proteinExpressionMap;
},
default: {},
});

readonly proteinExpressionProfiles = remoteData(
{
await: () => [this.molecularProfilesInStudy],
invoke: () => {
return Promise.resolve(
this.molecularProfilesInStudy.result.filter(
p => p.molecularAlterationType === 'PROTEIN_LEVEL'
)
);
},
},
[]
);

readonly analysisProteinExpressionProfiles = remoteData(
{
await: () => [this.proteinExpressionProfiles],
invoke: () => {
return Promise.resolve(
this.proteinExpressionProfiles.result.filter(
p => p.showProfileInAnalysisTab
)
);
},
},
[]
);

readonly isExpressionProfiledForPatient = remoteData({
await: () => [
this.mrnaExpressionProfiles,
this.proteinExpressionProfiles,
this.derivedUniquePatientKey,
this.coverageInformation,
],
invoke: () => {
const expressionProfileIds = [
...this.mrnaExpressionProfiles.result,
...this.proteinExpressionProfiles.result,
].map(p => p.molecularProfileId);
return Promise.resolve(
_.some(
isPatientProfiledInMultiple(
this.derivedUniquePatientKey.result,
expressionProfileIds,
this.coverageInformation.result
)
)
);
},
});

// public set patientIdsInCohort(cohortIds: string[]) {
// // cannot put action on setter
// runInAction(() => (this._patientIdsInCohort = cohortIds || []));
Expand Down Expand Up @@ -819,6 +1073,16 @@ export class PatientViewPageStore {
default: '',
});

readonly derivedUniquePatientKey = remoteData<string>({
await: () => [this.samples],
invoke: async () => {
for (let sample of this.samples.result)
return sample.uniquePatientKey;
return '';
},
default: '',
});

readonly clinicalDataPatient = remoteData({
await: () =>
this.pageMode === 'patient' ? [] : [this.derivedPatientId],
Expand Down
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