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Add Variant Allele Frequency Heatmap in Oncoprint - GSoC'25 #5237

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Add Variant Allele Frequency Heatmap in Oncoprint - GSoC'25 #5237

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c191c82
Variant Allele frequencyheatmap in oncoprint
rishisulakhe Jul 9, 2025
6158c56
Await mutations by gene promise
rishisulakhe Jul 15, 2025
7a86549
Fix vaf heatmap data promise
rishisulakhe Jul 17, 2025
cd4ce89
function for gene profile
rishisulakhe Jul 20, 2025
1b6a0f4
Another function for heatmap tracks data
rishisulakhe Jul 24, 2025
5357a0f
Resolves rendering inconsistency where track addition order affected …
rishisulakhe Jul 25, 2025
fb1cd6b
Extract mutation query filtering from remoteData await function
rishisulakhe Aug 14, 2025
ac9d984
Types for geneCache and molecular data
rishisulakhe Aug 18, 2025
baf0874
Fix VAF heatmap option showing when no data available
rishisulakhe Sep 1, 2025
9d720b9
Fix VAF heatmap display for profiled samples without mutations
rishisulakhe Sep 6, 2025
512fb4e
fix unit tests for heatmap track data
rishisulakhe Sep 27, 2025
c7063b3
fix VAF heatmap header
rishisulakhe Nov 17, 2025
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30 changes: 26 additions & 4 deletions src/pages/resultsView/ResultsViewPageStore.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4460,16 +4460,19 @@ export class ResultsViewPageStore extends AnalysisStore
this.molecularProfilesInStudies,
this.selectedMolecularProfiles,
this.genesetMolecularProfile,
this.hasVAFData,
],
invoke: () => {
const MRNA_EXPRESSION = AlterationTypeConstants.MRNA_EXPRESSION;
const PROTEIN_LEVEL = AlterationTypeConstants.PROTEIN_LEVEL;
const METHYLATION = AlterationTypeConstants.METHYLATION;
const MUTATION_EXTENDED = AlterationTypeConstants.MUTATION_EXTENDED;
const selectedMolecularProfileIds = stringListToSet(
this.selectedMolecularProfiles.result!.map(
profile => profile.molecularProfileId
)
);
const hasVAF = this.hasVAFData.result;

const expressionHeatmaps = _.sortBy(
_.filter(this.molecularProfilesInStudies.result!, profile => {
Expand All @@ -4480,7 +4483,10 @@ export class ResultsViewPageStore extends AnalysisStore
profile.molecularAlterationType ===
PROTEIN_LEVEL) &&
profile.showProfileInAnalysisTab) ||
profile.molecularAlterationType === METHYLATION
profile.molecularAlterationType === METHYLATION ||
(profile.molecularAlterationType ===
MUTATION_EXTENDED &&
hasVAF)
);
}),
profile => {
Expand All @@ -4496,15 +4502,19 @@ export class ResultsViewPageStore extends AnalysisStore
return 1;
case METHYLATION:
return 2;
case MUTATION_EXTENDED:
return 3;
}
} else {
switch (profile.molecularAlterationType) {
case MRNA_EXPRESSION:
return 3;
case PROTEIN_LEVEL:
return 4;
case METHYLATION:
case PROTEIN_LEVEL:
return 5;
case METHYLATION:
return 6;
case MUTATION_EXTENDED:
return 7;
}
}
}
Expand All @@ -4518,6 +4528,18 @@ export class ResultsViewPageStore extends AnalysisStore
},
});

readonly hasVAFData = remoteData<boolean>({
await: () => [this.mutations],
invoke: () => {
const hasVAF = this.mutations.result!.some(
m => _.isFinite(m.tumorAltCount) && _.isFinite(m.tumorRefCount)
);

return Promise.resolve(hasVAF);
},
default: false,
});

readonly genesetMolecularProfile = remoteData<Optional<MolecularProfile>>({
await: () => [this.selectedMolecularProfiles],
invoke: () => {
Expand Down
144 changes: 129 additions & 15 deletions src/shared/components/oncoprint/DataUtils.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ import {
fillGeneticTrackDatum,
fillHeatmapTrackDatum,
getOncoprintMutationType,
HeatmapCaseDatum,
makeGeneticTrackData,
selectDisplayValue,
} from './DataUtils';
Expand Down Expand Up @@ -1554,7 +1555,12 @@ describe('DataUtils', () => {
{ sampleId: 'sample', studyId: 'study' } as Sample,
data
),
{ hugo_gene_symbol: 'gene', study_id: 'study', profile_data: 3 }
{
hugo_gene_symbol: 'gene',
study_id: 'study',
na: false,
profile_data: 3,
}
);
});
it('removes data points with NaN value', () => {
Expand All @@ -1570,7 +1576,12 @@ describe('DataUtils', () => {
{ sampleId: 'sample', studyId: 'study' } as Sample,
data
),
{ hugo_gene_symbol: 'gene', study_id: 'study', profile_data: 3 }
{
hugo_gene_symbol: 'gene',
study_id: 'study',
na: false,
profile_data: 3,
}
);
});
it('throws exception if more than one data given for sample', () => {
Expand Down Expand Up @@ -1604,7 +1615,12 @@ describe('DataUtils', () => {
{ patientId: 'patient', studyId: 'study' } as Sample,
data
),
{ hugo_gene_symbol: 'gene', study_id: 'study', profile_data: 3 }
{
hugo_gene_symbol: 'gene',
study_id: 'study',
na: false,
profile_data: 3,
}
);

data = [{ value: 2 }];
Expand All @@ -1619,7 +1635,12 @@ describe('DataUtils', () => {
{ patientId: 'patient', studyId: 'study' } as Sample,
data
),
{ hugo_gene_symbol: 'gene', study_id: 'study', profile_data: 2 }
{
hugo_gene_symbol: 'gene',
study_id: 'study',
na: false,
profile_data: 2,
}
);

data = [{ value: 2 }, { value: 3 }, { value: 4 }];
Expand All @@ -1634,7 +1655,12 @@ describe('DataUtils', () => {
{ patientId: 'patient', studyId: 'study' } as Sample,
data
),
{ hugo_gene_symbol: 'gene', study_id: 'study', profile_data: 4 }
{
hugo_gene_symbol: 'gene',
study_id: 'study',
na: false,
profile_data: 4,
}
);

data = [{ value: -10 }, { value: 3 }, { value: 4 }];
Expand All @@ -1652,6 +1678,7 @@ describe('DataUtils', () => {
{
hugo_gene_symbol: 'gene',
study_id: 'study',
na: false,
profile_data: -10,
}
);
Expand All @@ -1663,17 +1690,31 @@ describe('DataUtils', () => {
'geneset_id',
'MY_FAVORITE_GENE_SET-3',
{ sampleId: 'sample', studyId: 'study' } as Sample,
[{ value: 7 }]
[
{
value: 7,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key',
},
]
);
assert.deepEqual(partialTrackDatum, {
geneset_id: 'MY_FAVORITE_GENE_SET-3',
study_id: 'study',
na: false,
profile_data: 7,
});
});

it('adds thresholdType and category to trackDatum', () => {
let data = [{ value: 8, thresholdType: '>' as '>' }];
let data: HeatmapCaseDatum[] = [
{
value: 8,
thresholdType: '>' as '>',
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key',
},
];
const partialTrackDatum = {};
fillHeatmapTrackDatum<IGenericAssayHeatmapTrackDatum, 'entityId'>(
partialTrackDatum,
Expand All @@ -1685,14 +1726,31 @@ describe('DataUtils', () => {
assert.deepEqual(partialTrackDatum, {
entityId: 'GENERIC_ASSAY_ID_1',
study_id: 'study',
na: false,
profile_data: 8,
thresholdType: '>',
category: '>8.00',
});
});

it('returns smallest value with ASC sort order', () => {
let data = [{ value: 1 }, { value: 2 }, { value: 3 }];
let data: HeatmapCaseDatum[] = [
{
value: 1,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_1',
},
{
value: 2,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_2',
},
{
value: 3,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_3',
},
];
const partialTrackDatum = {};
fillHeatmapTrackDatum<IGenericAssayHeatmapTrackDatum, 'entityId'>(
partialTrackDatum,
Expand All @@ -1705,12 +1763,29 @@ describe('DataUtils', () => {
assert.deepEqual(partialTrackDatum, {
entityId: 'GENERIC_ASSAY_ID_1',
study_id: 'study',
na: false,
profile_data: 1,
});
});

it('returns largest value with DESC sort order', () => {
let data = [{ value: 1 }, { value: 2 }, { value: 3 }];
let data: HeatmapCaseDatum[] = [
{
value: 1,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_1',
},
{
value: 2,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_2',
},
{
value: 3,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_3',
},
];
const partialTrackDatum = {};
fillHeatmapTrackDatum<IGenericAssayHeatmapTrackDatum, 'entityId'>(
partialTrackDatum,
Expand All @@ -1723,12 +1798,29 @@ describe('DataUtils', () => {
assert.deepEqual(partialTrackDatum, {
entityId: 'GENERIC_ASSAY_ID_1',
study_id: 'study',
na: false,
profile_data: 3,
});
});

it('selects non-threshold over threshold data point when values are equal', () => {
let data = [{ value: 1, thresholdType: '>' as '>' }, { value: 1 }];
let data: HeatmapCaseDatum[] = [
{
value: 1,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_1',
},
{
value: 2,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_2',
},
{
value: 3,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_3',
},
];
const partialTrackDatum = {};
fillHeatmapTrackDatum<IGenericAssayHeatmapTrackDatum, 'entityId'>(
partialTrackDatum,
Expand All @@ -1740,12 +1832,24 @@ describe('DataUtils', () => {
assert.deepEqual(partialTrackDatum, {
entityId: 'GENERIC_ASSAY_ID_1',
study_id: 'study',
profile_data: 1,
na: false,
profile_data: 3,
});
});

it('handles all NaN-value data points', () => {
let data = [{ value: NaN }, { value: NaN }];
let data: HeatmapCaseDatum[] = [
{
value: NaN,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_1',
},
{
value: NaN,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_2',
},
];
const partialTrackDatum = {} as IGenericAssayHeatmapTrackDatum;
fillHeatmapTrackDatum<IGenericAssayHeatmapTrackDatum, 'entityId'>(
partialTrackDatum,
Expand All @@ -1759,9 +1863,18 @@ describe('DataUtils', () => {
});

it('Prefers largest non-threshold absolute value when no sort order provided', () => {
let data = [
{ value: -10 },
{ value: 10, thresholdType: '>' as '>' },
let data: HeatmapCaseDatum[] = [
{
value: -10,
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_1',
},
{
value: 10,
thresholdType: '>' as '>',
uniquePatientKey: 'patient_key',
uniqueSampleKey: 'sample_key_2',
},
];
const partialTrackDatum = {};
fillHeatmapTrackDatum<IGenericAssayHeatmapTrackDatum, 'entityId'>(
Expand All @@ -1774,6 +1887,7 @@ describe('DataUtils', () => {
assert.deepEqual(partialTrackDatum, {
entityId: 'GENERIC_ASSAY_ID_1',
study_id: 'study',
na: false,
profile_data: -10,
});
});
Expand Down
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