From 075074e2e63643e772f1ec7436debac35b517081 Mon Sep 17 00:00:00 2001 From: Qi-Xuan Lu Date: Fri, 5 Apr 2024 14:40:27 -0400 Subject: [PATCH] Mutation pie chart and multi-selection table (#4794) * group gene selection options by alteration type * add mutation-data-counts endpoint and revamp renderAttributes giant switch statements * add sub menu options for mutation profile * get mutation data and fix display text on add chart * fix filter and show pill tags for mutation count data * add mutation type table and disable group comparison * get mutation table download data * support and fix intersect and union selection on mutation table * ui update for mutation chart * fix pilltags, apis, and select * cleanup code * resolve comments from Karthik * resolve Aaron's comments * resolve Study View Page missing data * fix selecting more rows in mutation counts table * fix pilltag errors on intersection selection * rename wild type to mutation type * fix type errors and conflicts * fix GenomicDataCount * fix e2e tests on SummaryTab * update any to Partial in SummaryTab * resolve Aaron's comments * remove categories grouping and change colors for mutation pie chart * fix mutation categories type assertion * revert colors.ts changes and add callback to change Mutated vs Wild Type pie chart --------- Co-authored-by: Qi-Xuan Lu --- ...ical_selector_element_chrome_1600x1000.png | Bin 22306 -> 22519 bytes .../src/generated/CBioPortalAPIInternal.ts | 171 ++- src/pages/studyView/StudyViewConfig.ts | 7 + src/pages/studyView/StudyViewPageStore.ts | 924 ++++++------- src/pages/studyView/StudyViewUtils.tsx | 626 ++++++++- src/pages/studyView/UserSelections.tsx | 91 +- .../addChartButton/AddChartButton.tsx | 3 +- .../geneLevelSelection/GeneLevelSelection.tsx | 100 +- src/pages/studyView/charts/ChartContainer.tsx | 78 +- .../studyPageHeader/StudyPageHeader.tsx | 3 + .../studyView/table/MultiSelectionTable.tsx | 59 +- src/pages/studyView/tabs/SummaryTab.tsx | 1157 +++++++++-------- 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a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts +++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts @@ -714,10 +714,10 @@ export type GenomicDataBinFilter = { export type GenomicDataCount = { 'count': number - 'label': string - 'uniqueCount': number + 'label': string + 'value': string }; @@ -907,9 +907,8 @@ export type MutationDataFilter = { 'profileType': string - 'values': Array < Array < DataFilterValue > - > - + 'values': Array < Array< DataFilterValue > > + }; export type MutationPositionIdentifier = { 'entrezGeneId': number @@ -4815,6 +4814,85 @@ export default class CBioPortalAPIInternal { return response.body; }); }; + + fetchMutationDataCountsUsingPOSTURL(parameters: { + 'genomicDataCountFilter': GenomicDataCountFilter, + $queryParameters ? : any + }): string { + let queryParameters: any = {}; + let path = '/api/mutation-data-counts/fetch'; + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + let keys = Object.keys(queryParameters); + return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); + }; + + /** + * Fetch mutation data counts by GenomicDataCountFilter + * @method + * @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST + * @param {} genomicDataCountFilter - Genomic data count filter + */ + fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters: { + 'genomicDataCountFilter': GenomicDataCountFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < request.Response > { + const domain = parameters.$domain ? parameters.$domain : this.domain; + const errorHandlers = this.errorHandlers; + const request = this.request; + let path = '/api/mutation-data-counts/fetch'; + let body: any; + let queryParameters: any = {}; + let headers: any = {}; + let form: any = {}; + return new Promise(function(resolve, reject) { + headers['Accept'] = 'application/json'; + headers['Content-Type'] = 'application/json'; + + if (parameters['genomicDataCountFilter'] !== undefined) { + body = parameters['genomicDataCountFilter']; + } + + if (parameters['genomicDataCountFilter'] === undefined) { + reject(new Error('Missing required parameter: genomicDataCountFilter')); + return; + } + + if (parameters.$queryParameters) { + Object.keys(parameters.$queryParameters).forEach(function(parameterName) { + var parameter = parameters.$queryParameters[parameterName]; + queryParameters[parameterName] = parameter; + }); + } + + request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); + + }); + }; + + /** + * Fetch mutation data counts by GenomicDataCountFilter + * @method + * @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST + * @param {} genomicDataCountFilter - Genomic data count filter + */ + fetchMutationDataCountsUsingPOST(parameters: { + 'genomicDataCountFilter': GenomicDataCountFilter, + $queryParameters ? : any, + $domain ? : string + }): Promise < Array < GenomicDataCountItem > + > { + return this.fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { + return response.body; + }); + }; + fetchMolecularProfileSampleCountsUsingPOSTURL(parameters: { 'studyViewFilter' ? : StudyViewFilter, $queryParameters ? : any @@ -5542,89 +5620,6 @@ export default class CBioPortalAPIInternal { return response.body; }); }; - fetchMutationDataCountsUsingPOSTURL(parameters: { - 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", - 'genomicDataCountFilter' ? : GenomicDataCountFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/mutation-data-counts/fetch'; - if (parameters['projection'] !== undefined) { - queryParameters['projection'] = parameters['projection']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Fetch mutation data counts by GenomicDataCountFilter - * @method - * @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST - * @param {string} projection - Level of detail of the response - * @param {} genomicDataCountFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters: { - 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", - 'genomicDataCountFilter' ? : GenomicDataCountFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/mutation-data-counts/fetch'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['projection'] !== undefined) { - queryParameters['projection'] = parameters['projection']; - } - - if (parameters['genomicDataCountFilter'] !== undefined) { - body = parameters['genomicDataCountFilter']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Fetch mutation data counts by GenomicDataCountFilter - * @method - * @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST - * @param {string} projection - Level of detail of the response - * @param {} genomicDataCountFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change. - */ - fetchMutationDataCountsUsingPOST(parameters: { - 'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META", - 'genomicDataCountFilter' ? : GenomicDataCountFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < ResponseEntityListGenomicDataCountItem > { - return this.fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; getAllReferenceGenomeGenesUsingGETURL(parameters: { 'genomeName': string, $queryParameters ? : any diff --git a/src/pages/studyView/StudyViewConfig.ts b/src/pages/studyView/StudyViewConfig.ts index 5c87f20b3aa..166ef974a1f 100644 --- a/src/pages/studyView/StudyViewConfig.ts +++ b/src/pages/studyView/StudyViewConfig.ts @@ -69,6 +69,7 @@ export enum ChartTypeEnum { SCATTER = 'SCATTER', VIOLIN_PLOT_TABLE = 'VIOLIN_PLOT_TABLE', MUTATED_GENES_TABLE = 'MUTATED_GENES_TABLE', + MUTATION_TYPE_COUNTS_TABLE = 'MUTATION_TYPE_COUNTS_TABLE', STRUCTURAL_VARIANT_GENES_TABLE = 'STRUCTURAL_VARIANT_GENES_TABLE', STRUCTURAL_VARIANTS_TABLE = 'STRUCTURAL_VARIANTS_TABLE', CNA_GENES_TABLE = 'CNA_GENES_TABLE', @@ -92,6 +93,7 @@ export enum ChartTypeNameEnum { SCATTER = 'density plot', VIOLIN_PLOT_TABLE = 'table', MUTATED_GENES_TABLE = 'table', + MUTATION_TYPE_COUNTS_TABLE = 'table', STRUCTURAL_VARIANT_GENES_TABLE = 'table', STRUCTURAL_VARIANTS_TABLE = 'table', CNA_GENES_TABLE = 'table', @@ -207,6 +209,11 @@ const studyViewFrontEnd = { h: 2, minW: 2, }, + [ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE]: { + w: 2, + h: 2, + minW: 2, + }, [ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE]: { w: 2, h: 2, diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts index 7cfca8f2d77..44e28488c05 100644 --- a/src/pages/studyView/StudyViewPageStore.ts +++ b/src/pages/studyView/StudyViewPageStore.ts @@ -45,8 +45,6 @@ import { GenericAssayData, GenericAssayDataBin, GenericAssayDataBinFilter, - GenericAssayDataCountFilter, - GenericAssayDataCountItem, GenericAssayDataFilter, GenericAssayDataMultipleStudyFilter, GenericAssayMeta, @@ -58,6 +56,7 @@ import { MolecularDataMultipleStudyFilter, MolecularProfile, MolecularProfileFilter, + MutationDataFilter, Mutation, MutationFilter, MutationMultipleStudyFilter, @@ -127,7 +126,6 @@ import { findInvalidMolecularProfileIds, geneFilterQueryFromOql, geneFilterQueryToOql, - generateXvsYScatterPlotDownloadData, getAllClinicalDataByStudyViewFilter, getBinBounds, getCategoricalFilterValues, @@ -135,7 +133,6 @@ import { getChartSettingsMap, getClinicalDataCountWithColorByClinicalDataCount, getCNAByAlteration, - getCNAColorByAlteration, getCNASamplesCount, getDataIntervalFilterValues, getDefaultPriorityByUniqueKey, @@ -143,7 +140,6 @@ import { getFilteredMolecularProfilesByAlterationType, getFilteredSampleIdentifiers, getFilteredStudiesWithSamples, - getFrequencyStr, getGenericAssayChartUniqueKey, getGenericAssayDataAsClinicalData, getGenomicChartUniqueKey, @@ -153,10 +149,8 @@ import { getMolecularProfileIdsFromUniqueKey, getNonZeroUniqueBins, getPriorityByClinicalAttribute, - getQValue, getRequestedAwaitPromisesForClinicalData, getSamplesByExcludingFiltersOnChart, - getSampleToClinicalData, getStructuralVariantSamplesCount, getUniqueKey, getUniqueKeyFromGeneFilterMolecularProfileIds, @@ -181,6 +175,13 @@ import { submitToPage, transformSampleDataToSelectedSampleClinicalData, updateCustomIntervalFilter, + invokeGenomicDataCount, + invokeMutationDataCount, + invokeGenericAssayDataCount, + getDefaultClinicalDataBinFilter, + getCustomChartDownloadData, + generateColorMapKey, + MutationCategorization, } from './StudyViewUtils'; import { SingleGeneQuery } from 'shared/lib/oql/oql-parser'; import autobind from 'autobind-decorator'; @@ -231,7 +232,7 @@ import { StudyViewComparisonGroup, } from '../groupComparison/GroupComparisonUtils'; import { LoadingPhase } from '../groupComparison/GroupComparisonLoading'; -import { sleep, sleepUntil } from '../../shared/lib/TimeUtils'; +import { sleepUntil } from '../../shared/lib/TimeUtils'; import ComplexKeyMap from '../../shared/lib/complexKeyDataStructures/ComplexKeyMap'; import MobxPromiseCache from 'shared/lib/MobxPromiseCache'; import { CancerGene, IndicatorQueryResp } from 'oncokb-ts-api-client'; @@ -248,6 +249,8 @@ import { StudyViewPageTabKeyEnum } from 'pages/studyView/StudyViewPageTabs'; import { AlterationTypeConstants, DataTypeConstants, + MutationOptionConstants, + MutationOptionConstantsLabel, REQUEST_ARG_ENUM, } from 'shared/constants'; import { @@ -456,6 +459,7 @@ export type GenomicChart = { profileType: string; hugoGeneSymbol: string; dataType?: string; + mutationOptionType?: string; }; export type GenericAssayChart = { @@ -1990,6 +1994,7 @@ export class StudyViewPageStore const chartInfo = this._geneSpecificChartMap.get( chartMeta.uniqueKey )!; + comparisonId = await this.createCnaGeneComparisonSession( chartMeta, [chartInfo.hugoGeneSymbol], @@ -2096,6 +2101,10 @@ export class StudyViewPageStore ChartUniqueKey, GenomicDataFilter >({}, { deep: false }); + private _mutationDataFilterSet = observable.map< + ChartUniqueKey, + MutationDataFilter + >({}, { deep: false }); private _genericAssayDataFilterSet = observable.map< ChartUniqueKey, GenericAssayDataFilter @@ -2275,6 +2284,20 @@ export class StudyViewPageStore }); } + if (!_.isEmpty(filters.mutationDataFilters)) { + filters.mutationDataFilters!.forEach(mutationDataFilter => { + const uniqueKey = getGenomicChartUniqueKey( + mutationDataFilter.hugoGeneSymbol, + mutationDataFilter.profileType, + mutationDataFilter.categorization + ); + this._mutationDataFilterSet.set( + uniqueKey, + _.clone(mutationDataFilter) + ); + }); + } + if (!_.isEmpty(filters.genericAssayDataFilters)) { filters.genericAssayDataFilters!.forEach(genericAssayDataFilter => { const uniqueKey = getGenericAssayChartUniqueKey( @@ -2465,6 +2488,9 @@ export class StudyViewPageStore public genomicDataCountPromises: { [id: string]: MobxPromise; } = {}; + public mutationDataCountPromises: { + [id: string]: MobxPromise; + } = {}; public genericAssayChartPromises: { [id: string]: MobxPromise; } = {}; @@ -2821,6 +2847,7 @@ export class StudyViewPageStore this._geneFilterSet.clear(); this._structVarFilterSet.clear(); this._genomicDataFilterSet.clear(); + this._mutationDataFilterSet.clear(); this._genericAssayDataFilterSet.clear(); this._chartSampleIdentifiersFilterSet.clear(); this.preDefinedCustomChartFilterSet.clear(); @@ -3102,13 +3129,116 @@ export class StudyViewPageStore ): void { trackStudyViewFilterEvent('genomicCategoricalData', this); + const chart = this._geneSpecificChartMap.get(uniqueKey); const dataFilterValues: DataFilterValue[] = getCategoricalFilterValues( values ); - this.updateGenomicDataFiltersByValues( - uniqueKey, - _.cloneDeep(dataFilterValues) + if (chart!.mutationOptionType) { + this.updateMutationDataFilters(uniqueKey, [_.cloneDeep(values)]); + } else { + this.updateGenomicDataFiltersByValues( + uniqueKey, + _.cloneDeep(dataFilterValues) + ); + } + } + + @action.bound + updateMutationDataFilters( + uniqueKey: string, + valueArrays: string[][] + ): void { + trackStudyViewFilterEvent('mutationCategoricalData', this); + + // valueArrays represent a two-dimensional array that supports union and + // intersection selection on samples + if (_.some(valueArrays, valueArray => valueArray.length !== 0)) { + const dataFilterValues: DataFilterValue[][] = valueArrays.map( + valueArray => + valueArray.map(value => { + return { value: value } as DataFilterValue; + }) + ); + const chart = this._geneSpecificChartMap.get(uniqueKey); + const mutationDataFilter: MutationDataFilter = { + hugoGeneSymbol: chart!.hugoGeneSymbol, + profileType: chart!.profileType, + values: dataFilterValues, + categorization: chart! + .mutationOptionType! as MutationCategorization, + }; + this._mutationDataFilterSet.set(uniqueKey, mutationDataFilter); + } else { + // delete mutationDataFilter if valueArrays is empty + this._mutationDataFilterSet.delete(uniqueKey); + } + } + + @action.bound + addMutationDataFilters(uniqueKey: string, valueArrays: string[][]): void { + trackStudyViewFilterEvent('mutationCategoricalData', this); + + let dataFilterValues: DataFilterValue[][] = valueArrays.map( + valueArray => + valueArray.map(value => { + return { value: value } as DataFilterValue; + }) ); + + if (this._mutationDataFilterSet.has(uniqueKey)) { + const values = toJS( + this._mutationDataFilterSet.get(uniqueKey)!.values + ); + + dataFilterValues = values.concat(dataFilterValues); + } + + const chart = this._geneSpecificChartMap.get(uniqueKey); + const mutationDataFilter: MutationDataFilter = { + hugoGeneSymbol: chart!.hugoGeneSymbol, + profileType: chart!.profileType, + values: dataFilterValues, + categorization: chart! + .mutationOptionType! as MutationCategorization, + }; + this._mutationDataFilterSet.set(uniqueKey, mutationDataFilter); + } + + @action.bound + removeMutationDataFilter(uniqueKey: string, toBeRemoved: string): void { + const dataFilterValues = toJS( + this._mutationDataFilterSet.get(uniqueKey)!.values + ); + + const newDataFilterValues = _.reduce( + dataFilterValues, + (acc, next: DataFilterValue[]) => { + const newGroup = next.filter( + dataFilterValue => dataFilterValue.value !== toBeRemoved + ); + if (newGroup.length > 0) { + acc.push(newGroup); + } + + return acc; + }, + [] as DataFilterValue[][] + ); + + if (newDataFilterValues.length === 0) { + this._mutationDataFilterSet.delete(uniqueKey); + } else { + const chart = this._geneSpecificChartMap.get(uniqueKey); + const newMutationDataFilter: MutationDataFilter = { + hugoGeneSymbol: chart!.hugoGeneSymbol, + profileType: chart!.profileType, + values: newDataFilterValues, + categorization: chart! + .mutationOptionType! as MutationCategorization, + }; + + this._mutationDataFilterSet.set(uniqueKey, newMutationDataFilter); + } } @action.bound @@ -3270,6 +3400,9 @@ export class StudyViewPageStore hugoGeneSymbol: chart!.hugoGeneSymbol, profileType: chart!.profileType, values: values, + ...(chart!.mutationOptionType + ? { categorization: chart!.mutationOptionType } + : {}), }; this._genomicDataFilterSet.set(uniqueKey, genomicDataFilter); } else { @@ -3503,6 +3636,19 @@ export class StudyViewPageStore return DataType.NUMBER; } + public getChartMetaDataType(uniqueKey: string): ChartMetaDataTypeEnum { + if (this.isGeneSpecificChart(uniqueKey)) { + return ChartMetaDataTypeEnum.GENE_SPECIFIC; + } else if (this.isGenericAssayChart(uniqueKey)) { + return ChartMetaDataTypeEnum.GENERIC_ASSAY; + } else if (this.isUserDefinedCustomDataChart(uniqueKey)) { + return ChartMetaDataTypeEnum.CUSTOM_DATA; + } else { + // Always returns CLINICAL chart if no other chart types matched + return ChartMetaDataTypeEnum.CLINICAL; + } + } + @action changeChartVisibility(uniqueKey: string, visible: boolean): void { if (visible) { @@ -3571,6 +3717,9 @@ export class StudyViewPageStore case ChartTypeEnum.CNA_GENES_TABLE: this.resetGeneFilter(chartUniqueKey); break; + case ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE: + this.updateMutationDataFilters(chartUniqueKey, [[]]); + break; case ChartTypeEnum.GENOMIC_PROFILES_TABLE: this.setGenomicProfilesFilter([]); break; @@ -3607,6 +3756,7 @@ export class StudyViewPageStore ); this.preDefinedCustomChartFilterSet.delete(chartUniqueKey); this._genomicDataFilterSet.delete(chartUniqueKey); + this._mutationDataFilterSet.delete(chartUniqueKey); this._genericAssayDataFilterSet.delete(chartUniqueKey); break; @@ -3653,6 +3803,8 @@ export class StudyViewPageStore case ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE: case ChartTypeEnum.CNA_GENES_TABLE: return this._geneFilterSet.has(chartUniqueKey); + case ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE: + return this._mutationDataFilterSet.has(chartUniqueKey); case ChartTypeEnum.STRUCTURAL_VARIANTS_TABLE: return this._structVarFilterSet.has(chartUniqueKey); case ChartTypeEnum.GENOMIC_PROFILES_TABLE: @@ -3951,6 +4103,10 @@ export class StudyViewPageStore return Array.from(this._genomicDataFilterSet.values()); } + @computed get mutationDataFilters(): MutationDataFilter[] { + return Array.from(this._mutationDataFilterSet.values()); + } + @computed get genericAssayDataFilters(): GenericAssayDataFilter[] { return Array.from(this._genericAssayDataFilterSet.values()); } @@ -3964,15 +4120,25 @@ export class StudyViewPageStore get filtersProxy(): StudyViewFilter { const filters: Partial = {}; - const genomicDataFilters = this.genomicDataFilters; + if (this.genomicDataFilters.length > 0) { + filters.genomicDataFilters = this.genomicDataFilters; + } - if (genomicDataFilters.length > 0) { - filters.genomicDataFilters = genomicDataFilters; + if (this.mutationDataFilters.length > 0) { + filters.mutationDataFilters = this.mutationDataFilters.map( + filter => { + return { + ...filter, + categorization: filter.categorization as + | 'MUTATED' + | 'MUTATION_TYPE', + }; + } + ); } - const genericAssayDataFilters = this.genericAssayDataFilters; - if (genericAssayDataFilters.length > 0) { - filters.genericAssayDataFilters = genericAssayDataFilters; + if (this.genericAssayDataFilters.length > 0) { + filters.genericAssayDataFilters = this.genericAssayDataFilters; } if (this.clinicalDataFilters.length > 0) { @@ -4191,6 +4357,15 @@ export class StudyViewPageStore : []; } + @autobind + public getMutationDataFiltersByUniqueKey(uniqueKey: string): string[][] { + return this._mutationDataFilterSet.has(uniqueKey) + ? this._mutationDataFilterSet.get(uniqueKey)!.values.map(value => { + return value.map(innerValue => innerValue.value); + }) + : []; + } + @autobind public getGenericAssayDataFiltersByUniqueKey( uniqueKey: string @@ -4488,6 +4663,63 @@ export class StudyViewPageStore this.changeChartVisibility(uniqueKey, false); } + public addColorToCategories( + counts: ClinicalDataCount[], + attributeId: string, + getDisplayedValue?: (value: string) => string, + getDisplayedColor?: (value: string) => string + ): ClinicalDataCountSummary[] { + return getClinicalDataCountWithColorByClinicalDataCount(counts).map( + item => { + if (getDisplayedValue) { + item.displayedValue = getDisplayedValue(item.value); + } + + if (getDisplayedColor) { + return { + ...item, + color: getDisplayedColor(item.value), + }; + } + + let colorMapKey = generateColorMapKey(attributeId, item.value); + // If the item doesn't has an assigned color + if (!this.chartItemToColor.has(colorMapKey)) { + // If the color has not been used + if ( + !this.chartToUsedColors + .get(attributeId) + ?.has(item.color) + ) { + this.chartItemToColor.set(colorMapKey, item.color); + this.chartToUsedColors + .get(attributeId) + ?.add(item.color); + } else { + // Pick up a new color if the color has been used + let d = { + value: item.value, + count: item.count, + }; + let newColor = pickNewColorForClinicData( + d, + this.chartToUsedColors.get(attributeId) || new Set() + ); + this.chartItemToColor.set(colorMapKey, newColor); + this.chartToUsedColors.get(attributeId)?.add(newColor); + item.color = newColor; + } + return item; + } else { + return { + ...item, + color: this.chartItemToColor.get(colorMapKey)!, + }; + } + } + ); + } + public getClinicalDataCount( chartMeta: ChartMeta ): MobxPromise { @@ -4577,66 +4809,6 @@ export class StudyViewPageStore return this.clinicalDataCountPromises[uniqueKey]; } - private addColorToCategories( - counts: ClinicalDataCount[], - attributeId: string, - getDisplayedValue?: (value: string) => string, - getDisplayedColor?: (value: string) => string - ): ClinicalDataCountSummary[] { - return getClinicalDataCountWithColorByClinicalDataCount(counts).map( - item => { - if (getDisplayedValue) { - item.displayedValue = getDisplayedValue(item.value); - } - - if (getDisplayedColor) { - return { - ...item, - color: getDisplayedColor(item.value), - }; - } - - let colorMapKey = this.generateColorMapKey( - attributeId, - item.value - ); - // If the item doesn't has an assigned color - if (!this.chartItemToColor.has(colorMapKey)) { - // If the color has not been used - if ( - !this.chartToUsedColors - .get(attributeId) - ?.has(item.color) - ) { - this.chartItemToColor.set(colorMapKey, item.color); - this.chartToUsedColors - .get(attributeId) - ?.add(item.color); - } else { - // Pick up a new color if the color has been used - let d = { - value: item.value, - count: item.count, - }; - let newColor = pickNewColorForClinicData( - d, - this.chartToUsedColors.get(attributeId) || new Set() - ); - this.chartItemToColor.set(colorMapKey, newColor); - this.chartToUsedColors.get(attributeId)?.add(newColor); - item.color = newColor; - } - return item; - } else { - return { - ...item, - color: this.chartItemToColor.get(colorMapKey)!, - }; - } - } - ); - } - public getCustomDataCount( chartMeta: ChartMeta ): MobxPromise { @@ -4752,7 +4924,7 @@ export class StudyViewPageStore invoke: async () => { let resultDataBins: DataBin[] = []; if (!this._customDataBinFilterSet.has(uniqueKey)) { - const attribute: ClinicalDataBinFilter = this.getDefaultClinicalDataBinFilter( + const attribute: ClinicalDataBinFilter = getDefaultClinicalDataBinFilter( chartMeta.clinicalAttribute! ); const result = await internalClient.fetchCustomDataBinCountsUsingPOST( @@ -4850,47 +5022,31 @@ export class StudyViewPageStore ] = remoteData({ await: () => [], invoke: async () => { - let res: ClinicalDataCountSummary[] = []; + const res: ClinicalDataCountSummary[] = []; const chartInfo = this._genericAssayChartMap.get( chartMeta.uniqueKey ); if (chartInfo) { - let result: GenericAssayDataCountItem[] = []; - - result = await internalClient.fetchGenericAssayDataCountsUsingPOST( - { - genericAssayDataCountFilter: { - genericAssayDataFilters: [ - { - stableId: - chartInfo.genericAssayEntityId, - profileType: chartInfo.profileType, - } as GenericAssayDataFilter, - ], - studyViewFilter: this.filters, - } as GenericAssayDataCountFilter, - } + const result = await invokeGenericAssayDataCount( + chartInfo, + this.filters ); - let data = result.find( - d => d.stableId === chartInfo.genericAssayEntityId - ); - let counts: ClinicalDataCount[] = []; - let stableId: string = ''; - if (data !== undefined) { - counts = data.counts.map(c => { - return { - count: c.count, - value: c.value, - } as ClinicalDataCount; - }); - stableId = data.stableId; - if (!this.chartToUsedColors.has(stableId)) { - this.chartToUsedColors.set(stableId, new Set()); - } + if (_.isEmpty(result)) { + return res; } - return this.addColorToCategories(counts, stableId); + if (!this.chartToUsedColors.has(result!.stableId)) { + this.chartToUsedColors.set( + result!.stableId, + new Set() + ); + } + + return this.addColorToCategories( + result!.counts, + result!.stableId + ); } return res; }, @@ -4911,53 +5067,26 @@ export class StudyViewPageStore >({ await: () => [this.selectedSamples], invoke: async () => { - let res: ClinicalDataCountSummary[] = []; + const res: ClinicalDataCountSummary[] = []; const chartInfo = this._geneSpecificChartMap.get( chartMeta.uniqueKey ); //only invoke if there are filtered samples if (chartInfo && this.hasFilteredSamples) { - const result = await internalClient.fetchGenomicDataCountsUsingPOST( - { - genomicDataCountFilter: { - genomicDataFilters: [ - { - hugoGeneSymbol: - chartInfo.hugoGeneSymbol, - profileType: chartInfo.profileType, - }, - ] as any, - studyViewFilter: this.filters, - }, - } - ); - - let data = result.find( - d => - d.hugoGeneSymbol === chartInfo.hugoGeneSymbol && - d.profileType === chartInfo.profileType + const result = await invokeGenomicDataCount( + chartInfo, + this.filters ); - let counts: ClinicalDataCount[] = []; - let profileType: string = ''; - if (data !== undefined) { - counts = data.counts.map(c => { - return { - count: c.count, - value: c.value, - } as ClinicalDataCount; - }); - profileType = data.profileType; + if (_.isEmpty(result)) { + return res; } return this.addColorToCategories( - counts, - profileType, - getCNAByAlteration, - value => - getCNAColorByAlteration( - getCNAByAlteration(value) - ) + result!.counts, + result!.profileType, + result!.getDisplayedValue, + result!.getDisplayedColor ); } return res; @@ -4969,8 +5098,36 @@ export class StudyViewPageStore return this.genomicDataCountPromises[chartMeta.uniqueKey]; } - private generateColorMapKey(id: string, value: string): string { - return `${id}.${value}`; + public getMutationTypeChartDataCount( + chartMeta: ChartMeta + ): MobxPromise { + if ( + !this.mutationDataCountPromises.hasOwnProperty(chartMeta.uniqueKey) + ) { + this.mutationDataCountPromises[chartMeta.uniqueKey] = remoteData< + MultiSelectionTableRow[] + >({ + await: () => [this.selectedSamples], + invoke: async () => { + const res: MultiSelectionTableRow[] = []; + const chartInfo = this._geneSpecificChartMap.get( + chartMeta.uniqueKey + ); + // only invoke if there are filtered samples + if (chartInfo && this.hasFilteredSamples) { + return invokeMutationDataCount( + chartInfo, + this.filters, + this.selectedSamples.result.length + ); + } + return res; + }, + onError: () => {}, + default: [], + }); + } + return this.mutationDataCountPromises[chartMeta.uniqueKey]; } @autobind @@ -5583,18 +5740,6 @@ export class StudyViewPageStore ); } - private getDefaultClinicalDataBinFilter( - attribute: ClinicalAttribute - ): ClinicalDataBinFilter & { - showNA?: boolean | undefined; - } { - return { - attributeId: attribute.clinicalAttributeId, - disableLogScale: false, - showNA: false, - } as ClinicalDataBinFilter & { showNA?: boolean }; - } - readonly resourceDefinitions = remoteData({ await: () => [this.queriedPhysicalStudies], invoke: () => { @@ -5697,7 +5842,7 @@ export class StudyViewPageStore clinicalAttributes.forEach((obj: ClinicalAttribute) => { if (obj.datatype === DataType.NUMBER) { const uniqueKey = getUniqueKey(obj); - let filter = this.getDefaultClinicalDataBinFilter(obj); + let filter = getDefaultClinicalDataBinFilter(obj); if (STUDY_VIEW_CONFIG.initialBins[uniqueKey]) { filter.customBins = @@ -6238,7 +6383,8 @@ export class StudyViewPageStore newCharts.forEach(newChart => { const uniqueKey = getGenomicChartUniqueKey( newChart.hugoGeneSymbol, - newChart.profileType + newChart.profileType, + newChart.mutationOptionType ); if (this._geneSpecificChartMap.has(uniqueKey)) { @@ -6255,6 +6401,9 @@ export class StudyViewPageStore patientAttribute: false, renderWhenDataChange: false, priority: 0, + ...(newChart.mutationOptionType + ? { mutationOptionType: newChart.mutationOptionType } + : {}), }; this._geneSpecificCharts.set(uniqueKey, chartMeta); @@ -6272,6 +6421,21 @@ export class StudyViewPageStore profileType: newChart.profileType, } as any); this.chartsDimension.set(uniqueKey, { w: 2, h: 1 }); + } else if ( + newChart.mutationOptionType && + newChart.mutationOptionType === + MutationOptionConstants.MUTATION_TYPE + ) { + this.chartsType.set( + uniqueKey, + ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE + ); + this.chartsDimension.set( + uniqueKey, + STUDY_VIEW_CONFIG.layout.dimensions[ + ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE + ] + ); } else { this.chartsType.set(uniqueKey, ChartTypeEnum.PIE_CHART); this.chartsDimension.set( @@ -6769,6 +6933,9 @@ export class StudyViewPageStore if (!_.isEmpty(this.initialFilters.genomicDataFilters)) { pending = pending || this.molecularProfileOptions.isPending; } + if (!_.isEmpty(this.initialFilters.mutationDataFilters)) { + pending = pending || this.molecularProfileOptions.isPending; + } if (!_.isEmpty(this.initialFilters.genericAssayDataFilters)) { pending = pending || this.genericAssayProfileOptionsByType.isPending; @@ -7101,6 +7268,16 @@ export class StudyViewPageStore dataType: molecularProfileOption?.dataType || DataType.NUMBER, + ...(chartUserSettings.profileType === + MolecularAlterationType_filenameSuffix.MUTATION_EXTENDED + ? { + mutationOptionType: + chartUserSettings.chartType === + ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE + ? MutationOptionConstants.MUTATION_TYPE + : MutationOptionConstants.MUTATED, + } + : {}), }, ], true @@ -7701,7 +7878,7 @@ export class StudyViewPageStore invoke: async () => { return _.chain(this.defaultVisibleAttributes.result) .filter(attr => attr.datatype === DataType.NUMBER) - .map(this.getDefaultClinicalDataBinFilter) + .map(getDefaultClinicalDataBinFilter) .uniqBy(attr => attr.attributeId) .value(); }, @@ -7793,6 +7970,49 @@ export class StudyViewPageStore } ); } + + if (!_.isEmpty(this.initialFilters.mutationDataFilters)) { + const molecularProfileOptionByTypeMap = _.keyBy( + this.molecularProfileOptions.result, + molecularProfileOption => molecularProfileOption.value + ); + _.each( + this.initialFilters.mutationDataFilters, + mutationDataFilter => { + if ( + molecularProfileOptionByTypeMap[ + mutationDataFilter.profileType + ] !== undefined + ) { + const molecularProfileOption = + molecularProfileOptionByTypeMap[ + mutationDataFilter.profileType + ]; + this.addGeneSpecificCharts( + [ + { + name: `${ + mutationDataFilter.hugoGeneSymbol + }: ${mutationDataFilter.profileType}: ${ + MutationOptionConstantsLabel[ + mutationDataFilter.categorization + ] + }`, + description: molecularProfileOption.label, + profileType: mutationDataFilter.profileType, + hugoGeneSymbol: + mutationDataFilter.hugoGeneSymbol, + dataType: molecularProfileOption.dataType, + mutationOptionType: + mutationDataFilter.categorization, + }, + ], + true + ); + } + } + ); + } } @action @@ -8725,7 +8945,12 @@ export class StudyViewPageStore public async getChartAllDataDownload(chartMeta: ChartMeta) { // handle custom chart if (this.isUserDefinedCustomDataChart(chartMeta.uniqueKey)) { - return this.getCustomChartDownloadData(chartMeta); + return getCustomChartDownloadData( + chartMeta, + this.selectedSamples.result!, + this.selectedPatients, + this._customChartsSelectedCases.get(chartMeta.uniqueKey) + ); } let clinicalDataList: ClinicalData[] = []; @@ -8819,354 +9044,6 @@ export class StudyViewPageStore ); } - public getCustomChartDownloadData(chartMeta: ChartMeta): Promise { - return new Promise(resolve => { - if (chartMeta && chartMeta.uniqueKey) { - let isPatientChart = chartMeta.patientAttribute; - let header = ['Study ID', 'Patient ID']; - - if (!isPatientChart) { - header.push('Sample ID'); - } - header.push(chartMeta.displayName); - let data = [header.join('\t')]; - if ( - chartMeta.uniqueKey === - SpecialChartsUniqueKeyEnum.CANCER_STUDIES - ) { - data = data.concat( - this.selectedSamples.result!.map((sample: Sample) => { - return [ - sample.studyId || Datalabel.NA, - sample.patientId || Datalabel.NA, - sample.sampleId || Datalabel.NA, - sample.studyId, - ].join('\t'); - }) - ); - } else if ( - this._customChartsSelectedCases.has(chartMeta.uniqueKey) - ) { - if (isPatientChart) { - data = data.concat( - this.selectedPatients.map((patient: Patient) => { - let record = _.find( - this._customChartsSelectedCases.get( - chartMeta.uniqueKey - ), - ( - caseIdentifier: CustomChartIdentifierWithValue - ) => { - return ( - caseIdentifier.studyId === - patient.studyId && - patient.patientId === - caseIdentifier.patientId - ); - } - ); - return [ - patient.studyId || Datalabel.NA, - patient.patientId || Datalabel.NA, - record === undefined ? 'NA' : record.value, - ].join('\t'); - }) - ); - } else { - data = data.concat( - this.selectedSamples.result!.map( - (sample: Sample) => { - let record = _.find( - this._customChartsSelectedCases.get( - chartMeta.uniqueKey - ), - ( - caseIdentifier: CustomChartIdentifierWithValue - ) => { - return ( - caseIdentifier.studyId === - sample.studyId && - sample.sampleId === - caseIdentifier.sampleId - ); - } - ); - return [ - sample.studyId || Datalabel.NA, - sample.patientId || Datalabel.NA, - sample.sampleId || Datalabel.NA, - record === undefined - ? 'NA' - : record.value, - ].join('\t'); - } - ) - ); - } - } - - resolve(data.join('\n')); - } else { - resolve(''); - } - }); - } - - public async getScatterDownloadData( - chartUniqueKey: ChartUniqueKey - ): Promise { - const chartInfo = this.getXvsYScatterChartInfo(chartUniqueKey)!; - const selectedSamples = await toPromise(this.selectedSamples); - const [xData, yData] = await Promise.all([ - getSampleToClinicalData(selectedSamples, chartInfo.xAttr), - getSampleToClinicalData(selectedSamples, chartInfo.yAttr), - ]); - return generateXvsYScatterPlotDownloadData( - chartInfo.xAttr, - chartInfo.yAttr, - selectedSamples, - xData, - yData - ); - } - - public getSurvivalDownloadData(chartMeta: ChartMeta): string { - const matchedPlot = _.find( - this.survivalPlots.result, - plot => plot.id === chartMeta.uniqueKey - ); - if (matchedPlot && this.survivalData.result) { - const data: string[] = []; - - // find the unique clinical attribute ids - const uniqueClinicalAttributeIds = matchedPlot.associatedAttrs; - - // add the header row - data.push( - ['Study ID', 'Patient ID', ...uniqueClinicalAttributeIds].join( - '\t' - ) - ); - - // add the data rows - const selectedPatientMap = _.reduce( - this.selectedPatients, - (acc, next) => { - acc[next.uniquePatientKey] = next; - return acc; - }, - {} as { [uniquePatientKey: string]: Patient } - ); - this.selectedPatientKeys.result.forEach(uniquePatientKey => { - const clinicalDataList = this.survivalData.result[ - uniquePatientKey - ]; - const row: string[] = []; - - if (clinicalDataList && clinicalDataList.length > 0) { - row.push(clinicalDataList[0].studyId || Datalabel.NA); - row.push(clinicalDataList[0].patientId || Datalabel.NA); - const keyed = _.keyBy( - clinicalDataList, - 'clinicalAttributeId' - ); - - _.each(uniqueClinicalAttributeIds, id => { - row.push( - keyed[id] - ? keyed[id].value || Datalabel.NA - : Datalabel.NA - ); - }); - } else { - const selectedPatient = - selectedPatientMap[uniquePatientKey]; - if (selectedPatient) { - row.push(selectedPatient.studyId || Datalabel.NA); - row.push(selectedPatient.patientId || Datalabel.NA); - - _.each(uniqueClinicalAttributeIds, () => { - row.push(Datalabel.NA); - }); - } - } - - data.push(row.join('\t')); - }); - - return data.join('\n'); - } else { - return ''; - } - } - - public async getMutatedGenesDownloadData(): Promise { - if (this.mutatedGeneTableRowData.result) { - let header = [ - 'Gene', - 'MutSig(Q-value)', - '# Mut', - '#', - 'Profiled Samples', - 'Freq', - ]; - if (this.oncokbCancerGeneFilterEnabled) { - header.push('Is Cancer Gene (source: OncoKB)'); - } - let data = [header.join('\t')]; - _.each( - this.mutatedGeneTableRowData.result, - (record: MultiSelectionTableRow) => { - let rowData = [ - record.label, - record.qValue === undefined - ? '' - : getQValue(record.qValue), - record.totalCount, - record.numberOfAlteredCases, - record.numberOfProfiledCases, - getFrequencyStr( - (record.numberOfAlteredCases / - record.numberOfProfiledCases) * - 100 - ), - ]; - if (this.oncokbCancerGeneFilterEnabled) { - rowData.push( - this.oncokbCancerGeneFilterEnabled - ? record.isCancerGene - ? 'Yes' - : 'No' - : 'NA' - ); - } - data.push(rowData.join('\t')); - } - ); - return data.join('\n'); - } else return ''; - } - - public getStructuralVariantGenesDownloadData(): string { - if (this.structuralVariantGeneTableRowData.result) { - const header = [ - 'Gene', - '# Structural Variant', - '#', - 'Profiled Samples', - 'Freq', - ]; - if (this.oncokbCancerGeneFilterEnabled) { - header.push('Is Cancer Gene (source: OncoKB)'); - } - const data = [header.join('\t')]; - _.each( - this.structuralVariantGeneTableRowData.result, - (record: MultiSelectionTableRow) => { - const rowData = [ - record.label, - record.totalCount, - record.numberOfAlteredCases, - record.numberOfProfiledCases, - getFrequencyStr( - (record.numberOfAlteredCases / - record.numberOfProfiledCases) * - 100 - ), - ]; - if (this.oncokbCancerGeneFilterEnabled) { - rowData.push( - this.oncokbCancerGeneFilterEnabled - ? record.isCancerGene - ? 'Yes' - : 'No' - : 'NA' - ); - } - data.push(rowData.join('\t')); - } - ); - return data.join('\n'); - } else return ''; - } - - public async getGenesCNADownloadData(): Promise { - if (this.cnaGeneTableRowData.result) { - let header = [ - 'Gene', - 'Gistic(Q-value)', - 'Cytoband', - 'CNA', - 'Profiled Samples', - '#', - 'Freq', - ]; - if (this.oncokbCancerGeneFilterEnabled) { - header.push('Is Cancer Gene (source: OncoKB)'); - } - let data = [header.join('\t')]; - _.each( - this.cnaGeneTableRowData.result, - (record: MultiSelectionTableRow) => { - let rowData = [ - record.label, - record.qValue === undefined - ? '' - : getQValue(record.qValue), - record.cytoband, - getCNAByAlteration(record.alteration!), - record.numberOfAlteredCases, - record.numberOfProfiledCases, - getFrequencyStr( - (record.numberOfAlteredCases / - record.numberOfProfiledCases) * - 100 - ), - ]; - if (this.oncokbCancerGeneFilterEnabled) { - rowData.push( - this.oncokbCancerGeneFilterEnabled - ? record.isCancerGene - ? 'Yes' - : 'No' - : 'NA' - ); - } - data.push(rowData.join('\t')); - } - ); - return data.join('\n'); - } else return ''; - } - public async getPatientTreatmentDownloadData(): Promise { - if (this.patientTreatments.result) { - const header = ['Treatment', '#']; - let data = [header.join('\t')]; - _.each( - this.patientTreatments.result, - (record: PatientTreatmentRow) => { - let rowData = [record.treatment, record.count]; - data.push(rowData.join('\t')); - } - ); - return data.join('\n'); - } else return ''; - } - public async getSampleTreatmentDownloadData(): Promise { - if (this.sampleTreatments.result) { - const header = ['Treatment', 'Pre/Post', '#']; - let data = [header.join('\t')]; - _.each( - this.sampleTreatments.result, - (record: SampleTreatmentRow) => { - let rowData = [record.treatment, record.time, record.count]; - data.push(rowData.join('\t')); - } - ); - return data.join('\n'); - } else return ''; - } - readonly survivalEntryMonths = remoteData< { [uniquePatientKey: string]: number } | undefined >({ @@ -9431,6 +9308,7 @@ export class StudyViewPageStore AlterationTypeConstants.PROTEIN_LEVEL, AlterationTypeConstants.METHYLATION, AlterationTypeConstants.COPY_NUMBER_ALTERATION, + AlterationTypeConstants.MUTATION_EXTENDED, ].includes(molecularProfile.molecularAlterationType); }); }, @@ -9448,8 +9326,10 @@ export class StudyViewPageStore if (!acc.has(profileType)) { acc.set( profileType, - DataTypeConstants.DISCRETE === - molecularProfile.datatype + [ + DataTypeConstants.DISCRETE, + DataTypeConstants.MAF, + ].includes(molecularProfile.datatype) ? DataType.STRING : DataType.NUMBER ); @@ -9466,10 +9346,16 @@ export class StudyViewPageStore await: () => [ this.molecularProfileTypeToDataType, this.molecularProfileSampleCounts, + this.molecularProfiles, ], invoke: async () => { const profileTypeToDataTypeSet = this.molecularProfileTypeToDataType .result; + const profileTypeToAlterationTypeSet = _.keyBy( + this.molecularProfiles.result, + molecularProfile => + getSuffixOfMolecularProfile(molecularProfile) + ); return this.molecularProfileSampleCounts.result .filter(datum => profileTypeToDataTypeSet.has(datum.uniqueKey)) @@ -9482,6 +9368,9 @@ export class StudyViewPageStore dataType: profileTypeToDataTypeSet.get(datum.uniqueKey) || DataType.STRING, + alterationType: + profileTypeToAlterationTypeSet[datum.uniqueKey] + .molecularAlterationType, }; }); }, @@ -10232,7 +10121,8 @@ export class StudyViewPageStore let count = 0; if (this.molecularProfileSampleCountSet.result !== undefined) { switch (chartType) { - case ChartTypeEnum.MUTATED_GENES_TABLE: { + case ChartTypeEnum.MUTATED_GENES_TABLE: + case ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE: { count = this.molecularProfileSampleCountSet.result[ MolecularAlterationType_filenameSuffix.MUTATION_EXTENDED! ] diff --git a/src/pages/studyView/StudyViewUtils.tsx b/src/pages/studyView/StudyViewUtils.tsx index 0816244612e..cb62d6c4e44 100644 --- a/src/pages/studyView/StudyViewUtils.tsx +++ b/src/pages/studyView/StudyViewUtils.tsx @@ -17,15 +17,19 @@ import { GenePanelData, GenericAssayData, GenericAssayDataBin, + GenericAssayDataFilter, GenericAssayDataMultipleStudyFilter, GenomicDataBin, GenomicDataCount, MolecularDataMultipleStudyFilter, MolecularProfile, NumericGeneMolecularData, + Patient, PatientIdentifier, + PatientTreatmentRow, Sample, SampleIdentifier, + SampleTreatmentRow, StructuralVariantFilterQuery, StudyViewFilter, } from 'cbioportal-ts-api-client'; @@ -36,6 +40,7 @@ import { BinMethodOption, GenericAssayChart, GenomicChart, + SurvivalType, XvsYChartSettings, XvsYScatterChart, XvsYViolinChart, @@ -65,7 +70,13 @@ import { stringListToIndexSet, toPromise, } from 'cbioportal-frontend-commons'; -import { DEFAULT_NA_COLOR, getClinicalValueColor } from 'shared/lib/Colors'; +import { + CLI_NO_COLOR, + CLI_YES_COLOR, + DEFAULT_NA_COLOR, + DEFAULT_UNKNOWN_COLOR, + getClinicalValueColor, +} from 'shared/lib/Colors'; import { StudyViewComparisonGroup } from '../groupComparison/GroupComparisonUtils'; import styles from './styles.module.scss'; import { getGroupParameters } from 'pages/groupComparison/comparisonGroupManager/ComparisonGroupManagerUtils'; @@ -88,10 +99,21 @@ import { import { getServerConfig } from 'config/config'; import joinJsx from 'shared/lib/joinJsx'; import { BoundType, NumberRange } from 'range-ts'; -import { ClinicalEventTypeCount } from 'cbioportal-ts-api-client/dist/generated/CBioPortalAPIInternal'; +import { + ClinicalEventTypeCount, + GenericAssayDataCountFilter, + GenericAssayDataCountItem, + GenomicDataCountFilter, + GenomicDataFilter, +} from 'cbioportal-ts-api-client/dist/generated/CBioPortalAPIInternal'; import { queryContainsStructVarAlteration } from 'shared/lib/oql/oqlfilter'; import { toast } from 'react-toastify'; import { useCallback } from 'react'; +import { MutationOptionConstants } from 'shared/constants'; +import { MolecularAlterationType_filenameSuffix } from 'shared/lib/StoreUtils'; +import { MultiSelectionTableRow } from './table/MultiSelectionTable'; +import Survival from 'pages/groupComparison/Survival'; +import { StructVarMultiSelectionTableRow } from './table/StructuralVariantMultiSelectionTable'; // Cannot use ClinicalDataTypeEnum here for the strong type. The model in the type is not strongly typed export enum ClinicalDataTypeEnum { @@ -151,6 +173,7 @@ export enum ChartMetaDataTypeEnum { export type ChartMeta = { clinicalAttribute?: ClinicalAttribute; genericAssayType?: string; + mutationOptionType?: string; uniqueKey: string; displayName: string; description: string; @@ -189,6 +212,7 @@ export type MolecularProfileOption = { label: string; description: string; dataType: string; + alterationType: string; patientLevel?: boolean; }; @@ -201,6 +225,8 @@ export type DataBin = { start: number; }; +export type MutationCategorization = 'MUTATED' | 'MUTATION_TYPE'; + export const SPECIAL_CHARTS: ChartMetaWithDimensionAndChartType[] = [ { uniqueKey: SpecialChartsUniqueKeyEnum.CANCER_STUDIES, @@ -786,9 +812,12 @@ export function getUniqueKey(attribute: ClinicalAttribute): string { export function getGenomicChartUniqueKey( hugoGeneSymbol: string, - profileType: string + profileType: string, + mutationOptionType?: string ): string { - return hugoGeneSymbol + '_' + profileType; + return mutationOptionType + ? hugoGeneSymbol + '_' + profileType + '_' + mutationOptionType + : hugoGeneSymbol + '_' + profileType; } export function getGenericAssayChartUniqueKey( @@ -989,6 +1018,28 @@ export function getVirtualStudyDescription( } }); + _.each(filter.mutationDataFilters || [], mutationDataFilter => { + const uniqueKey = getGenomicChartUniqueKey( + mutationDataFilter.hugoGeneSymbol, + mutationDataFilter.profileType, + mutationDataFilter.categorization + ); + + const name = attributeNamesSet[uniqueKey]; + + if (name) { + _.each(mutationDataFilter.values || [], value => { + filterLines.push( + `- ${name}: ${intervalFiltersDisplayValue( + value, + () => {}, + true + )}` + ); + }); + } + }); + _.each( filter.genericAssayDataFilters || [], genericAssayDataFilters => { @@ -1043,6 +1094,7 @@ export function isFiltered( _.isEmpty(filter.structuralVariantFilters) && _.isEmpty(filter.genomicProfiles) && _.isEmpty(filter.genomicDataFilters) && + _.isEmpty(filter.mutationDataFilters) && _.isEmpty(filter.genericAssayDataFilters) && _.isEmpty(filter.caseLists) && _.isEmpty(filter.customDataFilters) && @@ -1860,6 +1912,32 @@ export function getCNAColorByAlteration(alteration: string): string { } } +export function transformMutatedType(type: string): string { + if (type === undefined || type === 'NA') return type; + + // Split the input string by underscores + var words = type.split('_'); + + // Capitalize the first letter of each word + var capitalizedWords = words.map(_.capitalize); + + // Join the words back together with a space between them + return capitalizedWords.join(' '); +} + +export function getMutationColorByCategorization(type: string): string { + switch (type) { + case 'Mutated': + return CLI_YES_COLOR; + case 'Not Mutated': + return CLI_NO_COLOR; + case 'Not Profiled': + return DEFAULT_NA_COLOR; + default: + return DEFAULT_UNKNOWN_COLOR; + } +} + export function getDefaultChartTypeByClinicalAttribute( clinicalAttribute: ClinicalAttribute ): ChartType | undefined { @@ -4006,3 +4084,543 @@ function ToastSuppressor(props: any) { ); } + +export function getDefaultClinicalDataBinFilter( + attribute: ClinicalAttribute +): ClinicalDataBinFilter & { + showNA?: boolean | undefined; +} { + return { + attributeId: attribute.clinicalAttributeId, + disableLogScale: false, + showNA: false, + } as ClinicalDataBinFilter & { showNA?: boolean }; +} + +export function generateColorMapKey(id: string, value: string): string { + return `${id}.${value}`; +} + +export async function invokeGenericAssayDataCount( + chartInfo: GenericAssayChart, + filters: StudyViewFilter +) { + const result: GenericAssayDataCountItem[] = await internalClient.fetchGenericAssayDataCountsUsingPOST( + { + genericAssayDataCountFilter: { + genericAssayDataFilters: [ + { + stableId: chartInfo.genericAssayEntityId, + profileType: chartInfo.profileType, + } as GenericAssayDataFilter, + ], + studyViewFilter: filters, + } as GenericAssayDataCountFilter, + } + ); + + let data = result.find(d => d.stableId === chartInfo.genericAssayEntityId); + let counts: ClinicalDataCount[] = []; + let stableId: string = ''; + if (data !== undefined) { + counts = data.counts.map(c => { + return { + count: c.count, + value: c.value, + } as ClinicalDataCount; + }); + stableId = data.stableId; + + return { stableId: stableId, counts: counts }; + } + + return undefined; +} + +export async function invokeGenomicDataCount( + chartInfo: GenomicChart, + filters: StudyViewFilter +) { + let result = []; + let getDisplayedValue; + let getDisplayedColor; + let params = { + genomicDataCountFilter: { + genomicDataFilters: [ + { + hugoGeneSymbol: chartInfo.hugoGeneSymbol, + profileType: chartInfo.profileType, + } as GenomicDataFilter, + ], + studyViewFilter: filters, + }, + } as any; + + // mutation data counts (pie chart) + if ( + chartInfo.profileType === + MolecularAlterationType_filenameSuffix.MUTATION_EXTENDED + ) { + params = { + ...params, + $queryParameters: { + projection: 'SUMMARY', + }, + }; + result = await internalClient.fetchMutationDataCountsUsingPOST(params); + getDisplayedValue = transformMutatedType; + getDisplayedColor = (value: string) => + getMutationColorByCategorization(transformMutatedType(value)); + } else { + result = await internalClient.fetchGenomicDataCountsUsingPOST(params); + getDisplayedValue = getCNAByAlteration; + getDisplayedColor = (value: string | number) => + getCNAColorByAlteration(getCNAByAlteration(value)); + } + + const data = result.find( + d => + d.hugoGeneSymbol === chartInfo.hugoGeneSymbol && + d.profileType === chartInfo.profileType + ); + + let counts: ClinicalDataCount[] = []; + let profileType: string = ''; + if (data !== undefined) { + counts = data.counts.map(c => { + return { + count: c.count, + value: c.value, + } as ClinicalDataCount; + }); + profileType = data.profileType; + + return { + counts: counts, + profileType: profileType, + getDisplayedValue: getDisplayedValue, + getDisplayedColor: getDisplayedColor, + }; + } + + return undefined; +} + +export async function invokeMutationDataCount( + chartInfo: GenomicChart, + filters: StudyViewFilter, + profiledCases: number +) { + const params = { + genomicDataCountFilter: { + genomicDataFilters: [ + { + hugoGeneSymbol: chartInfo.hugoGeneSymbol, + profileType: chartInfo.profileType, + } as GenomicDataFilter, + ], + studyViewFilter: filters, + }, + $queryParameters: { + projection: 'DETAILED', + }, + } as any; + + const result = await internalClient.fetchMutationDataCountsUsingPOST( + params + ); + + const data = result.find( + d => + d.hugoGeneSymbol === chartInfo.hugoGeneSymbol && + d.profileType === chartInfo.profileType + ); + + let counts: MultiSelectionTableRow[] = []; + if (data !== undefined) { + counts = data.counts.map(c => { + return { + uniqueKey: c.value, + label: c.label, + // "Altered" and "Profiled" really just mean + // "numerator" and "denominator" in percent + // calculation of table. Here, they mean + // "# filtered samples in profile" and "# filtered samples overall" + numberOfAlteredCases: c.uniqueCount, + numberOfProfiledCases: profiledCases, + totalCount: c.count, + } as MultiSelectionTableRow; + }); + } + + return counts; +} + +export async function getCustomChartDownloadData( + chartMeta: ChartMeta, + selectedSamples: Sample[], + selectedPatients: Patient[], + caseIdentifiers?: CustomChartIdentifierWithValue[] +): Promise { + return new Promise(resolve => { + if (chartMeta && chartMeta.uniqueKey) { + let isPatientChart = chartMeta.patientAttribute; + let header = ['Study ID', 'Patient ID']; + + if (!isPatientChart) { + header.push('Sample ID'); + } + header.push(chartMeta.displayName); + let data = [header.join('\t')]; + if ( + chartMeta.uniqueKey === + SpecialChartsUniqueKeyEnum.CANCER_STUDIES + ) { + data = data.concat( + selectedSamples.map((sample: Sample) => { + return [ + sample.studyId || Datalabel.NA, + sample.patientId || Datalabel.NA, + sample.sampleId || Datalabel.NA, + sample.studyId, + ].join('\t'); + }) + ); + } else if (!_.isEmpty(caseIdentifiers)) { + if (isPatientChart) { + data = data.concat( + selectedPatients.map((patient: Patient) => { + let record = _.find( + caseIdentifiers, + ( + caseIdentifier: CustomChartIdentifierWithValue + ) => { + return ( + caseIdentifier.studyId === + patient.studyId && + patient.patientId === + caseIdentifier.patientId + ); + } + ); + return [ + patient.studyId || Datalabel.NA, + patient.patientId || Datalabel.NA, + record === undefined ? 'NA' : record.value, + ].join('\t'); + }) + ); + } else { + data = data.concat( + selectedSamples.map((sample: Sample) => { + let record = _.find( + caseIdentifiers, + ( + caseIdentifier: CustomChartIdentifierWithValue + ) => { + return ( + caseIdentifier.studyId === + sample.studyId && + sample.sampleId === + caseIdentifier.sampleId + ); + } + ); + return [ + sample.studyId || Datalabel.NA, + sample.patientId || Datalabel.NA, + sample.sampleId || Datalabel.NA, + record === undefined ? 'NA' : record.value, + ].join('\t'); + }) + ); + } + } + + resolve(data.join('\n')); + } else { + resolve(''); + } + }); +} + +export async function getScatterDownloadData( + chartInfo: XvsYScatterChart, + promise: MobxPromise +): Promise { + const selectedSamples = await toPromise(promise); + const [xData, yData] = await Promise.all([ + getSampleToClinicalData(selectedSamples, chartInfo.xAttr), + getSampleToClinicalData(selectedSamples, chartInfo.yAttr), + ]); + return generateXvsYScatterPlotDownloadData( + chartInfo.xAttr, + chartInfo.yAttr, + selectedSamples, + xData, + yData + ); +} + +export function getSurvivalDownloadData( + chartMeta: ChartMeta, + survivalPlots: SurvivalType[], + survivalDataMap: { [id: string]: ClinicalData[] }, + selectedPatients: Patient[], + selectedPatientKeys: string[] +): string { + const matchedPlot = _.find( + survivalPlots, + plot => plot.id === chartMeta.uniqueKey + ); + if (matchedPlot && survivalDataMap) { + const data: string[] = []; + + // find the unique clinical attribute ids + const uniqueClinicalAttributeIds = matchedPlot.associatedAttrs; + + // add the header row + data.push( + ['Study ID', 'Patient ID', ...uniqueClinicalAttributeIds].join('\t') + ); + + // add the data rows + const selectedPatientMap = _.reduce( + selectedPatients, + (acc, next) => { + acc[next.uniquePatientKey] = next; + return acc; + }, + {} as { [uniquePatientKey: string]: Patient } + ); + selectedPatientKeys.forEach(uniquePatientKey => { + const clinicalDataList = survivalDataMap[uniquePatientKey]; + const row: string[] = []; + + if (clinicalDataList && clinicalDataList.length > 0) { + row.push(clinicalDataList[0].studyId || Datalabel.NA); + row.push(clinicalDataList[0].patientId || Datalabel.NA); + const keyed = _.keyBy(clinicalDataList, 'clinicalAttributeId'); + + _.each(uniqueClinicalAttributeIds, id => { + row.push( + keyed[id] + ? keyed[id].value || Datalabel.NA + : Datalabel.NA + ); + }); + } else { + const selectedPatient = selectedPatientMap[uniquePatientKey]; + if (selectedPatient) { + row.push(selectedPatient.studyId || Datalabel.NA); + row.push(selectedPatient.patientId || Datalabel.NA); + + _.each(uniqueClinicalAttributeIds, () => { + row.push(Datalabel.NA); + }); + } + } + + data.push(row.join('\t')); + }); + + return data.join('\n'); + } else { + return ''; + } +} + +export async function getMutatedGenesDownloadData( + promise: MobxPromise, + oncokbCancerGeneFilterEnabled: boolean +): Promise { + if (promise.result) { + let header = [ + 'Gene', + 'MutSig(Q-value)', + '# Mut', + '#', + 'Profiled Samples', + 'Freq', + ]; + if (oncokbCancerGeneFilterEnabled) { + header.push('Is Cancer Gene (source: OncoKB)'); + } + let data = [header.join('\t')]; + _.each(promise.result, (record: MultiSelectionTableRow) => { + let rowData = [ + record.label, + record.qValue === undefined ? '' : getQValue(record.qValue), + record.totalCount, + record.numberOfAlteredCases, + record.numberOfProfiledCases, + getFrequencyStr( + (record.numberOfAlteredCases / + record.numberOfProfiledCases) * + 100 + ), + ]; + if (oncokbCancerGeneFilterEnabled) { + rowData.push( + oncokbCancerGeneFilterEnabled + ? record.isCancerGene + ? 'Yes' + : 'No' + : 'NA' + ); + } + data.push(rowData.join('\t')); + }); + return data.join('\n'); + } else return ''; +} + +export function getStructuralVariantGenesDownloadData( + promise: + | MobxPromise + | MobxPromise, + oncokbCancerGeneFilterEnabled: boolean +): string { + if (promise.result) { + const header = [ + 'Gene', + '# Structural Variant', + '#', + 'Profiled Samples', + 'Freq', + ]; + if (oncokbCancerGeneFilterEnabled) { + header.push('Is Cancer Gene (source: OncoKB)'); + } + const data = [header.join('\t')]; + _.each(promise.result, (record: MultiSelectionTableRow) => { + const rowData = [ + record.label, + record.totalCount, + record.numberOfAlteredCases, + record.numberOfProfiledCases, + getFrequencyStr( + (record.numberOfAlteredCases / + record.numberOfProfiledCases) * + 100 + ), + ]; + if (oncokbCancerGeneFilterEnabled) { + rowData.push( + oncokbCancerGeneFilterEnabled + ? record.isCancerGene + ? 'Yes' + : 'No' + : 'NA' + ); + } + data.push(rowData.join('\t')); + }); + return data.join('\n'); + } else return ''; +} + +export async function getGenesCNADownloadData( + promise: MobxPromise, + oncokbCancerGeneFilterEnabled: boolean +): Promise { + if (promise.result) { + let header = [ + 'Gene', + 'Gistic(Q-value)', + 'Cytoband', + 'CNA', + 'Profiled Samples', + '#', + 'Freq', + ]; + if (oncokbCancerGeneFilterEnabled) { + header.push('Is Cancer Gene (source: OncoKB)'); + } + let data = [header.join('\t')]; + _.each(promise.result, (record: MultiSelectionTableRow) => { + let rowData = [ + record.label, + record.qValue === undefined ? '' : getQValue(record.qValue), + record.cytoband, + getCNAByAlteration(record.alteration!), + record.numberOfAlteredCases, + record.numberOfProfiledCases, + getFrequencyStr( + (record.numberOfAlteredCases / + record.numberOfProfiledCases) * + 100 + ), + ]; + if (oncokbCancerGeneFilterEnabled) { + rowData.push( + oncokbCancerGeneFilterEnabled + ? record.isCancerGene + ? 'Yes' + : 'No' + : 'NA' + ); + } + data.push(rowData.join('\t')); + }); + return data.join('\n'); + } else return ''; +} + +export async function getPatientTreatmentDownloadData( + promise: MobxPromise +): Promise { + if (promise.result) { + const header = ['Treatment', '#']; + let data = [header.join('\t')]; + _.each(promise.result, (record: PatientTreatmentRow) => { + let rowData = [record.treatment, record.count]; + data.push(rowData.join('\t')); + }); + return data.join('\n'); + } else return ''; +} + +export async function getSampleTreatmentDownloadData( + promise: MobxPromise +): Promise { + if (promise.result) { + const header = ['Treatment', 'Pre/Post', '#']; + let data = [header.join('\t')]; + _.each(promise.result, (record: SampleTreatmentRow) => { + let rowData = [record.treatment, record.time, record.count]; + data.push(rowData.join('\t')); + }); + return data.join('\n'); + } else return ''; +} + +export async function getMutationTypesDownloadData( + promise: MobxPromise +): Promise { + if (promise.result) { + let header = [ + 'Mutation Event', + '# Mut', + '#', + 'Profiled Samples', + 'Freq', + ]; + let data = [header.join('\t')]; + _.each(promise.result, (record: MultiSelectionTableRow) => { + let rowData = [ + record.label, + record.totalCount, + record.numberOfAlteredCases, + record.numberOfProfiledCases, + getFrequencyStr( + (record.numberOfAlteredCases / + record.numberOfProfiledCases) * + 100 + ), + ]; + data.push(rowData.join('\t')); + }); + return data.join('\n'); + } else return ''; +} diff --git a/src/pages/studyView/UserSelections.tsx b/src/pages/studyView/UserSelections.tsx index 790d66622df..cea8a51a53e 100644 --- a/src/pages/studyView/UserSelections.tsx +++ b/src/pages/studyView/UserSelections.tsx @@ -1,5 +1,5 @@ import * as React from 'react'; -import _ from 'lodash'; +import _, { filter } from 'lodash'; import { observer } from 'mobx-react'; import { computed, makeObservable, runInAction } from 'mobx'; import styles from './styles.module.scss'; @@ -77,6 +77,7 @@ export interface IUserSelectionsProps { uniqueKey: string, values: DataFilterValue[] ) => void; + removeMutationDataFilter: (uniqueKey: string, value: string) => void; updateGenericAssayDataFilter: ( uniqueKey: string, values: DataFilterValue[] @@ -220,7 +221,7 @@ export default class UserSelections extends React.Component< } ); - // Genomic Bar chart filters + // Genomic chart filters _.reduce( this.props.filter.genomicDataFilters || [], (acc, genomicDataFilter) => { @@ -290,6 +291,62 @@ export default class UserSelections extends React.Component< components ); + // Mutation chart filters + _.reduce( + this.props.filter.mutationDataFilters || [], + (acc, mutationDataFilter) => { + const uniqueKey = getGenomicChartUniqueKey( + mutationDataFilter.hugoGeneSymbol, + mutationDataFilter.profileType, + mutationDataFilter.categorization + ); + const chartMeta = this.props.attributesMetaSet[uniqueKey]; + if (chartMeta) { + const filters = mutationDataFilter.values.map( + dataFilterValues => { + return ( + 1} + /> + ); + } + ); + + acc.push( +
+ + {chartMeta.displayName} + , + 1} + />, + ]} + operation={':'} + group={false} + /> +
+ ); + } + return acc; + }, + components + ); + // Generic Assay chart filters let genericAssayFilterComponents: JSX.Element[] = []; if (this.props.filter.genericAssayDataFilters) { @@ -969,6 +1026,36 @@ export default class UserSelections extends React.Component< }); } + private groupedMutationDataFilters( + dataFilterValues: DataFilterValue[], + chartMeta: ChartMeta & { chartType: ChartType } + ): JSX.Element { + return ( + { + return ( + + this.props.removeMutationDataFilter( + chartMeta.uniqueKey, + dataFilterValue.value + ) + } + store={this.props.store} + /> + ); + })} + operation={'or'} + group={false} + /> + ); + } + submitHesitantFilters() { this.props.store.submitQueuedFilterUpdates(); } diff --git a/src/pages/studyView/addChartButton/AddChartButton.tsx b/src/pages/studyView/addChartButton/AddChartButton.tsx index 9fd8215ef84..5fb6dd2f153 100644 --- a/src/pages/studyView/addChartButton/AddChartButton.tsx +++ b/src/pages/studyView/addChartButton/AddChartButton.tsx @@ -849,7 +849,8 @@ class AddChartTabs extends React.Component { if (charts.length === 1) { const uniqueKey = getGenomicChartUniqueKey( charts[0].hugoGeneSymbol, - charts[0].profileType + charts[0].profileType, + charts[0].mutationOptionType ); this.updateInfoMessage( `${charts[0].name} ${ diff --git a/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx b/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx index ffe9a2556af..d4b9a06958a 100644 --- a/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx +++ b/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx @@ -1,5 +1,5 @@ import * as React from 'react'; -import _ from 'lodash'; +import _, { List } from 'lodash'; import { GenomicChart } from 'pages/studyView/StudyViewPageStore'; import { observer } from 'mobx-react'; import { action, computed, makeObservable, observable } from 'mobx'; @@ -17,6 +17,12 @@ import LoadingIndicator from 'shared/components/loadingIndicator/LoadingIndicato import ErrorMessage from 'shared/components/ErrorMessage'; import { Gene } from 'cbioportal-ts-api-client'; import { MolecularProfileOption } from 'pages/studyView/StudyViewUtils'; +import { + AlterationTypeConstants, + MutationOptionConstants, + MutationOptionConstantsLabel, +} from 'shared/constants'; +import autobind from 'autobind-decorator'; export interface IGeneLevelSelectionProps { molecularProfileOptionsPromise: MobxPromise; @@ -25,6 +31,20 @@ export interface IGeneLevelSelectionProps { containerWidth: number; } +const molecularProfileSubOptions = [ + { + value: MutationOptionConstants.MUTATED, + label: MutationOptionConstantsLabel[MutationOptionConstants.MUTATED], + profileType: AlterationTypeConstants.MUTATION_EXTENDED, + }, + { + value: MutationOptionConstants.MUTATION_TYPE, + label: + MutationOptionConstantsLabel[MutationOptionConstants.MUTATION_TYPE], + profileType: AlterationTypeConstants.MUTATION_EXTENDED, + }, +]; + @observer export default class GeneLevelSelection extends React.Component< IGeneLevelSelectionProps, @@ -40,6 +60,12 @@ export default class GeneLevelSelection extends React.Component< profileName: string; description: string; dataType: string; + alterationType: string; + }; + + @observable private _selectedSubProfileOption?: { + value: string; + label: string; }; @observable private _oql?: { @@ -61,14 +87,14 @@ export default class GeneLevelSelection extends React.Component< if (this.selectedOption !== undefined) { const charts = this.validGenes.map(gene => { return { - name: - gene.hugoGeneSymbol + - ': ' + - this.selectedOption!.profileName, + name: this.getChartName(gene.hugoGeneSymbol), description: this.selectedOption!.description, profileType: this.selectedOption!.value, hugoGeneSymbol: gene.hugoGeneSymbol, dataType: this.selectedOption!.dataType, + ...(this.selectedSubOption + ? { mutationOptionType: this.selectedSubOption.value } + : {}), }; }); this.props.onSubmit(charts); @@ -80,6 +106,31 @@ export default class GeneLevelSelection extends React.Component< if (option && option.value) { this._selectedProfileOption = option; } + + if ( + !molecularProfileSubOptions + .map(subOption => subOption.label) + .includes(option.alterationType) + ) { + this._selectedSubProfileOption = undefined; + } + } + + @action.bound + private handleSubSelect(option: any) { + if (option && option.value) { + this._selectedSubProfileOption = option; + } + } + + @autobind + private getChartName(hugoGeneSymbol: string): string { + return ( + hugoGeneSymbol + + ': ' + + this.selectedOption!.profileName + + (this.selectedSubOption ? ': ' + this.selectedSubOption!.label : '') + ); } @computed @@ -93,6 +144,24 @@ export default class GeneLevelSelection extends React.Component< return undefined; } + @computed + private get selectedSubOption() { + if (this._selectedSubProfileOption !== undefined) { + return this._selectedSubProfileOption; + } + + if ( + this.selectedOption !== undefined && + molecularProfileSubOptions + .map(option => option.profileType) + .includes(this.selectedOption.alterationType) + ) { + return molecularProfileSubOptions[0]; + } + + return undefined; + } + @computed private get isQueryInvalid() { return ( @@ -175,7 +244,8 @@ export default class GeneLevelSelection extends React.Component<
+ + {this.selectedOption && + molecularProfileSubOptions + .map(option => option.profileType) + .includes(this.selectedOption.alterationType) && ( +
+ +
+ )} + {/*
*/} diff --git a/src/pages/studyView/charts/ChartContainer.tsx b/src/pages/studyView/charts/ChartContainer.tsx index eaad4c0e4ae..ab3c4ea2c8f 100644 --- a/src/pages/studyView/charts/ChartContainer.tsx +++ b/src/pages/studyView/charts/ChartContainer.tsx @@ -395,7 +395,8 @@ export class ChartContainer extends React.Component { return ( this.props.promise.isComplete && this.props.promise.result!.length > 1 && - COMPARISON_CHART_TYPES.indexOf(this.props.chartType) > -1 + COMPARISON_CHART_TYPES.indexOf(this.props.chartType) > -1 && + !this.props.chartMeta.mutationOptionType ); } @@ -486,7 +487,7 @@ export class ChartContainer extends React.Component { } @computed get comparisonButtonForTables() { - if (this.selectedRowsKeys!.length >= 2) { + if (this.selectedRowsKeys!.length >= 2 && this.comparisonPagePossible) { return { content: (
{ )} ref={this.handlers.ref} onUserSelection={this.handlers.onValueSelection} - openComparisonPage={this.openComparisonPage} + openComparisonPage={ + this.comparisonPagePossible + ? this.openComparisonPage + : undefined + } filters={this.props.filters} data={this.props.promise.result} placement={this.placement} @@ -661,6 +666,73 @@ export class ChartContainer extends React.Component { ); }; } + case ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE: { + return () => { + const numColumn: MultiSelectionTableColumn = { + columnKey: MultiSelectionTableColumnKey.NUMBER, + }; + if (this.props.store.isGlobalMutationFilterActive) { + numColumn.columnTooltip = ( + + Total number of mutations +
+ This table is filtered based on selections in + the Alteration Filter menu. + + ); + } + + return ( + + ); + }; + } case ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE: { return () => { const numColumn: MultiSelectionTableColumn = { diff --git a/src/pages/studyView/studyPageHeader/StudyPageHeader.tsx b/src/pages/studyView/studyPageHeader/StudyPageHeader.tsx index d24859600ae..2fc3db07271 100644 --- a/src/pages/studyView/studyPageHeader/StudyPageHeader.tsx +++ b/src/pages/studyView/studyPageHeader/StudyPageHeader.tsx @@ -95,6 +95,9 @@ export default class StudyPageHeader extends React.Component< updateGenomicDataFilter={ this.props.store.updateGenomicDataFiltersByValues } + removeMutationDataFilter={ + this.props.store.removeMutationDataFilter + } updateGenericAssayDataFilter={ this.props.store .updateGenericAssayDataFiltersByValues diff --git a/src/pages/studyView/table/MultiSelectionTable.tsx b/src/pages/studyView/table/MultiSelectionTable.tsx index 4cb9ad68a54..c2b17617273 100644 --- a/src/pages/studyView/table/MultiSelectionTable.tsx +++ b/src/pages/studyView/table/MultiSelectionTable.tsx @@ -56,6 +56,7 @@ export enum MultiSelectionTableColumnKey { GENE = 'Gene', MOLECULAR_PROFILE = 'Molecular Profile', CASE_LIST = 'Name', + MUTATION_TYPE = 'Mutation Type', NUMBER_STRUCTURAL_VARIANTS = '# SV', NUMBER_MUTATIONS = '# Mut', CYTOBAND = 'Cytoband', @@ -79,8 +80,8 @@ export type BaseMultiSelectionTableProps = { onChangeSelectedRows: (rowsKeys: string[]) => void; selectedRowsKeys: string[]; cancerGeneFilterEnabled?: boolean; - genePanelCache: MobxPromiseCache<{ genePanelId: string }, GenePanel>; - filterByCancerGenes: boolean; + genePanelCache?: MobxPromiseCache<{ genePanelId: string }, GenePanel>; + filterByCancerGenes?: boolean; onChangeCancerGeneFilter: (filtered: boolean) => void; alterationFilterEnabled?: boolean; filterAlterations?: boolean; @@ -92,8 +93,8 @@ export type MultiSelectionTableProps = BaseMultiSelectionTableProps & { extraButtons?: IFixedHeaderTableProps< MultiSelectionTableRow >['extraButtons']; - selectedGenes: string[]; - onGeneSelect: (hugoGeneSymbol: string) => void; + selectedGenes?: string[]; + onGeneSelect?: (hugoGeneSymbol: string) => void; columns: MultiSelectionTableColumn[]; promise: MobxPromise; }; @@ -104,6 +105,7 @@ const DEFAULT_COLUMN_WIDTH_RATIO: { [MultiSelectionTableColumnKey.GENE]: 0.35, [MultiSelectionTableColumnKey.MOLECULAR_PROFILE]: 0.6, [MultiSelectionTableColumnKey.CASE_LIST]: 0.6, + [MultiSelectionTableColumnKey.MUTATION_TYPE]: 0.35, [MultiSelectionTableColumnKey.NUMBER_MUTATIONS]: 0.25, [MultiSelectionTableColumnKey.NUMBER_STRUCTURAL_VARIANTS]: 0.2, [MultiSelectionTableColumnKey.NUMBER]: 0.25, @@ -174,7 +176,7 @@ export class MultiSelectionTable extends React.Component< return ( ); }, @@ -264,6 +266,39 @@ export class MultiSelectionTable extends React.Component< }, width: columnWidth, }, + [MultiSelectionTableColumnKey.MUTATION_TYPE]: { + name: columnKey, + headerRender: () => { + return ( +
+ {columnKey} +
+ ); + }, + render: (data: MultiSelectionTableRow) => { + return ( +
+ +
+ ); + }, + sortBy: (data: MultiSelectionTableRow) => data.label, + defaultSortDirection: 'asc' as 'asc', + filter: ( + data: MultiSelectionTableRow, + filterString: string, + filterStringUpper: string + ) => { + return data.label.toUpperCase().includes(filterStringUpper); + }, + width: columnWidth, + }, [MultiSelectionTableColumnKey.NUMBER]: { name: columnKey, tooltip: {getTooltip(this.props.tableType, false)}, @@ -482,6 +517,7 @@ export class MultiSelectionTable extends React.Component< [MultiSelectionTableColumnKey.GENE]: 0, [MultiSelectionTableColumnKey.MOLECULAR_PROFILE]: 0, [MultiSelectionTableColumnKey.CASE_LIST]: 0, + [MultiSelectionTableColumnKey.MUTATION_TYPE]: 0, [MultiSelectionTableColumnKey.NUMBER_MUTATIONS]: correctMargin( getFixedHeaderNumberCellMargin( columnWidth, @@ -748,9 +784,14 @@ export class MultiSelectionTable extends React.Component< return _.reduce( this.props.filters, (acc, next, index) => { - next.forEach(key => { - acc[key] = index; - }); + if (Array.isArray(next)) { + next.forEach(key => { + acc[key] = index; + }); + } else { + acc[next] = index; + } + return acc; }, {} as { [id: string]: number } diff --git a/src/pages/studyView/tabs/SummaryTab.tsx b/src/pages/studyView/tabs/SummaryTab.tsx index db6b8d2d2ce..ee0c9fff2ee 100644 --- a/src/pages/studyView/tabs/SummaryTab.tsx +++ b/src/pages/studyView/tabs/SummaryTab.tsx @@ -33,6 +33,15 @@ import { DataBin, makeDensityScatterPlotTooltip, logScalePossible, + ChartMetaDataTypeEnum, + getMutationTypesDownloadData, + getScatterDownloadData, + getSurvivalDownloadData, + getMutatedGenesDownloadData, + getStructuralVariantGenesDownloadData, + getGenesCNADownloadData, + getPatientTreatmentDownloadData, + getSampleTreatmentDownloadData, } from '../StudyViewUtils'; import { DataType } from 'cbioportal-frontend-commons'; import DelayedRender from 'shared/components/DelayedRender'; @@ -53,6 +62,7 @@ export class StudySummaryTab extends React.Component< > { private store: StudyViewPageStore; private handlers: any; + private chartTypeConfig: any; @observable showErrorMessage = true; @@ -144,6 +154,21 @@ export class StudySummaryTab extends React.Component< values ); }, + onSetMutationDataValues: ( + chartMeta: ChartMeta, + values: string[][] + ) => { + this.store.updateMutationDataFilters( + chartMeta.uniqueKey, + values + ); + }, + onAddMutationDataValues: ( + chartMeta: ChartMeta, + values: string[][] + ) => { + this.store.addMutationDataFilters(chartMeta.uniqueKey, values); + }, onGenericAssayDataBinSelection: ( chartMeta: ChartMeta, dataBins: GenericAssayDataBin[] @@ -163,355 +188,424 @@ export class StudySummaryTab extends React.Component< ); }, }; - } - - renderAttributeChart = (chartMeta: ChartMeta) => { - const props: Partial = { - chartMeta: chartMeta, - chartType: this.props.store.chartsType.get(chartMeta.uniqueKey), - store: this.props.store, - dimension: this.store.chartsDimension.get(chartMeta.uniqueKey), - title: chartMeta.displayName, - filters: [], - onDeleteChart: this.handlers.onDeleteChart, - isNewlyAdded: this.handlers.isNewlyAdded, - studyViewFilters: this.store.filters, - analysisGroupsSettings: this.store.analysisGroupsSettings, - cancerGeneFilterEnabled: this.store.oncokbCancerGeneFilterEnabled, - setComparisonConfirmationModal: this.store - .setComparisonConfirmationModal, - }; - switch (this.store.chartsType.get(chartMeta.uniqueKey)) { - case ChartTypeEnum.PIE_CHART: { - //if the chart is one of the custom charts then get the appropriate promise - if ( - this.store.isUserDefinedCustomDataChart(chartMeta.uniqueKey) - ) { - props.filters = this.store + this.chartTypeConfig = ( + chartMeta: ChartMeta, + props: Partial + ) => ({ + [ChartTypeEnum.PIE_CHART]: () => ({ + commonProps: { + onChangeChartType: this.handlers.onChangeChartType, + getData: (dataType?: DataType) => + this.store.getChartDownloadableData( + chartMeta, + dataType + ), + downloadTypes: ['Summary Data', 'Full Data', 'SVG', 'PDF'], + }, + [ChartMetaDataTypeEnum.CUSTOM_DATA]: () => ({ + filters: this.store .getCustomDataFiltersByUniqueKey(chartMeta.uniqueKey) .map( clinicalDataFilterValue => clinicalDataFilterValue.value - ); - props.onValueSelection = this.handlers.setCustomChartCategoricalFilters; - props.onResetSelection = this.handlers.setCustomChartCategoricalFilters; - props.promise = this.store.getCustomDataCount(chartMeta); - } else if ( - this.store.isGenericAssayChart(chartMeta.uniqueKey) - ) { - props.filters = this.store + ), + onValueSelection: this.handlers + .setCustomChartCategoricalFilters, + onResetSelection: this.handlers + .setCustomChartCategoricalFilters, + promise: this.store.getCustomDataCount(chartMeta), + }), + [ChartMetaDataTypeEnum.GENERIC_ASSAY]: () => ({ + filters: this.store .getGenericAssayDataFiltersByUniqueKey( - props.chartMeta!.uniqueKey + chartMeta.uniqueKey ) .map( genericAssayDataFilter => genericAssayDataFilter.value - ); - props.onValueSelection = this.handlers.onGenericAssayCategoricalValueSelection; - props.onResetSelection = this.handlers.onGenericAssayCategoricalValueSelection; - props.promise = this.store.getGenericAssayChartDataCount( + ), + onValueSelection: this.handlers + .onGenericAssayCategoricalValueSelection, + onResetSelection: this.handlers + .onGenericAssayCategoricalValueSelection, + promise: this.store.getGenericAssayChartDataCount( chartMeta - ); - } else if ( - this.store.isGeneSpecificChart(chartMeta.uniqueKey) - ) { - props.promise = this.store.getGenomicChartDataCount( - chartMeta - ); - props.filters = this.store - .getGenomicDataFiltersByUniqueKey(chartMeta.uniqueKey) - .map( - genomicDataFilterValue => - genomicDataFilterValue.value - ); - props.onValueSelection = this.handlers.onGenomicDataCategoricalValueSelection; - props.onResetSelection = this.handlers.onGenomicDataCategoricalValueSelection; - } else { - props.promise = this.store.getClinicalDataCount(chartMeta); - props.filters = this.store + ), + }), + [ChartMetaDataTypeEnum.GENE_SPECIFIC]: () => ({ + promise: this.store.getGenomicChartDataCount(chartMeta), + filters: chartMeta.mutationOptionType + ? this.store.getMutationDataFiltersByUniqueKey( + chartMeta.uniqueKey + ).length > 0 + ? this.store.getMutationDataFiltersByUniqueKey( + chartMeta.uniqueKey + )[0] + : [] + : this.store + .getGenomicDataFiltersByUniqueKey( + chartMeta.uniqueKey + ) + .map( + genomicDataFilterValue => + genomicDataFilterValue.value + ), + onValueSelection: this.handlers + .onGenomicDataCategoricalValueSelection, + onResetSelection: this.handlers + .onGenomicDataCategoricalValueSelection, + }), + [ChartMetaDataTypeEnum.CLINICAL]: () => ({ + promise: this.store.getClinicalDataCount(chartMeta), + filters: this.store .getClinicalDataFiltersByUniqueKey(chartMeta.uniqueKey) .map( clinicalDataFilterValue => clinicalDataFilterValue.value - ); - props.onValueSelection = this.handlers.onValueSelection; - props.onResetSelection = this.handlers.onValueSelection; - } - props.onChangeChartType = this.handlers.onChangeChartType; - props.getData = (dataType?: DataType) => - this.store.getChartDownloadableData(chartMeta, dataType); - props.downloadTypes = [ - 'Summary Data', - 'Full Data', - 'SVG', - 'PDF', - ]; - break; - } - case ChartTypeEnum.BAR_CHART: { - //if the chart is one of the custom charts then get the appropriate promise - if (this.store.isGeneSpecificChart(chartMeta.uniqueKey)) { - props.promise = this.store.getGenomicChartDataBin( - chartMeta - ); - props.filters = this.store.getGenomicDataFiltersByUniqueKey( - props.chartMeta!.uniqueKey - ); - props.onDataBinSelection = this.handlers.onGenomicDataBinSelection; - props.onResetSelection = this.handlers.onGenomicDataBinSelection; - props.getData = () => - this.store.getChartDownloadableData(chartMeta); - } else if ( - this.store.isGenericAssayChart(chartMeta.uniqueKey) - ) { - props.promise = this.store.getGenericAssayChartDataBin( - chartMeta - ); - props.filters = this.store.getGenericAssayDataFiltersByUniqueKey( - props.chartMeta!.uniqueKey - ); - props.onDataBinSelection = this.handlers.onGenericAssayDataBinSelection; - props.onResetSelection = this.handlers.onGenericAssayDataBinSelection; - props.getData = () => - this.store.getChartDownloadableData(chartMeta); - } else { - if ( - this.store.isUserDefinedCustomDataChart( - chartMeta.uniqueKey - ) - ) { - props.promise = this.store.getCustomDataNumerical( - chartMeta - ); - props.onDataBinSelection = this.handlers.onCustomChartDataBinSelection; - props.filters = this.store.getCustomDataFiltersByUniqueKey( - chartMeta.uniqueKey - ); - } else { - props.promise = this.store.getClinicalDataBin( - chartMeta - ); - props.onDataBinSelection = this.handlers.onDataBinSelection; - props.filters = this.store.getClinicalDataFiltersByUniqueKey( - chartMeta.uniqueKey - ); - } - props.onResetSelection = this.handlers.onDataBinSelection; - props.getData = () => - this.store.getChartDownloadableData(chartMeta); - } - props.onToggleLogScale = this.handlers.onToggleLogScale; - props.onToggleNAValue = this.handlers.onToggleNAValue; - props.showLogScaleToggle = this.store.isLogScaleToggleVisible( - chartMeta.uniqueKey, - props.promise!.result - ); - props.logScaleChecked = this.store.isLogScaleChecked( - chartMeta.uniqueKey - ); - props.isShowNAChecked = this.store.isShowNAChecked( - chartMeta.uniqueKey - ); - props.showNAToggle = this.store.isShowNAToggleVisible( - props.promise!.result - ); - props.downloadTypes = ['Data', 'SVG', 'PDF']; - break; - } - case ChartTypeEnum.TABLE: { - if ( - this.store.isUserDefinedCustomDataChart(chartMeta.uniqueKey) - ) { - props.filters = this.store + ), + onValueSelection: this.handlers.onValueSelection, + onResetSelection: this.handlers.onValueSelection, + }), + }), + [ChartTypeEnum.BAR_CHART]: () => ({ + commonProps: { + onToggleNAValue: this.handlers.onToggleNAValue, + logScaleChecked: this.store.isLogScaleChecked( + chartMeta.uniqueKey + ), + isShowNAChecked: this.store.isShowNAChecked( + chartMeta.uniqueKey + ), + downloadTypes: ['Data', 'SVG', 'PDF'], + }, + [ChartMetaDataTypeEnum.GENE_SPECIFIC]: () => ({ + promise: this.store.getGenomicChartDataBin(chartMeta), + filters: this.store.getGenomicDataFiltersByUniqueKey( + chartMeta.uniqueKey + ), + onDataBinSelection: this.handlers.onGenomicDataBinSelection, + onResetSelection: this.handlers.onGenomicDataBinSelection, + getData: () => + this.store.getChartDownloadableData(chartMeta), + showLogScaleToggle: this.store.isLogScaleToggleVisible( + chartMeta.uniqueKey, + this.store.getGenomicChartDataBin(chartMeta).result + ), + showNAToggle: this.store.isShowNAToggleVisible( + this.store.getGenomicChartDataBin(chartMeta).result! + ), + }), + [ChartMetaDataTypeEnum.GENERIC_ASSAY]: () => ({ + promise: this.store.getGenericAssayChartDataBin(chartMeta), + filters: this.store.getGenericAssayDataFiltersByUniqueKey( + chartMeta.uniqueKey + ), + onDataBinSelection: this.handlers + .onGenericAssayDataBinSelection, + onResetSelection: this.handlers + .onGenericAssayDataBinSelection, + getData: () => + this.store.getChartDownloadableData(chartMeta), + showLogScaleToggle: this.store.isLogScaleToggleVisible( + chartMeta.uniqueKey, + this.store.getGenericAssayChartDataBin(chartMeta).result + ), + showNAToggle: this.store.isShowNAToggleVisible( + this.store.getGenericAssayChartDataBin(chartMeta) + .result! + ), + }), + [ChartMetaDataTypeEnum.CUSTOM_DATA]: () => ({ + promise: this.store.getCustomDataNumerical(chartMeta), + onDataBinSelection: this.handlers + .onCustomChartDataBinSelection, + filters: this.store.getCustomDataFiltersByUniqueKey( + chartMeta.uniqueKey + ), + onResetSelection: this.handlers.onDataBinSelection, + getData: () => + this.store.getChartDownloadableData(chartMeta), + showLogScaleToggle: this.store.isLogScaleToggleVisible( + chartMeta.uniqueKey, + this.store.getCustomDataNumerical(chartMeta).result + ), + showNAToggle: this.store.isShowNAToggleVisible( + this.store.getCustomDataNumerical(chartMeta).result! + ), + }), + [ChartMetaDataTypeEnum.CLINICAL]: () => ({ + promise: this.store.getClinicalDataBin(chartMeta), + onDataBinSelection: this.handlers.onDataBinSelection, + filters: this.store.getClinicalDataFiltersByUniqueKey( + chartMeta.uniqueKey + ), + onResetSelection: this.handlers.onDataBinSelection, + getData: () => + this.store.getChartDownloadableData(chartMeta), + showLogScaleToggle: this.store.isLogScaleToggleVisible( + chartMeta.uniqueKey, + this.store.getClinicalDataBin(chartMeta).result + ), + showNAToggle: this.store.isShowNAToggleVisible( + this.store.getClinicalDataBin(chartMeta).result! + ), + }), + }), + [ChartTypeEnum.TABLE]: () => ({ + commonProps: { + onChangeChartType: this.handlers.onChangeChartType, + getData: () => + this.store.getChartDownloadableData(chartMeta), + downloadTypes: ['Data'], + }, + [ChartMetaDataTypeEnum.CUSTOM_DATA]: () => ({ + filters: this.store .getCustomDataFiltersByUniqueKey(chartMeta.uniqueKey) .map( clinicalDataFilterValue => clinicalDataFilterValue.value - ); - props.onValueSelection = this.handlers.setCustomChartCategoricalFilters; - props.onResetSelection = this.handlers.setCustomChartCategoricalFilters; - props.promise = this.store.getCustomDataCount(chartMeta); - } else if ( - this.store.isGenericAssayChart(chartMeta.uniqueKey) - ) { - props.filters = this.store + ), + onValueSelection: this.handlers + .setCustomChartCategoricalFilters, + onResetSelection: this.handlers + .setCustomChartCategoricalFilters, + promise: this.store.getCustomDataCount(chartMeta), + }), + [ChartMetaDataTypeEnum.GENERIC_ASSAY]: () => ({ + filters: this.store .getGenericAssayDataFiltersByUniqueKey( - props.chartMeta!.uniqueKey + chartMeta.uniqueKey ) .map( genericAssayDataFilter => genericAssayDataFilter.value - ); - props.onValueSelection = this.handlers.onGenericAssayCategoricalValueSelection; - props.onResetSelection = this.handlers.onGenericAssayCategoricalValueSelection; - props.promise = this.store.getGenericAssayChartDataCount( - chartMeta - ); - } else if ( - this.store.isGeneSpecificChart(chartMeta.uniqueKey) - ) { - props.promise = this.store.getGenomicChartDataCount( + ), + onValueSelection: this.handlers + .onGenericAssayCategoricalValueSelection, + onResetSelection: this.handlers + .onGenericAssayCategoricalValueSelection, + promise: this.store.getGenericAssayChartDataCount( chartMeta - ); - props.filters = this.store - .getGenomicDataFiltersByUniqueKey(chartMeta.uniqueKey) - .map( - genomicDataFilterValue => - genomicDataFilterValue.value - ); - props.onValueSelection = this.handlers.onGenomicDataCategoricalValueSelection; - props.onResetSelection = this.handlers.onGenomicDataCategoricalValueSelection; - } else { - props.filters = this.store + ), + }), + [ChartMetaDataTypeEnum.GENE_SPECIFIC]: () => ({ + promise: this.store.getGenomicChartDataCount(chartMeta), + filters: chartMeta.mutationOptionType + ? this.store.getMutationDataFiltersByUniqueKey( + chartMeta.uniqueKey + ).length > 0 + ? this.store.getMutationDataFiltersByUniqueKey( + chartMeta.uniqueKey + )[0] + : [] + : this.store + .getGenomicDataFiltersByUniqueKey( + chartMeta.uniqueKey + ) + .map( + genomicDataFilterValue => + genomicDataFilterValue.value + ), + onValueSelection: this.handlers + .onGenomicDataCategoricalValueSelection, + onResetSelection: this.handlers + .onGenomicDataCategoricalValueSelection, + }), + [ChartMetaDataTypeEnum.CLINICAL]: () => ({ + filters: this.store .getClinicalDataFiltersByUniqueKey(chartMeta.uniqueKey) .map( clinicalDataFilterValue => clinicalDataFilterValue.value - ); - props.promise = this.store.getClinicalDataCount(chartMeta); - props.onValueSelection = this.handlers.onValueSelection; - props.onResetSelection = this.handlers.onValueSelection; - } - props.onChangeChartType = this.handlers.onChangeChartType; - props.getData = dataType => - this.store.getChartDownloadableData(chartMeta, dataType); - props.downloadTypes = ['Summary Data', 'Full Data']; - break; - } - case ChartTypeEnum.MUTATED_GENES_TABLE: { - props.filters = this.store.getGeneFiltersByUniqueKey( + ), + promise: this.store.getClinicalDataCount(chartMeta), + onValueSelection: this.handlers.onValueSelection, + onResetSelection: this.handlers.onValueSelection, + }), + }), + [ChartTypeEnum.MUTATED_GENES_TABLE]: () => ({ + filters: this.store.getGeneFiltersByUniqueKey( chartMeta.uniqueKey - ); - props.promise = this.store.mutatedGeneTableRowData; - props.onValueSelection = this.store.addGeneFilters; - props.onResetSelection = () => - this.store.resetGeneFilter(chartMeta.uniqueKey); - props.selectedGenes = this.store.selectedGenes; - props.onGeneSelect = this.store.onCheckGene; - props.id = 'mutated-genes-table'; - props.title = this.store.getChartTitle( + ), + promise: this.store.mutatedGeneTableRowData, + onValueSelection: this.store.addGeneFilters, + onResetSelection: () => + this.store.resetGeneFilter(chartMeta.uniqueKey), + selectedGenes: this.store.selectedGenes, + onGeneSelect: this.store.onCheckGene, + id: 'mutated-genes-table', + title: this.store.getChartTitle( ChartTypeEnum.MUTATED_GENES_TABLE, props.title - ); - props.getData = () => this.store.getMutatedGenesDownloadData(); - props.genePanelCache = this.store.genePanelCache; - props.downloadTypes = ['Data']; - props.filterByCancerGenes = this.store.filterMutatedGenesTableByCancerGenes; - props.onChangeCancerGeneFilter = this.store.updateMutatedGenesTableByCancerGenesFilter; - props.alterationFilterEnabled = getServerConfig().skin_show_settings_menu; - props.filterAlterations = this.store.isGlobalMutationFilterActive; - break; - } - case ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE: { - props.filters = this.store.getGeneFiltersByUniqueKey( + ), + getData: () => + getMutatedGenesDownloadData( + this.store.mutatedGeneTableRowData, + this.store.oncokbCancerGeneFilterEnabled + ), + genePanelCache: this.store.genePanelCache, + downloadTypes: ['Data'], + filterByCancerGenes: this.store + .filterMutatedGenesTableByCancerGenes, + onChangeCancerGeneFilter: this.store + .updateMutatedGenesTableByCancerGenesFilter, + alterationFilterEnabled: getServerConfig() + .skin_show_settings_menu, + filterAlterations: this.store.isGlobalMutationFilterActive, + }), + [ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE]: () => ({ + filters: this.store.getMutationDataFiltersByUniqueKey( chartMeta.uniqueKey - ); - props.promise = this.store.structuralVariantGeneTableRowData; - props.onValueSelection = this.store.addGeneFilters; - props.onResetSelection = () => - this.store.resetGeneFilter(chartMeta.uniqueKey); - props.selectedGenes = this.store.selectedGenes; - props.onGeneSelect = this.store.onCheckGene; - props.title = this.store.getChartTitle( + ), + promise: this.store.getMutationTypeChartDataCount(chartMeta), + onValueSelection: this.handlers.onAddMutationDataValues, + onResetSelection: this.handlers.onSetMutationDataValues, + id: 'mutation-type-counts-table', + title: this.store.getChartTitle( + ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE, + props.title + ), + getData: () => + getMutationTypesDownloadData( + this.store.getMutationTypeChartDataCount(chartMeta) + ), + downloadTypes: ['Data'], + onChangeCancerGeneFilter: this.store + .updateMutatedGenesTableByCancerGenesFilter, + }), + [ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE]: () => ({ + filters: this.store.getGeneFiltersByUniqueKey( + chartMeta.uniqueKey + ), + promise: this.store.structuralVariantGeneTableRowData, + onValueSelection: this.store.addGeneFilters, + onResetSelection: () => + this.store.resetGeneFilter(chartMeta.uniqueKey), + selectedGenes: this.store.selectedGenes, + onGeneSelect: this.store.onCheckGene, + title: this.store.getChartTitle( ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE, props.title - ); - props.getData = () => - this.store.getStructuralVariantGenesDownloadData(); - props.genePanelCache = this.store.genePanelCache; - props.downloadTypes = ['Data']; - props.filterByCancerGenes = this.store.filterSVGenesTableByCancerGenes; - props.onChangeCancerGeneFilter = this.store.updateSVGenesTableByCancerGenesFilter; - props.alterationFilterEnabled = getServerConfig().skin_show_settings_menu; - props.filterAlterations = this.store.isGlobalMutationFilterActive; - break; - } - case ChartTypeEnum.STRUCTURAL_VARIANTS_TABLE: { - props.filters = this.store.getGeneFiltersByUniqueKey( + ), + getData: () => + getStructuralVariantGenesDownloadData( + this.store.structuralVariantGeneTableRowData, + this.store.oncokbCancerGeneFilterEnabled + ), + genePanelCache: this.store.genePanelCache, + downloadTypes: ['Data'], + filterByCancerGenes: this.store.filterSVGenesTableByCancerGenes, + onChangeCancerGeneFilter: this.store + .updateSVGenesTableByCancerGenesFilter, + alterationFilterEnabled: getServerConfig() + .skin_show_settings_menu, + filterAlterations: this.store.isGlobalMutationFilterActive, + }), + [ChartTypeEnum.STRUCTURAL_VARIANTS_TABLE]: () => ({ + filters: this.store.getGeneFiltersByUniqueKey( chartMeta.uniqueKey - ); - props.promise = this.store.structuralVariantTableRowData; - props.onValueSelection = this.store.addStructVarFilters; - props.onResetSelection = () => - this.store.resetGeneFilter(chartMeta.uniqueKey); - props.selectedStructuralVariants = this.store.selectedStructuralVariants; - props.onStructuralVariantSelect = this.store.onCheckStructuralVariant; - props.title = this.store.getChartTitle( + ), + promise: this.store.structuralVariantTableRowData, + onValueSelection: this.store.addStructVarFilters, + onResetSelection: () => + this.store.resetGeneFilter(chartMeta.uniqueKey), + selectedStructuralVariants: this.store + .selectedStructuralVariants, + onStructuralVariantSelect: this.store.onCheckStructuralVariant, + title: this.store.getChartTitle( ChartTypeEnum.STRUCTURAL_VARIANTS_TABLE, props.title - ); - props.getData = () => - this.store.getStructuralVariantGenesDownloadData(); - props.genePanelCache = this.store.genePanelCache; - props.downloadTypes = ['Data']; - props.filterByCancerGenes = this.store.filterStructVarsTableByCancerGenes; - props.onChangeCancerGeneFilter = this.store.updateStructVarsTableByCancerGenesFilter; - props.alterationFilterEnabled = getServerConfig().skin_show_settings_menu; - props.filterAlterations = this.store.isGlobalMutationFilterActive; - break; - } - case ChartTypeEnum.CNA_GENES_TABLE: { - props.filters = this.store.getGeneFiltersByUniqueKey( + ), + getData: () => + getStructuralVariantGenesDownloadData( + this.store.structuralVariantTableRowData, + this.store.oncokbCancerGeneFilterEnabled + ), + genePanelCache: this.store.genePanelCache, + downloadTypes: ['Data'], + filterByCancerGenes: this.store + .filterStructVarsTableByCancerGenes, + onChangeCancerGeneFilter: this.store + .updateStructVarsTableByCancerGenesFilter, + alterationFilterEnabled: getServerConfig() + .skin_show_settings_menu, + filterAlterations: this.store.isGlobalMutationFilterActive, + }), + [ChartTypeEnum.CNA_GENES_TABLE]: () => ({ + filters: this.store.getGeneFiltersByUniqueKey( chartMeta.uniqueKey - ); - props.promise = this.store.cnaGeneTableRowData; - props.onValueSelection = this.store.addGeneFilters; - props.onResetSelection = () => - this.store.resetGeneFilter(chartMeta.uniqueKey); - props.selectedGenes = this.store.selectedGenes; - props.onGeneSelect = this.store.onCheckGene; - props.title = this.store.getChartTitle( + ), + promise: this.store.cnaGeneTableRowData, + onValueSelection: this.store.addGeneFilters, + onResetSelection: () => + this.store.resetGeneFilter(chartMeta.uniqueKey), + selectedGenes: this.store.selectedGenes, + onGeneSelect: this.store.onCheckGene, + title: this.store.getChartTitle( ChartTypeEnum.CNA_GENES_TABLE, props.title - ); - props.getData = () => this.store.getGenesCNADownloadData(); - props.genePanelCache = this.store.genePanelCache; - props.downloadTypes = ['Data']; - props.filterByCancerGenes = this.store.filterCNAGenesTableByCancerGenes; - props.onChangeCancerGeneFilter = this.store.updateCNAGenesTableByCancerGenesFilter; - props.alterationFilterEnabled = getServerConfig().skin_show_settings_menu; - props.filterAlterations = this.store.isGlobalAlterationFilterActive; - break; - } - case ChartTypeEnum.GENOMIC_PROFILES_TABLE: { - props.filters = toJS(this.store.genomicProfilesFilter); - props.promise = this.store.molecularProfileSampleCounts; - props.onValueSelection = this.store.addGenomicProfilesFilter; - props.onResetSelection = () => { + ), + getData: () => + getGenesCNADownloadData( + this.store.cnaGeneTableRowData, + this.store.oncokbCancerGeneFilterEnabled + ), + genePanelCache: this.store.genePanelCache, + downloadTypes: ['Data'], + filterByCancerGenes: this.store + .filterCNAGenesTableByCancerGenes, + onChangeCancerGeneFilter: this.store + .updateCNAGenesTableByCancerGenesFilter, + alterationFilterEnabled: getServerConfig() + .skin_show_settings_menu, + filterAlterations: this.store.isGlobalAlterationFilterActive, + }), + [ChartTypeEnum.GENOMIC_PROFILES_TABLE]: () => ({ + filters: toJS(this.store.genomicProfilesFilter), + promise: this.store.molecularProfileSampleCounts, + onValueSelection: this.store.addGenomicProfilesFilter, + onResetSelection: () => { this.store.setGenomicProfilesFilter([]); - }; - break; - } - case ChartTypeEnum.CASE_LIST_TABLE: { - props.filters = toJS(this.store.caseListsFilter); - props.promise = this.store.caseListSampleCounts; - props.onValueSelection = this.store.addCaseListsFilter; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.CASE_LIST_TABLE]: () => ({ + filters: toJS(this.store.caseListsFilter), + promise: this.store.caseListSampleCounts, + onValueSelection: this.store.addCaseListsFilter, + onResetSelection: () => { this.store.setCaseListsFilter([]); + }, + }), + [ChartTypeEnum.SURVIVAL]: () => { + const props: Partial = { + promise: this.store.survivalPlots, + getData: () => + getSurvivalDownloadData( + chartMeta, + this.store.survivalPlots.result, + this.store.survivalData.result, + this.store.selectedPatients, + this.store.selectedPatientKeys.result + ), + patientToAnalysisGroup: this.store.patientToAnalysisGroup, + downloadTypes: ['Data', 'SVG', 'PDF'], + description: this.store.survivalDescriptions.result + ? this.store.survivalDescriptions.result[ + chartMeta.uniqueKey.substring( + 0, + chartMeta.uniqueKey.lastIndexOf('_SURVIVAL') + ) + ][0] + : undefined, + onToggleSurvivalPlotLeftTruncation: this.handlers + .onToggleSurvivalPlotLeftTruncation, + survivalPlotLeftTruncationChecked: this.store.survivalPlotLeftTruncationToggleMap?.get( + chartMeta.uniqueKey + ), + onDataBinSelection: this.handlers.onDataBinSelection, }; - break; - } - case ChartTypeEnum.SURVIVAL: { - props.promise = this.store.survivalPlots; - props.getData = () => - this.store.getSurvivalDownloadData(chartMeta); - props.patientToAnalysisGroup = this.store.patientToAnalysisGroup; - props.downloadTypes = ['Data', 'SVG', 'PDF']; - props.description = this.store.survivalDescriptions.result - ? this.store.survivalDescriptions.result![ - chartMeta.uniqueKey.substring( - 0, - chartMeta.uniqueKey.lastIndexOf('_SURVIVAL') - ) - ][0] - : undefined; - props.onToggleSurvivalPlotLeftTruncation = this.handlers.onToggleSurvivalPlotLeftTruncation; - props.survivalPlotLeftTruncationChecked = this.store.survivalPlotLeftTruncationToggleMap?.get( - chartMeta!.uniqueKey - ); - /* start of left truncation adjustment related settings */ - // Currently, left truncation is only appliable for Overall Survival data + if ( this.store.isLeftTruncationAvailable.result && new RegExp('OS_SURVIVAL').test(chartMeta.uniqueKey) @@ -521,237 +615,266 @@ export class StudySummaryTab extends React.Component< 'OS_SURVIVAL' ]?.survivalDataWithoutLeftTruncation; } - props.onDataBinSelection = this.handlers.onDataBinSelection; - /* end of left truncation adjustment related settings */ - break; - } - case ChartTypeEnum.VIOLIN_PLOT_TABLE: + + return props; + }, + [ChartTypeEnum.VIOLIN_PLOT_TABLE]: () => { const chartInfo = this.store.getXvsYViolinChartInfo( - props.chartMeta!.uniqueKey + chartMeta.uniqueKey )!; const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey + chartMeta.uniqueKey )!; - props.filters = [ - ...this.store.getClinicalDataFiltersByUniqueKey( - chartInfo.categoricalAttr.clinicalAttributeId - ), - ...this.store.getClinicalDataFiltersByUniqueKey( + const props: Partial = { + filters: [ + ...this.store.getClinicalDataFiltersByUniqueKey( + chartInfo.categoricalAttr.clinicalAttributeId + ), + ...this.store.getClinicalDataFiltersByUniqueKey( + chartInfo.numericalAttr.clinicalAttributeId + ), + ], + title: `${chartInfo.numericalAttr.displayName}${ + settings.violinLogScale ? ' (log)' : '' + } vs ${chartInfo.categoricalAttr.displayName}`, + promise: this.store.clinicalViolinDataCache.get({ + chartInfo, + violinLogScale: !!settings.violinLogScale, + }), + axisLabelX: chartInfo.categoricalAttr.displayName, + axisLabelY: chartInfo.numericalAttr.displayName, + showLogScaleToggle: logScalePossible( chartInfo.numericalAttr.clinicalAttributeId ), - ]; - props.title = `${chartInfo.numericalAttr.displayName}${ - settings.violinLogScale ? ' (log)' : '' - } vs ${chartInfo.categoricalAttr.displayName}`; - props.promise = this.store.clinicalViolinDataCache.get({ - chartInfo, - violinLogScale: !!settings.violinLogScale, - }); - props.axisLabelX = chartInfo.categoricalAttr.displayName; - props.axisLabelY = chartInfo.numericalAttr.displayName; - props.showLogScaleToggle = logScalePossible( - chartInfo.numericalAttr.clinicalAttributeId - ); - props.logScaleChecked = settings.violinLogScale; - props.onToggleLogScale = () => { - const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey - )!; - settings.violinLogScale = !settings.violinLogScale; - }; - props.showViolinPlotToggle = true; - props.violinPlotChecked = settings.showViolin; - props.onToggleViolinPlot = () => { - const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey - )!; - settings.showViolin = !settings.showViolin; - }; - props.showBoxPlotToggle = true; - props.boxPlotChecked = settings.showBox; - props.onToggleBoxPlot = () => { - const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey - )!; - settings.showBox = !settings.showBox; - }; - props.onValueSelection = ( - type: 'categorical' | 'numerical', - values: string[] | { start: number; end: number } - ) => { - switch (type) { - case 'categorical': - this.store.updateClinicalAttributeFilterByValues( - chartInfo.categoricalAttr.clinicalAttributeId, - (values as string[]).map( - value => ({ value } as DataFilterValue) - ) - ); - break; - case 'numerical': - this.store.updateClinicalDataCustomIntervalFilter( - chartInfo.numericalAttr.clinicalAttributeId, - values as { start: number; end: number } - ); - break; - } - }; - props.selectedCategories = this.store - .getClinicalDataFiltersByUniqueKey( - chartInfo.categoricalAttr.clinicalAttributeId - ) - .map(x => x.value); - props.onResetSelection = () => { - this.store.updateClinicalAttributeFilterByValues( - chartInfo.categoricalAttr.clinicalAttributeId, - [] - ); - this.store.updateClinicalAttributeFilterByValues( - chartInfo.numericalAttr.clinicalAttributeId, - [] - ); + logScaleChecked: settings.violinLogScale, + onToggleLogScale: () => { + const settings = this.store.getXvsYChartSettings( + chartMeta.uniqueKey + )!; + settings.violinLogScale = !settings.violinLogScale; + }, + showViolinPlotToggle: true, + violinPlotChecked: settings.showViolin, + onToggleViolinPlot: () => { + const settings = this.store.getXvsYChartSettings( + chartMeta.uniqueKey + )!; + settings.showViolin = !settings.showViolin; + }, + showBoxPlotToggle: true, + boxPlotChecked: settings.showBox, + onToggleBoxPlot: () => { + const settings = this.store.getXvsYChartSettings( + chartMeta.uniqueKey + )!; + settings.showBox = !settings.showBox; + }, + onValueSelection: ( + type: 'categorical' | 'numerical', + values: string[] | { start: number; end: number } + ) => { + switch (type) { + case 'categorical': + this.store.updateClinicalAttributeFilterByValues( + chartInfo.categoricalAttr + .clinicalAttributeId, + (values as string[]).map( + value => ({ value } as DataFilterValue) + ) + ); + break; + case 'numerical': + this.store.updateClinicalDataCustomIntervalFilter( + chartInfo.numericalAttr.clinicalAttributeId, + values as { start: number; end: number } + ); + break; + } + }, + selectedCategories: this.store + .getClinicalDataFiltersByUniqueKey( + chartInfo.categoricalAttr.clinicalAttributeId + ) + .map(x => x.value), + onResetSelection: () => { + this.store.updateClinicalAttributeFilterByValues( + chartInfo.categoricalAttr.clinicalAttributeId, + [] + ); + this.store.updateClinicalAttributeFilterByValues( + chartInfo.numericalAttr.clinicalAttributeId, + [] + ); + }, }; - break; - case ChartTypeEnum.SCATTER: { - props.filters = this.store.getScatterPlotFiltersByUniqueKey( - props.chartMeta!.uniqueKey - ); + return props; + }, + [ChartTypeEnum.SCATTER]: () => { const chartInfo = this.store.getXvsYScatterChartInfo( - props.chartMeta!.uniqueKey + chartMeta.uniqueKey )!; const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey + chartMeta.uniqueKey )!; - props.title = props.chartMeta!.displayName; - props.promise = this.store.clinicalDataDensityCache.get({ - chartInfo, - xAxisLogScale: !!settings.xLogScale, - yAxisLogScale: !!settings.yLogScale, - }); - props.showLogScaleXToggle = logScalePossible( - chartInfo.xAttr.clinicalAttributeId - ); - props.showLogScaleYToggle = logScalePossible( - chartInfo.yAttr.clinicalAttributeId - ); - props.logScaleXChecked = settings.xLogScale; - props.logScaleYChecked = settings.yLogScale; - props.onToggleLogScaleX = () => { - const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey - )!; - settings.xLogScale = !settings.xLogScale; - }; - props.onToggleLogScaleY = () => { - const settings = this.store.getXvsYChartSettings( - props.chartMeta!.uniqueKey - )!; - settings.yLogScale = !settings.yLogScale; - }; - props.onSwapAxes = () => { - this.store.swapXvsYChartAxes(props.chartMeta!.uniqueKey); - }; - props.plotDomain = chartInfo.plotDomain; - props.axisLabelX = `${chartInfo.xAttr.displayName}${ - settings.xLogScale ? ' (log)' : '' - }`; - props.axisLabelY = `${chartInfo.yAttr.displayName}${ - settings.yLogScale ? ' (log)' : '' - }`; - props.tooltip = makeDensityScatterPlotTooltip( - chartInfo, - settings - ); - props.onValueSelection = (bounds: RectangleBounds) => { - this.store.updateScatterPlotFilterByValues( - props.chartMeta!.uniqueKey, - bounds - ); - }; - props.onResetSelection = () => { - this.store.updateScatterPlotFilterByValues( - props.chartMeta!.uniqueKey - ); + const props: Partial = { + filters: this.store.getScatterPlotFiltersByUniqueKey( + chartMeta.uniqueKey + ), + title: chartMeta.displayName, + promise: this.store.clinicalDataDensityCache.get({ + chartInfo, + xAxisLogScale: !!settings.xLogScale, + yAxisLogScale: !!settings.yLogScale, + }), + showLogScaleXToggle: logScalePossible( + chartInfo.xAttr.clinicalAttributeId + ), + showLogScaleYToggle: logScalePossible( + chartInfo.yAttr.clinicalAttributeId + ), + logScaleXChecked: settings.xLogScale, + logScaleYChecked: settings.yLogScale, + onToggleLogScaleX: () => { + const settings = this.store.getXvsYChartSettings( + chartMeta.uniqueKey + )!; + settings.xLogScale = !settings.xLogScale; + }, + onToggleLogScaleY: () => { + const settings = this.store.getXvsYChartSettings( + chartMeta.uniqueKey + )!; + settings.yLogScale = !settings.yLogScale; + }, + onSwapAxes: () => { + this.store.swapXvsYChartAxes(chartMeta.uniqueKey); + }, + plotDomain: chartInfo.plotDomain, + axisLabelX: `${chartInfo.xAttr.displayName}${ + settings.xLogScale ? ' (log)' : '' + }`, + axisLabelY: `${chartInfo.yAttr.displayName}${ + settings.yLogScale ? ' (log)' : '' + }`, + tooltip: makeDensityScatterPlotTooltip(chartInfo, settings), + onValueSelection: (bounds: RectangleBounds) => { + this.store.updateScatterPlotFilterByValues( + chartMeta.uniqueKey, + bounds + ); + }, + onResetSelection: () => { + this.store.updateScatterPlotFilterByValues( + chartMeta.uniqueKey + ); + }, + sampleToAnalysisGroup: this.store.sampleToAnalysisGroup, + getData: () => + getScatterDownloadData( + chartInfo, + this.store.selectedSamples + ), + downloadTypes: ['Data', 'SVG', 'PDF'], }; - props.sampleToAnalysisGroup = this.store.sampleToAnalysisGroup; - props.getData = () => - this.store.getScatterDownloadData( - props.chartMeta!.uniqueKey - ); - props.downloadTypes = ['Data', 'SVG', 'PDF']; - break; - } - case ChartTypeEnum.SAMPLE_TREATMENTS_TABLE: { - props.filters = this.store.sampleTreatmentFiltersAsStrings; - props.promise = this.store.sampleTreatments; - props.onValueSelection = this.store.onTreatmentSelection; - props.getData = () => - this.store.getSampleTreatmentDownloadData(); - props.downloadTypes = ['Data']; - props.onResetSelection = () => { + return props; + }, + [ChartTypeEnum.SAMPLE_TREATMENTS_TABLE]: () => ({ + filters: this.store.sampleTreatmentFiltersAsStrings, + promise: this.store.sampleTreatments, + onValueSelection: this.store.onTreatmentSelection, + getData: () => + getSampleTreatmentDownloadData(this.store.sampleTreatments), + downloadTypes: ['Data'], + onResetSelection: () => { this.store.clearSampleTreatmentFilters(); - }; - break; - } - case ChartTypeEnum.SAMPLE_TREATMENT_GROUPS_TABLE: { - props.filters = this.store.sampleTreatmentGroupFiltersAsStrings; - props.promise = this.store.sampleTreatmentGroups; - props.onValueSelection = this.store.onTreatmentSelection; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.SAMPLE_TREATMENT_GROUPS_TABLE]: () => ({ + filters: this.store.sampleTreatmentGroupFiltersAsStrings, + promise: this.store.sampleTreatmentGroups, + onValueSelection: this.store.onTreatmentSelection, + onResetSelection: () => { this.store.clearSampleTreatmentGroupFilters(); - }; - break; - } - case ChartTypeEnum.SAMPLE_TREATMENT_TARGET_TABLE: { - props.filters = this.store.sampleTreatmentTargetFiltersAsStrings; - props.promise = this.store.sampleTreatmentTarget; - props.onValueSelection = this.store.onTreatmentSelection; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.SAMPLE_TREATMENT_TARGET_TABLE]: () => ({ + filters: this.store.sampleTreatmentTargetFiltersAsStrings, + promise: this.store.sampleTreatmentTarget, + onValueSelection: this.store.onTreatmentSelection, + onResetSelection: () => { this.store.clearSampleTreatmentTargetFilters(); - }; - break; - } - case ChartTypeEnum.PATIENT_TREATMENTS_TABLE: { - props.filters = this.store.patientTreatmentFiltersAsStrings; - props.promise = this.store.patientTreatments; - props.onValueSelection = this.store.onTreatmentSelection; - props.getData = () => - this.store.getPatientTreatmentDownloadData(); - props.downloadTypes = ['Data']; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.PATIENT_TREATMENTS_TABLE]: () => ({ + filters: this.store.patientTreatmentFiltersAsStrings, + promise: this.store.patientTreatments, + onValueSelection: this.store.onTreatmentSelection, + getData: () => + getPatientTreatmentDownloadData( + this.store.patientTreatments + ), + downloadTypes: ['Data'], + onResetSelection: () => { this.store.clearPatientTreatmentFilters(); - }; - break; - } - case ChartTypeEnum.PATIENT_TREATMENT_GROUPS_TABLE: { - props.filters = this.store.patientTreatmentGroupFiltersAsStrings; - props.promise = this.store.patientTreatmentGroups; - props.onValueSelection = this.store.onTreatmentSelection; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.PATIENT_TREATMENT_GROUPS_TABLE]: () => ({ + filters: this.store.patientTreatmentGroupFiltersAsStrings, + promise: this.store.patientTreatmentGroups, + onValueSelection: this.store.onTreatmentSelection, + onResetSelection: () => { this.store.clearPatientTreatmentGroupFilters(); - }; - break; - } - case ChartTypeEnum.PATIENT_TREATMENT_TARGET_TABLE: { - props.filters = this.store.patientTreatmentTargetFiltersAsStrings; - props.promise = this.store.patientTreatmentTarget; - props.onValueSelection = this.store.onTreatmentSelection; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.PATIENT_TREATMENT_TARGET_TABLE]: () => ({ + filters: this.store.patientTreatmentTargetFiltersAsStrings, + promise: this.store.patientTreatmentTarget, + onValueSelection: this.store.onTreatmentSelection, + onResetSelection: () => { this.store.clearPatientTreatmentTargetFilters(); - }; - break; - } - case ChartTypeEnum.CLINICAL_EVENT_TYPE_COUNTS_TABLE: { - props.filters = this.store.clinicalEventTypeFiltersRawStrings; - props.promise = this.store.clinicalEventTypeCounts; - props.onValueSelection = this.store.addClinicalEventTypeFilter; - props.onResetSelection = () => { + }, + }), + [ChartTypeEnum.CLINICAL_EVENT_TYPE_COUNTS_TABLE]: () => ({ + filters: this.store.clinicalEventTypeFiltersRawStrings, + promise: this.store.clinicalEventTypeCounts, + onValueSelection: this.store.addClinicalEventTypeFilter, + onResetSelection: () => { this.store.resetClinicalEventTypeFilter(); - }; - break; - } - default: - break; + }, + }), + }); + } + + renderAttributeChart = (chartMeta: ChartMeta) => { + let props: Partial = { + chartMeta: chartMeta, + chartType: this.props.store.chartsType.get(chartMeta.uniqueKey), + store: this.props.store, + dimension: this.store.chartsDimension.get(chartMeta.uniqueKey), + title: chartMeta.displayName, + filters: [], + onDeleteChart: this.handlers.onDeleteChart, + isNewlyAdded: this.handlers.isNewlyAdded, + studyViewFilters: this.store.filters, + analysisGroupsSettings: this.store.analysisGroupsSettings, + cancerGeneFilterEnabled: this.store.oncokbCancerGeneFilterEnabled, + setComparisonConfirmationModal: this.store + .setComparisonConfirmationModal, + }; + + const chartType = this.store.chartsType.get(chartMeta.uniqueKey)!; + const subTypeProps = this.chartTypeConfig(chartMeta, props)[ + chartType + ](); + + if (subTypeProps.commonProps) { + // charts that have sub types + const subProps = subTypeProps[ + this.store.getChartMetaDataType(chartMeta.uniqueKey) + ](); + props = { ...props, ...subProps, ...subTypeProps.commonProps }; + } else { + props = { ...props, ...subTypeProps }; } // Using custom component inside of the GridLayout creates too many chaos as mentioned here diff --git a/src/shared/constants.ts b/src/shared/constants.ts index c311c6ae065..cbe918b94fb 100644 --- a/src/shared/constants.ts +++ b/src/shared/constants.ts @@ -129,3 +129,13 @@ export const DataTypeConstants = { }; export const SUPPORTED_DAT_METHODS = ['oauth2', 'uuid']; + +export const MutationOptionConstants = { + MUTATED: 'MUTATED', + MUTATION_TYPE: 'MUTATION_TYPE', +}; + +export const MutationOptionConstantsLabel = { + [MutationOptionConstants.MUTATED]: 'Mutated vs Not Mutated', + [MutationOptionConstants.MUTATION_TYPE]: 'Mutation Types', +};