From 5f850c231b97afe810c0bb2042d4956bad9ada78 Mon Sep 17 00:00:00 2001 From: Bryan Lai <56288120+gblaih@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:48:56 -0500 Subject: [PATCH] Add user color configuration for oncoprinter (#4817) * add color chooser to oncoprinter * add tests and screenshots --------- Co-authored-by: Bryan Lai --- ...efault_colors_element_chrome_1600x1000.png | Bin 0 -> 40317 bytes ...lected_colors_element_chrome_1600x1000.png | Bin 0 -> 40375 bytes .../specs/core/oncoprinterColorConfig.spec.js | 130 +++++++++++++++ src/pages/resultsView/ResultsViewPageStore.ts | 10 +- .../tools/oncoprinter/Oncoprinter.tsx | 113 ++++++++++++- .../OncoprinterClinicalAndHeatmapUtils.ts | 40 ++++- .../tools/oncoprinter/OncoprinterStore.ts | 49 ++++++ .../tools/oncoprinter/OncoprinterToolUtils.ts | 27 ++++ .../oncoprint/ClinicalTrackColorPicker.tsx | 4 - src/shared/components/oncoprint/DeltaUtils.ts | 3 - src/shared/components/oncoprint/Oncoprint.tsx | 2 - .../oncoprint/OncoprintColorModal.tsx | 107 +++++++++++++ .../oncoprint/ResultsViewOncoprint.tsx | 151 ++++-------------- 13 files changed, 499 insertions(+), 137 deletions(-) create mode 100644 end-to-end-test/remote/screenshots/reference/oncoprinter_reflects_default_colors_element_chrome_1600x1000.png create mode 100644 end-to-end-test/remote/screenshots/reference/oncoprinter_reflects_user_selected_colors_element_chrome_1600x1000.png create mode 100644 end-to-end-test/remote/specs/core/oncoprinterColorConfig.spec.js create mode 100644 src/shared/components/oncoprint/OncoprintColorModal.tsx diff --git a/end-to-end-test/remote/screenshots/reference/oncoprinter_reflects_default_colors_element_chrome_1600x1000.png b/end-to-end-test/remote/screenshots/reference/oncoprinter_reflects_default_colors_element_chrome_1600x1000.png new file mode 100644 index 0000000000000000000000000000000000000000..f04271fc518905abed4837fb2eacca97f02918fe GIT binary patch literal 40317 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z&?|DFIk!7_*dasaVy0xesXtpF8#A68Ep4Il(GAZtf(iT70=RKW<^)QEgY%$@#cbL1 zdA)x1d1)P69;iR@ds?;5hR?IQo?Cs@Zuao>2b!@Lz06`WybJ3645wX7*^riRxhu%9 zY{saAXCp`acDacljWC3gefIBvWFP4i5qo>uawE%xaoXWt=D{8AUU#eRTG!6fF!pWh z@{j}dajlzPILo>#zni#Z!3dA(w|_sJwbjRPWaeU@^cuHoXaCX5vRCYgZ#Z=t{#o|> fzwKXnV!OqEb8XeO$^HMrzX_i@+U@;#uK#}nPdk@b literal 0 HcmV?d00001 diff --git a/end-to-end-test/remote/specs/core/oncoprinterColorConfig.spec.js b/end-to-end-test/remote/specs/core/oncoprinterColorConfig.spec.js new file mode 100644 index 00000000000..52fc007dc61 --- /dev/null +++ b/end-to-end-test/remote/specs/core/oncoprinterColorConfig.spec.js @@ -0,0 +1,130 @@ +var assertScreenShotMatch = require('../../../shared/lib/testUtils') + .assertScreenShotMatch; +var assert = require('assert'); +var waitForOncoprint = require('../../../shared/specUtils').waitForOncoprint; +var goToUrlAndSetLocalStorage = require('../../../shared/specUtils') + .goToUrlAndSetLocalStorage; +var getNthOncoprintTrackOptionsElements = require('../../../shared/specUtils') + .getNthOncoprintTrackOptionsElements; +var { + checkOncoprintElement, + getElementByTestHandle, +} = require('../../../shared/specUtils.js'); + +const TIMEOUT = 6000; + +const ONCOPRINT_TIMEOUT = 60000; + +const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, ''); + +describe('oncoprinter clinical example data, color configuration', () => { + it('oncoprinter color configuration modal reflects user selected colors', function() { + goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/oncoprinter`); + $('.oncoprinterClinicalExampleData').waitForExist(); + $('.oncoprinterClinicalExampleData').click(); + $('.oncoprinterSubmit').click(); + waitForOncoprint(TIMEOUT); + + var trackOptionsElts = getNthOncoprintTrackOptionsElements(2); + // open menu + $(trackOptionsElts.button_selector).click(); + $(trackOptionsElts.dropdown_selector).waitForDisplayed({ + timeout: 1000, + }); + // click "Edit Colors" to open modal + $(trackOptionsElts.dropdown_selector + ' li:nth-child(11)').click(); + browser.pause(1000); + + // select new colors for track values + getElementByTestHandle('color-picker-icon').click(); + $('.circle-picker').waitForDisplayed({ timeout: 1000 }); + $('.circle-picker [title="#990099"]').click(); + waitForOncoprint(ONCOPRINT_TIMEOUT); + getElementByTestHandle('color-picker-icon').waitForDisplayed(); + getElementByTestHandle('color-picker-icon').click(); + $('.circle-picker').waitForDisplayed({ reverse: true }); + + $$('[data-test="color-picker-icon"]')[1].click(); + $('.circle-picker').waitForDisplayed({ timeout: 1000 }); + $('.circle-picker [title="#109618"]').click(); + waitForOncoprint(ONCOPRINT_TIMEOUT); + getElementByTestHandle('color-picker-icon').waitForDisplayed(); + $$('[data-test="color-picker-icon"]')[1].click(); + $('.circle-picker').waitForDisplayed({ reverse: true }); + + $$('[data-test="color-picker-icon"]')[2].click(); + $('.circle-picker').waitForDisplayed({ timeout: 1000 }); + $('.circle-picker [title="#8b0707"]').click(); + waitForOncoprint(ONCOPRINT_TIMEOUT); + + assert.strictEqual( + $('[data-test="color-picker-icon"] rect').getAttribute('fill'), + '#990099' + ); + assert.strictEqual( + $$('[data-test="color-picker-icon"] rect')[1].getAttribute('fill'), + '#109618' + ); + assert.strictEqual( + $$('[data-test="color-picker-icon"] rect')[2].getAttribute('fill'), + '#8b0707' + ); + }); + + it('oncoprinter reflects user selected colors', () => { + // close modal + $('a.tabAnchor_oncoprint').click(); + var res = checkOncoprintElement(); + assertScreenShotMatch(res); + }); + + it('oncoprinter reset colors button is visible when default colors not used', () => { + // click "Edit Colors" to open modal and check "Reset Colors" button in modal + var trackOptionsElts = getNthOncoprintTrackOptionsElements(2); + $(trackOptionsElts.button_selector).click(); + $(trackOptionsElts.dropdown_selector).waitForDisplayed({ + timeout: 1000, + }); + $(trackOptionsElts.dropdown_selector + ' li:nth-child(11)').click(); + getElementByTestHandle('resetColors').waitForDisplayed(); + }); + + it('oncoprinter color configuration modal reflects default colors', () => { + // click "Reset Colors" track + getElementByTestHandle('resetColors').click(); + waitForOncoprint(ONCOPRINT_TIMEOUT); + + assert.strictEqual( + $('[data-test="color-picker-icon"] rect').getAttribute('fill'), + '#dc3912' + ); + assert.strictEqual( + $$('[data-test="color-picker-icon"] rect')[1].getAttribute('fill'), + '#3366cc' + ); + assert.strictEqual( + $$('[data-test="color-picker-icon"] rect')[2].getAttribute('fill'), + '#ff9900' + ); + }); + + it('oncoprinter reflects default colors', () => { + // close modal + $('a.tabAnchor_oncoprint').click(); + var res = checkOncoprintElement(); + assertScreenShotMatch(res); + }); + + it('oncoprinter reset colors button is hidden when default colors are used', () => { + // click "Edit Colors" to open modal and check "Reset Colors" button in modal + var trackOptionsElts = getNthOncoprintTrackOptionsElements(2); + $(trackOptionsElts.button_selector).click(); + $(trackOptionsElts.dropdown_selector).waitForDisplayed({ + timeout: 1000, + }); + $(trackOptionsElts.dropdown_selector + ' li:nth-child(11)').click(); + getElementByTestHandle('resetColors').waitForDisplayed({ + reverse: true, + }); + }); +}); diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts index 4c154922fcb..82500ac82ee 100644 --- a/src/pages/resultsView/ResultsViewPageStore.ts +++ b/src/pages/resultsView/ResultsViewPageStore.ts @@ -435,6 +435,8 @@ interface IResultsViewExclusionSettings { ) => void; } +const ONCOPRINT_COLOR_CONFIG = 'clinicalTracksColorConfig'; + /* fields and methods in the class below are ordered based on roughly /* chronological setup concerns, rather than on encapsulation and public API */ /* tslint:disable: member-ordering */ @@ -496,7 +498,7 @@ export class ResultsViewPageStore extends AnalysisStore ); const clinicalTracksColorConfig = localStorage.getItem( - 'clinicalTracksColorConfig' + ONCOPRINT_COLOR_CONFIG ); if (clinicalTracksColorConfig !== null) { this._userSelectedStudiesToClinicalTracksColors = JSON.parse( @@ -589,8 +591,8 @@ export class ResultsViewPageStore extends AnalysisStore @observable _userSelectedStudiesToClinicalTracksColors: { [studies: string]: { - [label: string]: { - [value: string]: RGBAColor; + [trackLabel: string]: { + [attributeValue: string]: RGBAColor; }; }; } = { global: {} }; @@ -641,7 +643,7 @@ export class ResultsViewPageStore extends AnalysisStore ] = color; } localStorage.setItem( - 'clinicalTracksColorConfig', + ONCOPRINT_COLOR_CONFIG, JSON.stringify(this._userSelectedStudiesToClinicalTracksColors) ); } diff --git a/src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx b/src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx index 158d82a988a..eaa6db3ca3a 100644 --- a/src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx +++ b/src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx @@ -8,7 +8,7 @@ import OncoprintControls, { } from 'shared/components/oncoprint/controls/OncoprintControls'; import { percentAltered } from '../../../../shared/components/oncoprint/OncoprintUtils'; import { getServerConfig } from 'config/config'; -import { OncoprintJS } from 'oncoprintjs'; +import { OncoprintJS, RGBAColor } from 'oncoprintjs'; import fileDownload from 'react-file-download'; import { FadeInteraction, svgToPdfDownload } from 'cbioportal-frontend-commons'; import classNames from 'classnames'; @@ -19,12 +19,34 @@ import WindowStore from '../../../../shared/components/window/WindowStore'; import { getGeneticTrackKey } from './OncoprinterGeneticUtils'; import InfoBanner from '../../../../shared/components/banners/InfoBanner'; import '../../../../globalStyles/oncoprintStyles.scss'; +import _ from 'lodash'; +import { + MUTATION_SPECTRUM_CATEGORIES, + MUTATION_SPECTRUM_FILLS, +} from 'shared/cache/ClinicalDataCache'; +import { + hexToRGBA, + RESERVED_CLINICAL_VALUE_COLORS, + rgbaToHex, +} from 'shared/lib/Colors'; +import { + getClinicalTrackColor, + getClinicalTrackValues, +} from 'shared/components/oncoprint/ResultsViewOncoprint'; +import { Modal } from 'react-bootstrap'; +import ClinicalTrackColorPicker from 'shared/components/oncoprint/ClinicalTrackColorPicker'; +import classnames from 'classnames'; +import { getDefaultClinicalAttributeColoringForStringDatatype } from './OncoprinterToolUtils'; +import { OncoprintColorModal } from 'shared/components/oncoprint/OncoprintColorModal'; interface IOncoprinterProps { divId: string; store: OncoprinterStore; } +const DEFAULT_UNKNOWN_COLOR = [255, 255, 255, 1]; +const DEFAULT_MIXED_COLOR = [220, 57, 18, 1]; + @observer export default class Oncoprinter extends React.Component< IOncoprinterProps, @@ -379,9 +401,92 @@ export default class Oncoprinter extends React.Component< return WindowStore.size.width - 75; } + @action.bound + public handleSelectedClinicalTrackColorChange( + value: string, + color: RGBAColor | undefined + ) { + if (this.selectedClinicalTrack) { + this.props.store.setUserSelectedClinicalTrackColor( + this.selectedClinicalTrack.label, + value, + color + ); + } + } + + @observable trackKeySelectedForEdit: string | null = null; + + @action.bound + setTrackKeySelectedForEdit(key: string | null) { + this.trackKeySelectedForEdit = key; + } + + // if trackKeySelectedForEdit is null ('Edit Colors' has not been selected in an individual track menu), + // selectedClinicalTrack will be undefined + @computed get selectedClinicalTrack() { + return _.find( + this.props.store.clinicalTracks, + t => t.key === this.trackKeySelectedForEdit + ); + } + + @computed get defaultClinicalAttributeColoringForStringDatatype() { + if (this.selectedClinicalTrack) { + return _.mapValues( + getDefaultClinicalAttributeColoringForStringDatatype( + this.selectedClinicalTrack.data + ), + hexToRGBA + ); + } + return _.mapValues(RESERVED_CLINICAL_VALUE_COLORS, hexToRGBA); + } + + @autobind + private getSelectedClinicalTrackDefaultColorForValue( + attributeValue: string + ) { + if (!this.selectedClinicalTrack) { + return DEFAULT_UNKNOWN_COLOR; + } + switch (this.selectedClinicalTrack.datatype) { + case 'counts': + return MUTATION_SPECTRUM_FILLS[ + _.indexOf(MUTATION_SPECTRUM_CATEGORIES, attributeValue) + ]; + case 'string': + // Mixed refers to when an event has multiple values (i.e. Sample Type for a patient event may have both Primary and Recurrence values) + if (attributeValue === 'Mixed') { + return DEFAULT_MIXED_COLOR; + } else { + return this + .defaultClinicalAttributeColoringForStringDatatype[ + attributeValue + ]; + } + default: + return DEFAULT_UNKNOWN_COLOR; + } + } + public render() { return (
+ {this.selectedClinicalTrack && ( + + )}
diff --git a/src/pages/staticPages/tools/oncoprinter/OncoprinterClinicalAndHeatmapUtils.ts b/src/pages/staticPages/tools/oncoprinter/OncoprinterClinicalAndHeatmapUtils.ts index 65ef8e2e723..a84d0334dd5 100644 --- a/src/pages/staticPages/tools/oncoprinter/OncoprinterClinicalAndHeatmapUtils.ts +++ b/src/pages/staticPages/tools/oncoprinter/OncoprinterClinicalAndHeatmapUtils.ts @@ -11,6 +11,9 @@ import { MUTATION_SPECTRUM_FILLS } from '../../../../shared/cache/ClinicalDataCa import { MolecularProfile } from 'cbioportal-ts-api-client'; import { AlterationTypeConstants } from 'shared/constants'; import { capitalize } from 'cbioportal-frontend-commons'; +import { hexToRGBA } from 'shared/lib/Colors'; +import { RGBAColor } from 'oncoprintjs'; +import { getDefaultClinicalAttributeColoringForStringDatatype } from './OncoprinterToolUtils'; export const ONCOPRINTER_VAL_NA = 'N/A'; @@ -470,6 +473,11 @@ export function getHeatmapTrackKey(attributeName: string) { export function getClinicalTracks( attributes: OncoprinterClinicalTrackSpec[], parsedLines: OncoprinterOrderedValuesInputLine[], + userSelectedClinicalTracksColors: { + [label: string]: { + [value: string]: RGBAColor; + }; + }, excludedSampleIds?: string[] ) { let attributeToOncoprintData = getClinicalOncoprintData( @@ -486,10 +494,20 @@ export function getClinicalTracks( attributes.map(attr => { const data = attributeToOncoprintData[attr.trackName]; - let datatype, numberRange, countsCategoryFills; + let datatype, category_to_color, numberRange, countsCategoryFills; switch (attr.datatype) { case ClinicalTrackDataType.STRING: datatype = 'string'; + category_to_color = Object.assign( + {}, + _.mapValues( + getDefaultClinicalAttributeColoringForStringDatatype( + data + ), + hexToRGBA + ), + userSelectedClinicalTracksColors[attr.trackName] + ); break; case ClinicalTrackDataType.NUMBER: case ClinicalTrackDataType.LOG_NUMBER: @@ -503,7 +521,24 @@ export function getClinicalTracks( attr.countsCategories!.length === MUTATION_SPECTRUM_FILLS.length ) { - countsCategoryFills = MUTATION_SPECTRUM_FILLS; + countsCategoryFills = attr.countsCategories!.map( + (label, i) => { + if ( + userSelectedClinicalTracksColors[ + attr.trackName + ] && + userSelectedClinicalTracksColors[ + attr.trackName + ][label] + ) { + return userSelectedClinicalTracksColors[ + attr.trackName + ][label]; + } else { + return MUTATION_SPECTRUM_FILLS[i]; + } + } + ); } break; } @@ -511,6 +546,7 @@ export function getClinicalTracks( key: getClinicalTrackKey(attr.trackName), attributeId: attr.trackName, label: attr.trackName, + category_to_color, data, datatype, description: '', diff --git a/src/pages/staticPages/tools/oncoprinter/OncoprinterStore.ts b/src/pages/staticPages/tools/oncoprinter/OncoprinterStore.ts index 9d6cecf9826..81de7451567 100644 --- a/src/pages/staticPages/tools/oncoprinter/OncoprinterStore.ts +++ b/src/pages/staticPages/tools/oncoprinter/OncoprinterStore.ts @@ -39,6 +39,7 @@ import { parseHeatmapInput, } from './OncoprinterClinicalAndHeatmapUtils'; import internalClient from 'shared/api/cbioportalInternalClientInstance'; +import { RGBAColor } from 'oncoprintjs'; export type OncoprinterDriverAnnotationSettings = Pick< DriverAnnotationSettings, @@ -54,6 +55,8 @@ function genomeNexusKey2(l:{chromosome:string, start:number, end:number, referen return `${l.chromosome}_${l.start}_${l.end}_${l.referenceAllele}_${l.variantAllele}`; }*/ +const ONCOPRINTER_COLOR_CONFIG = 'oncoprinterClinicalTracksColorConfig'; + export default class OncoprinterStore { // NOTE: we are not annotating hotspot because that needs nucleotide positions // we are not annotating COSMIC because that needs keywords @@ -70,9 +73,24 @@ export default class OncoprinterStore { @observable hideGermlineMutations = false; @observable customDriverWarningHidden: boolean; + @observable _userSelectedClinicalTracksColors: { + [trackLabel: string]: { + [attributeValue: string]: RGBAColor; + }; + } = {}; + constructor() { makeObservable(this); this.initialize(); + + const clinicalTracksColorConfig = localStorage.getItem( + ONCOPRINTER_COLOR_CONFIG + ); + if (clinicalTracksColorConfig !== null) { + this._userSelectedClinicalTracksColors = JSON.parse( + clinicalTracksColorConfig + ); + } } private initialize() { @@ -572,6 +590,7 @@ export default class OncoprinterStore { return getClinicalTracks( result.headers, result.data, + this.userSelectedClinicalTracksColors, this.sampleIdsNotInInputOrder ); } @@ -589,4 +608,34 @@ export default class OncoprinterStore { this.sampleIdsNotInInputOrder ); } + + @action.bound + public setUserSelectedClinicalTrackColor( + label: string, + value: string, + color: RGBAColor | undefined + ) { + // if color is undefined, delete color from userSelectedClinicalAttributeColors if exists + // else, set the color in userSelectedClinicalAttributeColors + if ( + !color && + this._userSelectedClinicalTracksColors[label] && + this._userSelectedClinicalTracksColors[label][value] + ) { + delete this._userSelectedClinicalTracksColors[label][value]; + } else if (color) { + if (!this._userSelectedClinicalTracksColors[label]) { + this._userSelectedClinicalTracksColors[label] = {}; + } + this._userSelectedClinicalTracksColors[label][value] = color; + } + localStorage.setItem( + ONCOPRINTER_COLOR_CONFIG, + JSON.stringify(this._userSelectedClinicalTracksColors) + ); + } + + @computed get userSelectedClinicalTracksColors() { + return this._userSelectedClinicalTracksColors; + } } diff --git a/src/pages/staticPages/tools/oncoprinter/OncoprinterToolUtils.ts b/src/pages/staticPages/tools/oncoprinter/OncoprinterToolUtils.ts index 7e6dbae7a94..df24ba05c09 100644 --- a/src/pages/staticPages/tools/oncoprinter/OncoprinterToolUtils.ts +++ b/src/pages/staticPages/tools/oncoprinter/OncoprinterToolUtils.ts @@ -1,3 +1,8 @@ +import _ from 'lodash'; +import { ClinicalTrackDatum } from 'shared/components/oncoprint/Oncoprint'; +import { makeUniqueColorGetter } from 'shared/components/plots/PlotUtils'; +import { RESERVED_CLINICAL_VALUE_COLORS } from 'shared/lib/Colors'; + export function getDataForSubmission( fileInput: HTMLInputElement | null, stringInput: string @@ -21,3 +26,25 @@ export function getDataForSubmission( } }); } + +export function getDefaultClinicalAttributeColoringForStringDatatype( + data: ClinicalTrackDatum[] +) { + const colorGetter = makeUniqueColorGetter( + _.values(RESERVED_CLINICAL_VALUE_COLORS) + ); + let categoryToColor: { [value: string]: string } = {}; + for (const d of data) { + if ( + (d.attr_val as string) !== '' && + !((d.attr_val as string) in categoryToColor) + ) { + categoryToColor[d.attr_val as string] = colorGetter(); + } + } + categoryToColor = Object.assign( + categoryToColor, + RESERVED_CLINICAL_VALUE_COLORS + ); + return categoryToColor; +} diff --git a/src/shared/components/oncoprint/ClinicalTrackColorPicker.tsx b/src/shared/components/oncoprint/ClinicalTrackColorPicker.tsx index 4e211c696db..9aaba2ad5ff 100644 --- a/src/shared/components/oncoprint/ClinicalTrackColorPicker.tsx +++ b/src/shared/components/oncoprint/ClinicalTrackColorPicker.tsx @@ -15,19 +15,16 @@ import { rgbaToHex, } from 'shared/lib/Colors'; import { COLORS } from 'pages/studyView/StudyViewUtils'; -import { ResultsViewPageStore } from 'pages/resultsView/ResultsViewPageStore'; import { RGBAColor } from 'oncoprintjs'; import _ from 'lodash'; export interface IGroupCheckboxProps { - store: ResultsViewPageStore; handleClinicalTrackColorChange?: ( value: string, color: RGBAColor | undefined ) => void; clinicalTrackValue: any; color: RGBAColor; - setClinicalTrackColorChanged: (changed: boolean) => void; } const COLOR_UNDEFINED = '#FFFFFF'; @@ -59,7 +56,6 @@ export default class ClinicalTrackColorPicker extends React.Component< ); } // set changed track key - this.props.setClinicalTrackColorChanged(true); }; @computed get colorList() { diff --git a/src/shared/components/oncoprint/DeltaUtils.ts b/src/shared/components/oncoprint/DeltaUtils.ts index f8bbffb20f8..2a121f72877 100644 --- a/src/shared/components/oncoprint/DeltaUtils.ts +++ b/src/shared/components/oncoprint/DeltaUtils.ts @@ -1345,7 +1345,6 @@ function transitionClinicalTrack( // update ruleset if color has changed for selected track if ( - nextProps.clinicalTrackColorChanged && nextProps.trackKeySelectedForEdit && getTrackSpecKeyToTrackId()[nextProps.trackKeySelectedForEdit] === trackId @@ -1355,8 +1354,6 @@ function transitionClinicalTrack( rule_set_params.exclude_from_legend = !nextProps.showClinicalTrackLegends; rule_set_params.na_legend_label = nextSpec.na_legend_label; oncoprint.setRuleSet(trackId, rule_set_params); - nextProps.setClinicalTrackColorChanged && - nextProps.setClinicalTrackColorChanged(false); } } } diff --git a/src/shared/components/oncoprint/Oncoprint.tsx b/src/shared/components/oncoprint/Oncoprint.tsx index 52dbebbfe13..4bd8795493d 100644 --- a/src/shared/components/oncoprint/Oncoprint.tsx +++ b/src/shared/components/oncoprint/Oncoprint.tsx @@ -301,8 +301,6 @@ export interface IOncoprintProps { trackKeySelectedForEdit?: string | null; setTrackKeySelectedForEdit?: (key: string | null) => void; - clinicalTrackColorChanged?: boolean; - setClinicalTrackColorChanged?: (changed: boolean) => void; suppressRendering?: boolean; onSuppressRendering?: () => void; diff --git a/src/shared/components/oncoprint/OncoprintColorModal.tsx b/src/shared/components/oncoprint/OncoprintColorModal.tsx new file mode 100644 index 00000000000..4fcc84b4b92 --- /dev/null +++ b/src/shared/components/oncoprint/OncoprintColorModal.tsx @@ -0,0 +1,107 @@ +import { action, makeObservable, observable } from 'mobx'; +import { observer } from 'mobx-react'; +import * as React from 'react'; +import { ClinicalTrackSpec } from './Oncoprint'; +import { + getClinicalTrackColor, + getClinicalTrackValues, +} from './ResultsViewOncoprint'; +import { Modal } from 'react-bootstrap'; +import ClinicalTrackColorPicker from './ClinicalTrackColorPicker'; +import { RGBAColor } from 'oncoprintjs'; +import classnames from 'classnames'; +import _ from 'lodash'; +import { rgbaToHex } from 'shared/lib/Colors'; + +interface IOncoprintColorModalProps { + setTrackKeySelectedForEdit: (key: string | null) => void; + selectedClinicalTrack: ClinicalTrackSpec; + handleSelectedClinicalTrackColorChange: ( + value: string, + color: RGBAColor | undefined + ) => void; + getSelectedClinicalTrackDefaultColorForValue: (value: string) => number[]; +} + +export const OncoprintColorModal: React.FC = observer( + ({ + setTrackKeySelectedForEdit, + selectedClinicalTrack, + handleSelectedClinicalTrackColorChange, + getSelectedClinicalTrackDefaultColorForValue, + }: IOncoprintColorModalProps) => { + const clinicalTrackValues = getClinicalTrackValues( + selectedClinicalTrack + ); + + return ( + setTrackKeySelectedForEdit(null)}> + + + Color Configuration: {selectedClinicalTrack.label} + + + + + + + + + + + + {clinicalTrackValues.map(value => ( + + + + + ))} + +
ValueColor
{value} + +
+ + + + ); + } +); diff --git a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx index c31f1a9ff74..fde9efce8e2 100644 --- a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx +++ b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx @@ -96,6 +96,7 @@ import { Modal } from 'react-bootstrap'; import ClinicalTrackColorPicker from './ClinicalTrackColorPicker'; import { hexToRGBA, rgbaToHex } from 'shared/lib/Colors'; import classnames from 'classnames'; +import { OncoprintColorModal } from './OncoprintColorModal'; interface IResultsViewOncoprintProps { divId: string; @@ -104,6 +105,9 @@ interface IResultsViewOncoprintProps { addOnBecomeVisibleListener?: (callback: () => void) => void; } +const DEFAULT_UNKNOWN_COLOR = [255, 255, 255, 1]; +const DEFAULT_MIXED_COLOR = [48, 97, 194, 1]; + export enum SortByUrlParamValue { CASE_ID = 'case_id', CASE_LIST = 'case_list', @@ -147,7 +151,7 @@ export function getClinicalTrackValues(track: ClinicalTrackSpec): any[] { const values = _(track.data) .map(d => d.attr_val) .uniq() - .without(undefined) + .without(undefined, '') .value(); return values.sort((a: string, b: string) => a < b ? -1 : a > b ? 1 : 0 @@ -166,11 +170,11 @@ export function getClinicalTrackColor( return track.countsCategoryFills[valueIndex]; } else if (track.datatype === 'string' && track.category_to_color) { if (value === 'Mixed') { - return track.category_to_color[value] || [48, 97, 194, 1]; + return track.category_to_color[value] || DEFAULT_MIXED_COLOR; } return track.category_to_color[value]; } else { - return [255, 255, 255, 1] as RGBAColor; + return DEFAULT_UNKNOWN_COLOR as RGBAColor; } } @@ -1890,6 +1894,8 @@ export default class ResultsViewOncoprint extends React.Component< this.trackKeySelectedForEdit = key; } + // if trackKeySelectedForEdit is null ('Edit Colors' has not been selected in an individual track menu), + // selectedClinicalTrack will be undefined @computed get selectedClinicalTrack() { return _.find( this.clinicalTracks.result, @@ -1898,42 +1904,30 @@ export default class ResultsViewOncoprint extends React.Component< } @autobind - private getDefaultSelectedClinicalTrackColor(value: string) { + private getSelectedClinicalTrackDefaultColorForValue( + attributeValue: string + ) { if (!this.selectedClinicalTrack) { - return [255, 255, 255, 1]; + return DEFAULT_UNKNOWN_COLOR; } if (this.selectedClinicalTrack.datatype === 'counts') { return MUTATION_SPECTRUM_FILLS[ - _.indexOf(MUTATION_SPECTRUM_CATEGORIES, value) + _.indexOf(MUTATION_SPECTRUM_CATEGORIES, attributeValue) ]; } else if (this.selectedClinicalTrack.datatype === 'string') { // Mixed refers to when an event has multiple values (i.e. Sample Type for a patient event may have both Primary and Recurrence values) - if (value === 'Mixed') { - return [48, 97, 194, 1]; + if (attributeValue === 'Mixed') { + return DEFAULT_MIXED_COLOR; } else { return hexToRGBA( this.props.store.clinicalDataCache.get( this.props.store.clinicalAttributeIdToClinicalAttribute .result![this.selectedClinicalTrack!.attributeId] - ).result!.categoryToColor![value] + ).result!.categoryToColor![attributeValue] ); } } - return [255, 255, 255, 1]; - } - - @computed get selectedClinicalTrackValues() { - if (this.selectedClinicalTrack) { - return getClinicalTrackValues(this.selectedClinicalTrack); - } - return []; - } - - @observable clinicalTrackColorChanged: boolean = false; - - @action.bound - setClinicalTrackColorChanged(changed: boolean) { - this.clinicalTrackColorChanged = changed; + return DEFAULT_UNKNOWN_COLOR; } public render() { @@ -1974,97 +1968,18 @@ export default class ResultsViewOncoprint extends React.Component< {this.selectedClinicalTrack && ( - this.setTrackKeySelectedForEdit(null)} - > - - - Color Configuration:{' '} - {this.selectedClinicalTrack.label} - - - - - - - - - - - - {this.selectedClinicalTrackValues.map( - value => ( - - - - - ) - )} - -
ValueColor
{value} - -
- - - + )}