✨ Add Time Range Selection to KM Plots on Study View

src/pages/resultsView/survival/SurvivalChart.tsx

@@ -16,6 +16,7 @@ import {
     VictoryLabel,
     VictoryScatter,
     VictoryZoomContainer,
+    VictorySelectionContainer,
 } from 'victory';
 import {
     getSurvivalSummaries,
@@ -29,12 +30,13 @@ import {
     SurvivalPlotFilters,
     SurvivalSummary,
     SURVIVAL_COMPACT_MODE_THRESHOLD,
+    ScatterData,
 } from './SurvivalUtil';
 import { toConditionalPrecision } from 'shared/lib/NumberUtils';
 import { getPatientViewUrl } from '../../../shared/api/urls';
 import { DefaultTooltip, DownloadControls } from 'cbioportal-frontend-commons';
 import autobind from 'autobind-decorator';
-import { AnalysisGroup } from '../../studyView/StudyViewUtils';
+import { AnalysisGroup, DataBin } from '../../studyView/StudyViewUtils';
 import { AbstractChart } from '../../studyView/charts/ChartContainer';
 import { toSvgDomNodeWithLegend } from '../../studyView/StudyViewUtils';
 import classnames from 'classnames';
@@ -91,6 +93,8 @@ export interface ISurvivalChartProps {
     xAxisTickCount?: number;
     // Compact mode will hide censoring dots in the chart and do binning based on configuration
     compactMode?: boolean;
+    attributeId?: string;
+    onUserSelection?: (dataBins: DataBin[]) => void;
 }
 
 const MIN_GROUP_SIZE_FOR_LOGRANK = 10;
@@ -594,6 +598,51 @@ export default class SurvivalChart
         this.sliderValue = Number.parseFloat(text);
     }
 
+    @autobind
+    private onSelection(data: any[]) {
+        if (data.length < 2) {
+            console.error(
+                'Survival Plot onSelection Failure: Not enough elements to select'
+            );
+            return;
+        }
+
+        const scatterPoints: Array<ScatterData> = data[1].data;
+        if (scatterPoints.length > 2) {
+            const dataBin = generateFilterDataBin(
+                scatterPoints,
+                () => this.props.attributeId!
+            );
+            if (this.props.onUserSelection) {
+                this.props.onUserSelection([dataBin]);
+            }
+        }
+    }
+
+    @computed
+    get victoryChartContainer() {
+        return this.props.onUserSelection ? (
+            <VictorySelectionContainer
+                selectionDimension="x"
+                onSelection={this.onSelection}
+            />
+        ) : (
+            <VictoryZoomContainer
+                responsive={false}
+                disable={true}
+                zoomDomain={
+                    this.props.showSlider
+                        ? { x: [0, this.sliderValue] }
+                        : undefined
+                }
+                onZoomDomainChange={_.debounce((domain: any) => {
+                    this.scatterFilter = domain as SurvivalPlotFilters;
+                }, 1000)}
+                containerRef={(ref: any) => (this.svgContainer = ref)}
+            />
+        );
+    }
+
     @computed
     get chart() {
         return (
@@ -676,23 +725,7 @@ export default class SurvivalChart
                 </div>
 
                 <VictoryChart
-                    containerComponent={
-                        <VictoryZoomContainer
-                            responsive={false}
-                            disable={true}
-                            zoomDomain={
-                                this.props.showSlider
-                                    ? { x: [0, this.sliderValue] }
-                                    : undefined
-                            }
-                            onZoomDomainChange={_.debounce((domain: any) => {
-                                this.scatterFilter = domain as SurvivalPlotFilters;
-                            }, 1000)}
-                            containerRef={(ref: any) =>
-                                (this.svgContainer = ref)
-                            }
-                        />
-                    }
+                    containerComponent={this.victoryChartContainer}
                     height={this.styleOpts.height}
                     width={this.styleOpts.width}
                     padding={this.styleOpts.padding}
@@ -944,3 +977,16 @@ export default class SurvivalChart
         }
     }
 }
+
+export function generateFilterDataBin(
+    scatterPoints: Array<ScatterData>,
+    getAttributeId: () => string
+): DataBin {
+    const minX = scatterPoints[0].x;
+    const maxX = scatterPoints[scatterPoints.length - 1].x;
+    return {
+        id: getAttributeId(),
+        start: minX,
+        end: maxX,
+    } as DataBin;
+}

src/pages/studyView/StudyViewPageStore.ts

@@ -280,6 +280,11 @@ import {
     StudyViewFilterQueryExtractor,
     StudyViewQueryExtractor,
 } from './StudyViewQueryExtractor';
+import {
+    getAllowedSurvivalClinicalDataFilterId,
+    isSurvivalAttributeId,
+    isSurvivalChart,
+} from './charts/survival/StudyViewSurvivalUtils';
 
 export const STUDY_VIEW_FILTER_AUTOSUBMIT = 'study_view_filter_autosubmit';
 
@@ -2772,10 +2777,12 @@ export class StudyViewPageStore
         if (this.chartMetaSet[chartUniqueKey]) {
             let chartMeta = this.chartMetaSet[chartUniqueKey];
             trackStudyViewFilterEvent('clinicalDataFilters', this);
-            this.updateClinicalAttributeFilterByValues(
-                chartMeta.clinicalAttribute!.clinicalAttributeId,
-                values
-            );
+
+            const attributeId: string = isSurvivalChart(chartMeta.uniqueKey)
+                ? getAllowedSurvivalClinicalDataFilterId(chartMeta.uniqueKey)
+                : chartMeta.clinicalAttribute!.clinicalAttributeId;
+
+            this.updateClinicalAttributeFilterByValues(attributeId, values);
         }
     }
     @action.bound
@@ -6026,6 +6033,7 @@ export class StudyViewPageStore
                     dataType: getChartMetaDataType(survivalPlot.id),
                     patientAttribute: true,
                     displayName: survivalPlot.title,
+                    clinicalAttribute: survivalPlot.survivalStatusAttribute,
                     // use survival status attribute's priority as KM plot's priority for non-reserved plots
                     priority:
                         STUDY_VIEW_CONFIG.priority[survivalPlot.id] ||

src/pages/studyView/UserSelections.tsx

@@ -54,6 +54,10 @@ import {
 import { StudyViewPageStore } from 'pages/studyView/StudyViewPageStore';
 import classNames from 'classnames';
 import { StudyViewPageTabKeyEnum } from 'pages/studyView/StudyViewPageTabs';
+import {
+    getSurvivalChartMetaId,
+    isSurvivalAttributeId,
+} from './charts/survival/StudyViewSurvivalUtils';
 
 export interface IUserSelectionsProps {
     store: StudyViewPageStore;
@@ -547,9 +551,12 @@ export default class UserSelections extends React.Component<
         return _.reduce(
             filters || [],
             (acc, clinicalDataFilter) => {
-                const chartMeta = this.props.attributesMetaSet[
+                const attributeId = isSurvivalAttributeId(
                     clinicalDataFilter.attributeId
-                ];
+                )
+                    ? getSurvivalChartMetaId(clinicalDataFilter.attributeId)
+                    : clinicalDataFilter.attributeId;
+                const chartMeta = this.props.attributesMetaSet[attributeId];
                 if (chartMeta) {
                     const dataType = this.props.clinicalAttributeIdToDataType[
                         clinicalDataFilter.attributeId

src/pages/studyView/charts/ChartContainer.tsx

@@ -418,7 +418,8 @@ export class ChartContainer extends React.Component<IChartContainerProps, {}> {
                     this.props.chartMeta.uniqueKey
                 ]?.survivalData,
                 this.props.analysisGroupsSettings.groups,
-                this.props.patientToAnalysisGroup!.result!
+                this.props.patientToAnalysisGroup!.result!,
+                this.props.chartMeta.uniqueKey
             );
         } else {
             return undefined;
@@ -981,6 +982,8 @@ export class ChartContainer extends React.Component<IChartContainerProps, {}> {
                             yAxisTickCount={2}
                             xAxisTickCount={4}
                             compactMode={this.showCompactSurvivalChart}
+                            attributeId={data.attributeId}
+                            onUserSelection={this.handlers.onDataBinSelection}
                         />
                     );
                 } else {

src/pages/studyView/charts/survival/StudyViewSurvivalUtils.ts

@@ -1,5 +1,4 @@
 import { PatientSurvival } from '../../../../shared/model/PatientSurvival';
-import { IChartContainerProps } from '../ChartContainer';
 import { AnalysisGroup } from '../../StudyViewUtils';
 import _ from 'lodash';
 import { logRankTest } from 'pages/resultsView/survival/logRankTest';
@@ -8,7 +7,10 @@ import { sortPatientSurvivals } from 'pages/resultsView/survival/SurvivalUtil';
 export function makeSurvivalChartData(
     patientSurvivals: ReadonlyArray<PatientSurvival>,
     analysisGroups: ReadonlyArray<AnalysisGroup>,
-    patientToAnalysisGroup: { [uniquePatientKey: string]: string }
+    patientToAnalysisGroup: {
+        [uniquePatientKey: string]: string;
+    },
+    attributeId: string
 ) {
     let patientToAnalysisGroups = _.mapValues(patientToAnalysisGroup, group => [
         group,
@@ -48,7 +50,35 @@ export function makeSurvivalChartData(
         analysisGroups,
         sortedGroupedSurvivals,
         pValue,
+        attributeId,
     };
 }
 
 export function makeScatterPlotData() {}
+
+export function isSurvivalAttributeId(attributeId: string) {
+    return /_MONTHS|_STATUS$/i.test(attributeId);
+}
+
+export function isSurvivalChart(chartUniqueKey: string) {
+    return /_SURVIVAL$/i.test(chartUniqueKey);
+}
+
+export function getAllowedSurvivalClinicalDataFilterId(chartUniqueKey: string) {
+    const prefix = chartUniqueKey.substring(
+        0,
+        chartUniqueKey.indexOf('_SURVIVAL')
+    );
+    return `${prefix}_MONTHS`;
+}
+
+export function getSurvivalChartMetaId(attributeId: string) {
+    const survivalClinicalDataType = /_MONTHS$/i.test(attributeId)
+        ? '_MONTHS'
+        : '_STATUS';
+    const prefix = attributeId.substring(
+        0,
+        attributeId.indexOf(survivalClinicalDataType)
+    );
+    return `${prefix}_SURVIVAL`;
+}

src/pages/studyView/tabs/SummaryTab.tsx

@@ -459,6 +459,7 @@ export class StudySummaryTab extends React.Component<
                         'OS_SURVIVAL'
                     ]?.survivalDataWithoutLeftTruncation;
                 }
+                props.onDataBinSelection = this.handlers.onDataBinSelection;
                 /* end of left truncation adjustment related settings */
                 break;
             }