Merge pull request #4432 from gblaih/group-comparison-lollipop-plot-f…

…requency

Fix incorrect mutation frequency in group comparison lollipop plot

packages/react-mutation-mapper/src/store/DefaultMutationMapperStore.ts

@@ -378,7 +378,8 @@ class DefaultMutationMapperStore<T extends Mutation>
         return this.groupedMutationsByPosition.map(groupedMutations => ({
             group: groupedMutations.group,
             counts: this.countUniqueMutationsByPosition(
-                groupedMutations.mutations
+                groupedMutations.mutations,
+                groupedMutations.group
             ),
         }));
     }
@@ -393,24 +394,27 @@ class DefaultMutationMapperStore<T extends Mutation>
         );
     }
 
-    public countUniqueMutationsByPosition(mutationsByPosition: {
-        [pos: number]: T[];
-    }): { [pos: number]: number } {
+    public countUniqueMutationsByPosition(
+        mutationsByPosition: {
+            [pos: number]: T[];
+        },
+        group?: string
+    ): { [pos: number]: number } {
         const map: { [pos: number]: number } = {};
 
         Object.keys(mutationsByPosition).forEach(pos => {
             const position = parseInt(pos, 10);
             // for each position multiple mutations for the same patient is counted only once
             const mutations = mutationsByPosition[position];
             if (mutations) {
-                map[position] = this.countUniqueMutations(mutations);
+                map[position] = this.countUniqueMutations(mutations, group);
             }
         });
 
         return map;
     }
 
-    public countUniqueMutations(mutations: T[]): number {
+    public countUniqueMutations(mutations: T[], group?: string): number {
         // assume by default all mutations are unique
         // child classes need to override this method to have a custom way of counting unique mutations
         return this.config.getMutationCount

src/pages/groupComparison/GroupComparisonMutationsTabPlot.tsx

@@ -68,16 +68,20 @@ export default class GroupComparisonMutationsTabPlot extends React.Component<
     @computed get mutationMapperToolStore() {
         const store = new MutationMapperToolStore(this.props.mutations, {
             ...this.props.filters,
-            countUniqueMutations: this.countUniqueMutations,
+            countUniqueMutations: this.countUniqueMutationsInGroup,
         });
         return store;
     }
 
     @autobind
-    protected countUniqueMutations(mutations: Mutation[]) {
+    protected countUniqueMutationsInGroup(
+        mutations: Mutation[],
+        group: string
+    ) {
         return this.axisMode === AxisScale.PERCENT
             ? (countUniqueMutations(mutations) /
-                  this.props.store.profiledSamplesCount.result!) *
+                  this.props.store.groupToProfiledSamples.result![group]
+                      .length) *
                   100
             : countUniqueMutations(mutations);
     }
@@ -91,9 +95,9 @@ export default class GroupComparisonMutationsTabPlot extends React.Component<
         await: () => [
             this.props.store.mutations,
             this.props.store.mutationsByGroup,
-            this.props.store.profiledSamplesCount,
             this.mutationMapperToolStore.mutationMapperStores,
             this.props.store.coverageInformation,
+            this.props.store.groupToProfiledSamples,
         ],
         render: () => {
             if (

src/pages/groupComparison/GroupComparisonStore.ts

@@ -15,6 +15,7 @@ import {
     Mutation,
     Gene,
     GenePanelData,
+    Sample,
 } from 'cbioportal-ts-api-client';
 import { action, observable, makeObservable, computed } from 'mobx';
 import client from '../../shared/api/cbioportalClientInstance';
@@ -321,6 +322,46 @@ export default class GroupComparisonStore extends ComparisonStore {
         },
     });
 
+    public readonly groupToProfiledSamples = remoteData({
+        await: () => [
+            this._originalGroups,
+            this.sampleMap,
+            this.mutationEnrichmentProfiles,
+            this.coverageInformation,
+        ],
+        invoke: () => {
+            const sampleSet = this.sampleMap.result!;
+            const groups = this._originalGroups.result!;
+            const ret: {
+                [groupUid: string]: Sample[];
+            } = {};
+            for (const group of groups) {
+                for (const studyObject of group.studies) {
+                    const studyId = studyObject.id;
+                    for (const sampleId of studyObject.samples) {
+                        const sample = sampleSet.get({ sampleId, studyId });
+                        if (
+                            sample &&
+                            this.mutationEnrichmentProfiles.result!.some(p =>
+                                isSampleProfiled(
+                                    sample.uniqueSampleKey,
+                                    p.molecularProfileId,
+                                    this.activeMutationMapperGene!
+                                        .hugoGeneSymbol,
+                                    this.coverageInformation.result!
+                                )
+                            )
+                        ) {
+                            ret[group.name] = ret[group.name] || [];
+                            ret[group.name].push(sample);
+                        }
+                    }
+                }
+            }
+            return Promise.resolve(ret);
+        },
+    });
+
     readonly mutations = remoteData({
         await: () => [this.samples, this.mutationEnrichmentProfiles],
         invoke: async () => {
@@ -343,26 +384,6 @@ export default class GroupComparisonStore extends ComparisonStore {
         },
     });
 
-    readonly profiledSamplesCount = remoteData({
-        await: () => [
-            this.samples,
-            this.coverageInformation,
-            this.mutationEnrichmentProfiles,
-        ],
-        invoke: async () => {
-            return this.samples.result!.filter(s =>
-                this.mutationEnrichmentProfiles.result!.some(p =>
-                    isSampleProfiled(
-                        s.uniqueSampleKey,
-                        p.molecularProfileId,
-                        this.activeMutationMapperGene!.hugoGeneSymbol,
-                        this.coverageInformation.result!
-                    )
-                )
-            ).length;
-        },
-    });
-
     readonly allSamples = remoteData({
         await: () => [this._session],
         invoke: async () => {

src/shared/components/mutationMapper/MutationMapperStore.ts

@@ -64,7 +64,7 @@ export interface IMutationMapperStoreConfig {
         group: string;
         filter: DataFilter<any>;
     }[];
-    countUniqueMutations?: (mutations: Mutation[]) => number;
+    countUniqueMutations?: (mutations: Mutation[], group?: string) => number;
 }
 
 export default class MutationMapperStore extends DefaultMutationMapperStore<
@@ -207,9 +207,12 @@ export default class MutationMapperStore extends DefaultMutationMapperStore<
         return buildNamespaceColumnConfig(this.mutationData.result);
     }
 
-    public countUniqueMutations(mutations: Mutation[]): number {
+    public countUniqueMutations(mutations: Mutation[], group?: string): number {
         return this.mutationMapperStoreConfig.countUniqueMutations
-            ? this.mutationMapperStoreConfig.countUniqueMutations(mutations)
+            ? this.mutationMapperStoreConfig.countUniqueMutations(
+                  mutations,
+                  group
+              )
             : countUniqueMutations(mutations);
     }