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Updates based on comments
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@kalletlak
kalletlak committed Nov 20, 2019
1 parent d8637d8 commit bf2861e
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Showing 14 changed files with 352 additions and 309 deletions.
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6 changes: 3 additions & 3 deletions src/pages/groupComparison/ClinicalData.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,7 @@ export default class ClinicalData extends React.Component<IClinicalDataProps, {}
}
});

public readonly groupSampleAxisData = remoteData({
private readonly groupMembershipAxisData = remoteData({
await: () => [this.props.store.sampleSet, this.props.store.activeGroups],
invoke: async () => {
const categoryOrder = _.map(this.props.store.activeGroups.result!, group => group.nameWithOrdinal);
Expand Down Expand Up @@ -286,11 +286,11 @@ export default class ClinicalData extends React.Component<IClinicalDataProps, {}
});

@computed get vertAxisDataPromise() {
return this.swapAxes ? this.groupSampleAxisData : this.clinicalDataPromise;
return this.swapAxes ? this.groupMembershipAxisData : this.clinicalDataPromise;
}

@computed get horzAxisDataPromise() {
return this.swapAxes ? this.clinicalDataPromise : this.groupSampleAxisData;
return this.swapAxes ? this.clinicalDataPromise : this.groupMembershipAxisData;
}

@computed get horzLabel() {
Expand Down
25 changes: 12 additions & 13 deletions src/pages/groupComparison/CopyNumberEnrichments.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ import {MolecularProfile} from "../../shared/api/generated/CBioPortalAPI";
import {MakeMobxView} from "../../shared/components/MobxView";
import LoadingIndicator from "../../shared/components/loadingIndicator/LoadingIndicator";
import ErrorMessage from "../../shared/components/ErrorMessage";
import {MakeEnrichmentsTabUI, getNumSamples} from "./GroupComparisonUtils";
import {MakeEnrichmentsTabUI} from "./GroupComparisonUtils";
import { remoteData } from "public-lib/api/remoteData";
import _ from "lodash";
import { AlterationContainerType } from "pages/resultsView/enrichments/EnrichmentsUtil";
Expand All @@ -26,27 +26,26 @@ export default class CopyNumberEnrichments extends React.Component<ICopyNumberEn

readonly tabUI = MakeEnrichmentsTabUI(()=>this.props.store, ()=>this.enrichmentsUI, "copy-number", true, true, true);

private readonly enrichmentAnalysisGroups = remoteData({
await:()=>[this.props.store.activeGroups],
invoke:()=>{
const groups = _.map(this.props.store.activeGroups.result, group => {
private readonly copyNumberEnrichmentAnalysisGroups = remoteData({
await: () => [this.props.store.enrichmentAnalysisGroups],
invoke: () => {
return Promise.resolve(_.map(this.props.store.enrichmentAnalysisGroups.result, group => {
return {
name:group.nameWithOrdinal,
description:`Number (percentage) of ${this.props.store.usePatientLevelEnrichments ? "patients" : "samples"} in ${group.nameWithOrdinal} that have the listed alteration in the listed gene.`,
count: getNumSamples(group),
name: group.name,
description: `Number (percentage) of ${this.props.store.usePatientLevelEnrichments ? "patients" : "samples"} in ${group.name} that have the listed alteration in the listed gene.`,
count: group.count,
color: group.color
}
})
return Promise.resolve(groups);
}));
}
});

readonly enrichmentsUI = MakeMobxView({
await:()=>[
this.props.store.copyNumberEnrichmentData,
this.enrichmentAnalysisGroups,
this.copyNumberEnrichmentAnalysisGroups,
this.props.store.selectedStudyCopyNumberEnrichmentProfileMap,
this.enrichmentAnalysisGroups,
this.copyNumberEnrichmentAnalysisGroups,
this.props.store.studies
],
render:()=>{
Expand All @@ -65,7 +64,7 @@ export default class CopyNumberEnrichments extends React.Component<ICopyNumberEn
/>

<AlterationEnrichmentContainer data={this.props.store.copyNumberEnrichmentData.result!}
groups={this.enrichmentAnalysisGroups.result}
groups={this.copyNumberEnrichmentAnalysisGroups.result}
alteredVsUnalteredMode={false}
headerName={headerName}
showCNAInTable={true}
Expand Down
30 changes: 29 additions & 1 deletion src/pages/groupComparison/GroupComparisonStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ import {
GroupComparisonTab,
IOverlapComputations,
isGroupEmpty,
partitionCasesByGroupMembership
partitionCasesByGroupMembership,
getNumSamples
} from "./GroupComparisonUtils";
import {remoteData} from "../../public-lib/api/remoteData";
import {
Expand Down Expand Up @@ -360,6 +361,33 @@ export default class GroupComparisonStore {
invoke:()=>Promise.resolve(this.availableGroups.result!.filter(group=>this.isGroupSelected(group.uid) && !isGroupEmpty(group)))
});

readonly enrichmentAnalysisGroups = remoteData({
await: () => [this.activeGroups, this.sampleSet],
invoke: () => {
const sampleSet = this.sampleSet.result || new ComplexKeyMap<Sample>();
const groups = this.activeGroups.result!.map(group => {
const samples: Sample[] = [];
group.studies.forEach(studyEntry => {
const studyId = studyEntry.id;
studyEntry.samples.forEach(sampleId => {
if (sampleSet.has({ studyId: studyId, sampleId })) {
const sample = sampleSet.get({ studyId: studyId, sampleId })!;
samples.push(sample);
}
});
});
return {
name: group.nameWithOrdinal,
description: "",
count: getNumSamples(group),
color: group.color,
samples
}
});
return Promise.resolve(groups);
}
});

readonly _originalGroupsOverlapRemoved = remoteData<ComparisonGroup[]>({
await:()=>[this.overlapComputations, this._originalGroups],
invoke:()=>Promise.resolve(this.overlapComputations.result!.groups)
Expand Down
37 changes: 11 additions & 26 deletions src/pages/groupComparison/MRNAEnrichments.tsx
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
import * as React from "react";
import {observer} from "mobx-react";
import autobind from "autobind-decorator";
import {MolecularProfile, Sample} from "../../shared/api/generated/CBioPortalAPI";
import {MolecularProfile} from "../../shared/api/generated/CBioPortalAPI";
import {MakeMobxView} from "../../shared/components/MobxView";
import EnrichmentsDataSetDropdown from "../resultsView/enrichments/EnrichmentsDataSetDropdown";
import LoadingIndicator from "../../shared/components/loadingIndicator/LoadingIndicator";
import ErrorMessage from "../../shared/components/ErrorMessage";
import GroupComparisonStore from "./GroupComparisonStore";
import ExpressionEnrichmentContainer from "../resultsView/enrichments/ExpressionEnrichmentsContainer";
import {MakeEnrichmentsTabUI, getNumSamples} from "./GroupComparisonUtils";
import {MakeEnrichmentsTabUI} from "./GroupComparisonUtils";
import { remoteData } from "cbioportal-frontend-commons";
import ComplexKeyMap from "shared/lib/complexKeyDataStructures/ComplexKeyMap";
import * as _ from "lodash";

export interface IMRNAEnrichmentsProps {
store: GroupComparisonStore
Expand All @@ -23,30 +23,15 @@ export default class MRNAEnrichments extends React.Component<IMRNAEnrichmentsPro
this.props.store.setMRNAEnrichmentProfileMap(profileMap);
}

private readonly enrichmentAnalysisGroups = remoteData({
await: () => [this.props.store.activeGroups, this.props.store.sampleSet],
private readonly mrnaEnrichmentAnalysisGroups = remoteData({
await: () => [this.props.store.enrichmentAnalysisGroups],
invoke: () => {
const sampleSet = this.props.store.sampleSet.result || new ComplexKeyMap<Sample>();
const groups = this.props.store.activeGroups.result!.map(group => {
const uniqueSampleKeys: string[] = [];
group.studies.forEach(studyEntry => {
const studyId = studyEntry.id;
studyEntry.samples.forEach(sampleId => {
if (sampleSet.has({ studyId: studyId, sampleId })) {
const uniqueSampleKey = sampleSet.get({ studyId: studyId, sampleId })!.uniqueSampleKey;
uniqueSampleKeys.push(uniqueSampleKey);
}
});
});
return Promise.resolve(_.map(this.props.store.enrichmentAnalysisGroups.result, group => {
return {
name: group.nameWithOrdinal,
description: `samples in ${group.nameWithOrdinal}`,
count: getNumSamples(group),
color: group.color,
uniqueSampleKeys
...group,
description: `samples in ${group.name}`
}
});
return Promise.resolve(groups);
}));
}
});

Expand All @@ -56,7 +41,7 @@ export default class MRNAEnrichments extends React.Component<IMRNAEnrichmentsPro
await:()=>[
this.props.store.mRNAEnrichmentData,
this.props.store.selectedmRNAEnrichmentProfileMap,
this.enrichmentAnalysisGroups,
this.mrnaEnrichmentAnalysisGroups,
this.props.store.studies,
this.props.store.sampleKeyToSample
],
Expand All @@ -76,7 +61,7 @@ export default class MRNAEnrichments extends React.Component<IMRNAEnrichmentsPro
/>
<ExpressionEnrichmentContainer
data={this.props.store.mRNAEnrichmentData.result!}
groups={this.enrichmentAnalysisGroups.result}
groups={this.mrnaEnrichmentAnalysisGroups.result}
selectedProfile={selectedProfile}
alteredVsUnalteredMode={false}
sampleKeyToSample={this.props.store.sampleKeyToSample.result!}
Expand Down
24 changes: 11 additions & 13 deletions src/pages/groupComparison/MutationEnrichments.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,8 @@ import EnrichmentsDataSetDropdown from "../resultsView/enrichments/EnrichmentsDa
import AlterationEnrichmentContainer from "../resultsView/enrichments/AlterationEnrichmentsContainer";
import autobind from "autobind-decorator";
import { MakeMobxView } from "../../shared/components/MobxView";
import { MakeEnrichmentsTabUI, getNumSamples } from "./GroupComparisonUtils";
import { MakeEnrichmentsTabUI } from "./GroupComparisonUtils";
import { remoteData } from "public-lib/api/remoteData";
import { ResultsViewPageStore } from "../resultsView/ResultsViewPageStore";
import _ from "lodash";
import { AlterationContainerType } from "pages/resultsView/enrichments/EnrichmentsUtil";

Expand All @@ -28,26 +27,25 @@ export default class MutationEnrichments extends React.Component<IMutationEnrich

readonly tabUI = MakeEnrichmentsTabUI(()=>this.props.store, ()=>this.enrichmentsUI, "mutation", true, true, true);

private readonly enrichmentAnalysisGroups = remoteData({
await:()=>[this.props.store.activeGroups],
invoke:()=>{
const groups = _.map(this.props.store.activeGroups.result, group => {
private readonly mutationEnrichmentAnalysisGroups = remoteData({
await: () => [this.props.store.enrichmentAnalysisGroups],
invoke: () => {
return Promise.resolve(_.map(this.props.store.enrichmentAnalysisGroups.result, group => {
return {
name:group.nameWithOrdinal,
description:`Number (percentage) of ${this.props.store.usePatientLevelEnrichments ? "patients" : "samples"} in ${group.nameWithOrdinal} that have a mutation in the listed gene.`,
count: getNumSamples(group),
name: group.name,
description:`Number (percentage) of ${this.props.store.usePatientLevelEnrichments ? "patients" : "samples"} in ${group.name} that have a mutation in the listed gene.`,
count: group.count,
color: group.color
}
})
return Promise.resolve(groups);
}));
}
});

readonly enrichmentsUI = MakeMobxView({
await:()=>[
this.props.store.mutationEnrichmentData,
this.props.store.selectedStudyMutationEnrichmentProfileMap,
this.enrichmentAnalysisGroups,
this.mutationEnrichmentAnalysisGroups,
this.props.store.studies
],
render:()=>{
Expand All @@ -65,7 +63,7 @@ export default class MutationEnrichments extends React.Component<IMutationEnrich
studies={this.props.store.studies.result!}
/>
<AlterationEnrichmentContainer data={this.props.store.mutationEnrichmentData.result!}
groups={this.enrichmentAnalysisGroups.result}
groups={this.mutationEnrichmentAnalysisGroups.result}
alteredVsUnalteredMode={false}
headerName={headerName}
containerType={AlterationContainerType.MUTATION}
Expand Down
36 changes: 10 additions & 26 deletions src/pages/groupComparison/ProteinEnrichments.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,9 @@ import ExpressionEnrichmentContainer from "../resultsView/enrichments/Expression
import Loader from "../../shared/components/loadingIndicator/LoadingIndicator";
import ErrorMessage from "../../shared/components/ErrorMessage";
import GroupComparisonStore from "./GroupComparisonStore";
import {MakeEnrichmentsTabUI, getNumSamples} from "./GroupComparisonUtils";
import {MakeEnrichmentsTabUI} from "./GroupComparisonUtils";
import { remoteData } from "cbioportal-frontend-commons";
import ComplexKeyMap from "shared/lib/complexKeyDataStructures/ComplexKeyMap";
import { Sample } from "shared/api/generated/CBioPortalAPIInternal";
import * as _ from "lodash";

export interface IProteinEnrichmentsProps {
store: GroupComparisonStore
Expand All @@ -24,30 +23,15 @@ export default class ProteinEnrichments extends React.Component<IProteinEnrichme
this.props.store.setProteinEnrichmentProfileMap(profileMap);
}

private readonly enrichmentAnalysisGroups = remoteData({
await: () => [this.props.store.activeGroups, this.props.store.sampleSet],
private readonly proteinEnrichmentAnalysisGroups = remoteData({
await: () => [this.props.store.enrichmentAnalysisGroups],
invoke: () => {
const sampleSet = this.props.store.sampleSet.result || new ComplexKeyMap<Sample>();
const groups = this.props.store.activeGroups.result!.map(group => {
const uniqueSampleKeys: string[] = [];
group.studies.forEach(studyEntry => {
const studyId = studyEntry.id;
studyEntry.samples.forEach(sampleId => {
if (sampleSet.has({ studyId: studyId, sampleId })) {
const uniqueSampleKey = sampleSet.get({ studyId: studyId, sampleId })!.uniqueSampleKey;
uniqueSampleKeys.push(uniqueSampleKey);
}
});
});
return Promise.resolve(_.map(this.props.store.enrichmentAnalysisGroups.result, group => {
return {
name: group.nameWithOrdinal,
description: `samples in ${group.nameWithOrdinal}`,
count: getNumSamples(group),
color: group.color,
uniqueSampleKeys
...group,
description: `samples in ${group.name}`
}
});
return Promise.resolve(groups);
}));
}
});

Expand All @@ -57,7 +41,7 @@ export default class ProteinEnrichments extends React.Component<IProteinEnrichme
await:()=>[
this.props.store.proteinEnrichmentData,
this.props.store.selectedProteinEnrichmentProfileMap,
this.enrichmentAnalysisGroups,
this.proteinEnrichmentAnalysisGroups,
this.props.store.studies
],
render:()=>{
Expand All @@ -76,7 +60,7 @@ export default class ProteinEnrichments extends React.Component<IProteinEnrichme
/>
<ExpressionEnrichmentContainer
data={this.props.store.proteinEnrichmentData.result!}
groups={this.enrichmentAnalysisGroups.result}
groups={this.proteinEnrichmentAnalysisGroups.result}
selectedProfile={selectedProfile}
alteredVsUnalteredMode={false}
sampleKeyToSample={this.props.store.sampleKeyToSample.result!}
Expand Down

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