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Merge pull request #1432 from thehyve/gsva_plots
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Implement gene set option in plots tab
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@alisman
alisman authored Oct 4, 2018
2 parents 17db699 + 47bda20 commit 22770c9
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Showing 5 changed files with 221 additions and 30 deletions.
16 changes: 8 additions & 8 deletions package-lock.json
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19 changes: 18 additions & 1 deletion src/pages/resultsView/ResultsViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -54,10 +54,16 @@ import GeneMolecularDataCache from "../../shared/cache/GeneMolecularDataCache";
import GenesetMolecularDataCache from "../../shared/cache/GenesetMolecularDataCache";
import GenesetCorrelatedGeneCache from "../../shared/cache/GenesetCorrelatedGeneCache";
import GeneCache from "../../shared/cache/GeneCache";
import GenesetCache from "../../shared/cache/GenesetCache";
import {IHotspotIndex} from "../../shared/model/CancerHotspots";
import {IOncoKbData} from "../../shared/model/OncoKB";
import {generateQueryVariantId} from "../../shared/lib/OncoKbUtils";
import {CosmicMutation, AlterationEnrichment, ExpressionEnrichment} from "../../shared/api/generated/CBioPortalAPIInternal";
import {
CosmicMutation,
AlterationEnrichment,
ExpressionEnrichment,
Geneset
} from "../../shared/api/generated/CBioPortalAPIInternal";
import internalClient from "../../shared/api/cbioportalInternalClientInstance";
import {IndicatorQueryResp} from "../../shared/api/generated/OncoKbAPI";
import {getAlterationString} from "../../shared/lib/CopyNumberUtils";
Expand Down Expand Up @@ -1674,6 +1680,13 @@ export class ResultsViewPageStore {
}
});

readonly genesets = remoteData<Geneset[]>({
invoke: async () => internalClient.fetchGenesetsUsingPOST({genesetIds: this.genesetIds.slice()}),
onResult:(genesets:Geneset[])=>{
this.genesetCache.addData(genesets);
}
});

readonly entrezGeneIdToGene = remoteData<{[entrezGeneId:number]:Gene}>({
await: ()=>[this.genes],
invoke: ()=>Promise.resolve(_.keyBy(this.genes.result!, gene=>gene.entrezGeneId))
Expand Down Expand Up @@ -2454,6 +2467,10 @@ export class ResultsViewPageStore {
return new GeneCache();
}

@cached get genesetCache() {
return new GenesetCache();
}

public numericGeneMolecularDataCache = new MobxPromiseCache<{entrezGeneId:number, molecularProfileId:string}, NumericGeneMolecularData[]>(
q=>({
await: ()=>[
Expand Down
135 changes: 119 additions & 16 deletions src/pages/resultsView/plots/PlotsTab.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ import {
getCnaQueries, getMutationQueries, getScatterPlotDownloadData, getBoxPlotDownloadData, getTablePlotDownloadData,
mutationRenderPriority, mutationSummaryRenderPriority, MutationSummary, mutationSummaryToAppearance,
CNA_STROKE_WIDTH, PLOT_SIDELENGTH, CLIN_ATTR_DATA_TYPE,
sortMolecularProfilesForDisplay, scatterPlotZIndexSortBy
sortMolecularProfilesForDisplay, scatterPlotZIndexSortBy, GENESET_DATA_TYPE
} from "./PlotsTabUtils";
import {
ClinicalAttribute, MolecularProfile, Mutation,
Expand Down Expand Up @@ -73,7 +73,9 @@ export enum PlotType {

export type AxisMenuSelection = {
entrezGeneId?:number;
genesetId?:string;
selectedGeneOption?:{value:number, label:string}; // value is entrez id, label is hugo symbol
selectedGenesetOption?:{value:string, label:string};
dataType?:string;
dataSourceId?:string;
logScale: boolean;
Expand All @@ -91,6 +93,7 @@ class PlotsTabBoxPlot extends BoxScatterPlot<IBoxScatterPlotPoint> {}
const SVG_ID = "plots-tab-plot-svg";

export const SAME_GENE_OPTION_VALUE = "same";
export const SAME_GENESET_OPTION_VALUE = "same";

@observer
export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
Expand Down Expand Up @@ -312,7 +315,37 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
set logScale(v:boolean) {
this._logScale = v;
},
get genesetId() {
if (this.selectedGenesetOption) {
if (this.selectedGenesetOption.value === SAME_GENESET_OPTION_VALUE) {
return self.horzSelection.genesetId;
} else {
return this.selectedGenesetOption.value;
}
} else {
return undefined;
}
},
get selectedGenesetOption() {
const genesetOptions = (vertical ? self.vertGenesetOptions : self.horzGenesetOptions.result) || [];
if (this._selectedGenesetOption === undefined && genesetOptions.length) {
// select default if _selectedGenesetOption is undefined and theres defaults to choose from
return genesetOptions[0];
} else if (vertical && this._selectedGenesetOption && this._selectedGenesetOption.value === SAME_GENESET_OPTION_VALUE &&
self.horzSelection.dataType === CLIN_ATTR_DATA_TYPE) {
// if vertical gene set option is "same as horizontal", and horizontal is clinical, then use the actual
// gene set option value instead of "Same gene" option value, because that would be slightly weird UX
return self.horzSelection.selectedGenesetOption;
} else {
// otherwise, return stored value for this variable
return this._selectedGenesetOption;
}
},
set selectedGenesetOption(o:any) {
this._selectedGenesetOption = o;
},
_selectedGeneOption: undefined,
_selectedGenesetOption: undefined,
_dataType: undefined,
_dataSourceId: undefined,
_logScale: true
Expand Down Expand Up @@ -459,6 +492,16 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
this.horzSelection.selectedGeneOption = option;
}

@autobind
private onVerticalAxisGenesetSelect(option:any) {
this.vertSelection.selectedGenesetOption = option;
}

@autobind
private onHorizontalAxisGenesetSelect(option:any) {
this.horzSelection.selectedGenesetOption = option;
}

public test__selectGeneOption(vertical:boolean, optionValue:any) {
// for end to end testing
// optionValue is either entrez id or the code for same gene
Expand Down Expand Up @@ -493,13 +536,36 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
// option changes. if its remoteData, theres setTimeout(0)'s in the way and it causes unnecessarily an extra
// render which leads to a flash of the loading icon on the screen
let sameGeneOption = undefined;
if (this.horzSelection.selectedGeneOption && this.horzSelection.dataType !== CLIN_ATTR_DATA_TYPE) {
// show "Same gene" option as long as horzSelection has a selected option, and horz isnt clinical attribute, bc
// in that case theres no selected gene displayed so its confusing UX to have "Same gene" as an option
if (this.horzSelection.selectedGeneOption && this.horzSelection.dataType !== CLIN_ATTR_DATA_TYPE && this.horzSelection.dataType !== GENESET_DATA_TYPE) {
// show "Same gene" option as long as horzSelection has a selected option, and horz isnt clinical attribute or
// a gene set, bc in that case theres no selected gene displayed so its confusing UX to have "Same gene" as an option
sameGeneOption = [{ value: SAME_GENE_OPTION_VALUE, label: `Same gene (${this.horzSelection.selectedGeneOption.label})`}];
}
return (sameGeneOption || []).concat((this.horzGeneOptions.result || []) as any[]);
};
}

//readonly horzGenesetOptions = this.props.store.genesetIds.map(genesetId=>({ value: genesetId, label: genesetId }));
readonly horzGenesetOptions = remoteData({
await:()=>[this.props.store.genesets],
invoke:()=>{
return Promise.resolve(
this.props.store.genesets.result!.map(geneset=>({ value: geneset.genesetId, label: geneset.name }))
);
}
});

@computed get vertGenesetOptions() {
// computed instead of remoteData in order to make the rerender synchronous when the 'Same gene set (GENE SET)'
// option changes. if its remoteData, theres setTimeout(0)'s in the way and it causes unnecessarily an extra
// render which leads to a flash of the loading icon on the screen
let sameGenesetOption = undefined;
if (this.horzSelection.selectedGenesetOption && this.horzSelection.dataType === GENESET_DATA_TYPE) {
// show "Same gene set" option as long as horzSelection has a selected option, and horz is gene set attribute, bc
// in that case theres no selected gene displayed so its confusing UX to have "Same gene" as an option
sameGenesetOption = [{ value: SAME_GENESET_OPTION_VALUE, label: `Same gene set (${this.horzSelection.selectedGenesetOption.label})`}];
}
return (sameGenesetOption || []).concat((this.horzGenesetOptions.result || []) as {value:string, label:string}[]);
}

readonly clinicalAttributeIdToClinicalAttribute = remoteData<{[clinicalAttributeId:string]:ClinicalAttribute}>({
await:()=>[
Expand All @@ -515,8 +581,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
readonly clinicalAttributeOptions = remoteData({
await:()=>[this.props.store.clinicalAttributes],
invoke:()=>{
let _clinicalAttributes = _.sortBy<ClinicalAttribute>(this.props.store.clinicalAttributes.result!,

let _clinicalAttributes = _.sortBy<ClinicalAttribute>(this.props.store.clinicalAttributes.result!,
[(o: any)=>-o.priority, (o: any)=>o.label]).map(attribute=>(
{
value: attribute.clinicalAttributeId,
Expand Down Expand Up @@ -547,7 +613,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
readonly dataTypeOptions = remoteData<{value:string, label:string}[]>({
await:()=>[
this.props.store.nonMutationMolecularProfilesWithData,
this.clinicalAttributeOptions
this.clinicalAttributeOptions,
this.props.store.molecularProfilesInStudies
],
invoke:()=>{
const profiles = this.props.store.nonMutationMolecularProfilesWithData.result!;
Expand All @@ -562,6 +629,17 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
dataTypeIds.push(CLIN_ATTR_DATA_TYPE);
}

if (this.props.store.molecularProfilesInStudies.result!.length && this.horzGenesetOptions.result && this.horzGenesetOptions.result!.length > 0) {
// add geneset profile to list if the study contains it and the query contains gene sets
this.props.store.molecularProfilesInStudies.result.filter(p=>{
if (p.molecularAlterationType === AlterationTypeConstants[GENESET_DATA_TYPE]) {
if (dataTypeIds.indexOf(GENESET_DATA_TYPE) === -1) {
dataTypeIds.push(GENESET_DATA_TYPE);
}
}
});
}

return Promise.resolve(
_.sortBy(dataTypeIds, // sort them into display order
type=>dataTypeDisplayOrder.indexOf(type)
Expand All @@ -575,11 +653,11 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {

readonly dataTypeToDataSourceOptions = remoteData<{[dataType:string]:{value:string, label:string}[]}>({
await:()=>[
this.props.store.nonMutationMolecularProfilesWithData,
this.props.store.molecularProfileIdToMolecularProfile,
this.clinicalAttributeOptions
],
invoke:()=>{
const profiles = this.props.store.nonMutationMolecularProfilesWithData.result!;
const profiles = this.props.store.molecularProfileIdToMolecularProfile.result!;
const map = _.mapValues(
_.groupBy(profiles, profile=>profile.molecularAlterationType), // create a map from profile type to list of profiles of that type
profilesOfType=>(
Expand Down Expand Up @@ -637,6 +715,14 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
this.horzSelection.selectedGeneOption = vertOption;
this.vertSelection.selectedGeneOption = horzOption;
}

// only swap gene sets if vertSelection is not set to "Same gene set"
if (!this.vertSelection.selectedGenesetOption || (this.vertSelection.selectedGenesetOption.value.toString() !== SAME_GENESET_OPTION_VALUE)) {
const horzOption = this.horzSelection.selectedGenesetOption;
const vertOption = this.vertSelection.selectedGenesetOption;
this.horzSelection.selectedGenesetOption = vertOption;
this.vertSelection.selectedGenesetOption = horzOption;
}
}

@computed get bothAxesMolecularProfile() {
Expand Down Expand Up @@ -706,7 +792,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
this.props.store.entrezGeneIdToGene,
this.props.store.clinicalDataCache,
this.props.store.numericGeneMolecularDataCache,
this.props.store.studyToMutationMolecularProfile
this.props.store.studyToMutationMolecularProfile,
this.props.store.genesetMolecularDataCache
);
}

Expand All @@ -719,7 +806,8 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
this.props.store.entrezGeneIdToGene,
this.props.store.clinicalDataCache,
this.props.store.numericGeneMolecularDataCache,
this.props.store.studyToMutationMolecularProfile
this.props.store.studyToMutationMolecularProfile,
this.props.store.genesetMolecularDataCache
);
}

Expand Down Expand Up @@ -918,7 +1006,7 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
/> Apply Log Scale
</label></div>
)}
<div className="form-group" style={{opacity:(axisSelection.dataType === CLIN_ATTR_DATA_TYPE ? 0 : 1)}}>
{(axisSelection.dataType !== GENESET_DATA_TYPE) && (<div className="form-group" style={{opacity:(axisSelection.dataType === CLIN_ATTR_DATA_TYPE ? 0 : 1)}}>
<label>Gene</label>
<div style={{display:"flex", flexDirection:"row"}}>
<ReactSelect
Expand All @@ -929,10 +1017,25 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
options={this.horzGeneOptions.isComplete ? (vertical ? this.vertGeneOptions : this.horzGeneOptions.result) : []}
clearable={false}
searchable={false}
disabled={axisSelection.dataType === CLIN_ATTR_DATA_TYPE}
disabled={axisSelection.dataType === CLIN_ATTR_DATA_TYPE || axisSelection.dataType === GENESET_DATA_TYPE}
/>
</div>
</div>
</div>)}
{(axisSelection.dataType === GENESET_DATA_TYPE) && (<div className="form-group" style={{opacity:1}}>
<label>Gene Set</label>
<div style={{display:"flex", flexDirection:"row"}}>
<ReactSelect
name={`${vertical ? "v" : "h"}-geneset-selector`}
value={axisSelection.selectedGenesetOption ? axisSelection.selectedGenesetOption.value : undefined}
onChange={vertical ? this.onVerticalAxisGenesetSelect : this.onHorizontalAxisGenesetSelect}
isLoading={this.horzGenesetOptions.isPending}
options={this.horzGenesetOptions.isComplete ? (vertical ? this.vertGenesetOptions : this.horzGenesetOptions.result) : []}
clearable={false}
searchable={false}
disabled={axisSelection.dataType !== GENESET_DATA_TYPE}
/>
</div>
</div>)}
</div>
</form>
);
Expand Down Expand Up @@ -1327,4 +1430,4 @@ export default class PlotsTab extends React.Component<IPlotsTabProps,{}> {
</div>
);
}
}
}
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