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Mutation pie chart and multi-selection table (#4794)
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* group gene selection options by alteration type

* add mutation-data-counts endpoint and revamp renderAttributes giant switch statements

* add sub menu options for mutation profile

* get mutation data and fix display text on add chart

* fix filter and show pill tags for mutation count data

* add mutation type table and disable group comparison

* get mutation table download data

* support and fix intersect and union selection on mutation table

* ui update for mutation chart

* fix pilltags, apis, and select

* cleanup code

* resolve comments from Karthik

* resolve Aaron's comments

* resolve Study View Page missing data

* fix selecting more rows in mutation counts table

* fix pilltag errors on intersection selection

* rename wild type to mutation type

* fix type errors and conflicts

* fix GenomicDataCount

* fix e2e tests on SummaryTab

* update any to Partial in SummaryTab

* resolve Aaron's comments

* remove categories grouping and change colors for mutation pie chart

* fix mutation categories type assertion

* revert colors.ts changes and add callback to change Mutated vs Wild Type pie chart

---------

Co-authored-by: Qi-Xuan Lu <qlu@carisls.com>
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@7xuanlu @qlu-cls
7xuanlu and qlu-cls authored Apr 5, 2024
1 parent c9f73d8 commit 075074e
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Showing 13 changed files with 2,082 additions and 1,147 deletions.
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171 changes: 83 additions & 88 deletions packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -714,10 +714,10 @@ export type GenomicDataBinFilter = {
export type GenomicDataCount = {
'count': number

'label': string

'uniqueCount': number

'label': string

'value': string

};
Expand Down Expand Up @@ -907,9 +907,8 @@ export type MutationDataFilter = {

'profileType': string

'values': Array < Array < DataFilterValue >
>

'values': Array < Array< DataFilterValue > >

};
export type MutationPositionIdentifier = {
'entrezGeneId': number
Expand Down Expand Up @@ -4815,6 +4814,85 @@ export default class CBioPortalAPIInternal {
return response.body;
});
};

fetchMutationDataCountsUsingPOSTURL(parameters: {
'genomicDataCountFilter': GenomicDataCountFilter,
$queryParameters ? : any
}): string {
let queryParameters: any = {};
let path = '/api/mutation-data-counts/fetch';

if (parameters.$queryParameters) {
Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
var parameter = parameters.$queryParameters[parameterName];
queryParameters[parameterName] = parameter;
});
}
let keys = Object.keys(queryParameters);
return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : '');
};

/**
* Fetch mutation data counts by GenomicDataCountFilter
* @method
* @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST
* @param {} genomicDataCountFilter - Genomic data count filter
*/
fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters: {
'genomicDataCountFilter': GenomicDataCountFilter,
$queryParameters ? : any,
$domain ? : string
}): Promise < request.Response > {
const domain = parameters.$domain ? parameters.$domain : this.domain;
const errorHandlers = this.errorHandlers;
const request = this.request;
let path = '/api/mutation-data-counts/fetch';
let body: any;
let queryParameters: any = {};
let headers: any = {};
let form: any = {};
return new Promise(function(resolve, reject) {
headers['Accept'] = 'application/json';
headers['Content-Type'] = 'application/json';

if (parameters['genomicDataCountFilter'] !== undefined) {
body = parameters['genomicDataCountFilter'];
}

if (parameters['genomicDataCountFilter'] === undefined) {
reject(new Error('Missing required parameter: genomicDataCountFilter'));
return;
}

if (parameters.$queryParameters) {
Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
var parameter = parameters.$queryParameters[parameterName];
queryParameters[parameterName] = parameter;
});
}

request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers);

});
};

/**
* Fetch mutation data counts by GenomicDataCountFilter
* @method
* @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST
* @param {} genomicDataCountFilter - Genomic data count filter
*/
fetchMutationDataCountsUsingPOST(parameters: {
'genomicDataCountFilter': GenomicDataCountFilter,
$queryParameters ? : any,
$domain ? : string
}): Promise < Array < GenomicDataCountItem >
> {
return this.fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) {
return response.body;
});
};

fetchMolecularProfileSampleCountsUsingPOSTURL(parameters: {
'studyViewFilter' ? : StudyViewFilter,
$queryParameters ? : any
Expand Down Expand Up @@ -5542,89 +5620,6 @@ export default class CBioPortalAPIInternal {
return response.body;
});
};
fetchMutationDataCountsUsingPOSTURL(parameters: {
'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",
'genomicDataCountFilter' ? : GenomicDataCountFilter,
$queryParameters ? : any
}): string {
let queryParameters: any = {};
let path = '/api/mutation-data-counts/fetch';
if (parameters['projection'] !== undefined) {
queryParameters['projection'] = parameters['projection'];
}

if (parameters.$queryParameters) {
Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
var parameter = parameters.$queryParameters[parameterName];
queryParameters[parameterName] = parameter;
});
}
let keys = Object.keys(queryParameters);
return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : '');
};

/**
* Fetch mutation data counts by GenomicDataCountFilter
* @method
* @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST
* @param {string} projection - Level of detail of the response
* @param {} genomicDataCountFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
*/
fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters: {
'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",
'genomicDataCountFilter' ? : GenomicDataCountFilter,
$queryParameters ? : any,
$domain ? : string
}): Promise < request.Response > {
const domain = parameters.$domain ? parameters.$domain : this.domain;
const errorHandlers = this.errorHandlers;
const request = this.request;
let path = '/api/mutation-data-counts/fetch';
let body: any;
let queryParameters: any = {};
let headers: any = {};
let form: any = {};
return new Promise(function(resolve, reject) {
headers['Accept'] = 'application/json';
headers['Content-Type'] = 'application/json';

if (parameters['projection'] !== undefined) {
queryParameters['projection'] = parameters['projection'];
}

if (parameters['genomicDataCountFilter'] !== undefined) {
body = parameters['genomicDataCountFilter'];
}

if (parameters.$queryParameters) {
Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
var parameter = parameters.$queryParameters[parameterName];
queryParameters[parameterName] = parameter;
});
}

request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers);

});
};

/**
* Fetch mutation data counts by GenomicDataCountFilter
* @method
* @name CBioPortalAPIInternal#fetchMutationDataCountsUsingPOST
* @param {string} projection - Level of detail of the response
* @param {} genomicDataCountFilter - A web service for supplying JSON formatted data to cBioPortal clients. Please note that this API is currently in beta and subject to change.
*/
fetchMutationDataCountsUsingPOST(parameters: {
'projection' ? : "ID" | "SUMMARY" | "DETAILED" | "META",
'genomicDataCountFilter' ? : GenomicDataCountFilter,
$queryParameters ? : any,
$domain ? : string
}): Promise < ResponseEntityListGenomicDataCountItem > {
return this.fetchMutationDataCountsUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) {
return response.body;
});
};
getAllReferenceGenomeGenesUsingGETURL(parameters: {
'genomeName': string,
$queryParameters ? : any
Expand Down
7 changes: 7 additions & 0 deletions src/pages/studyView/StudyViewConfig.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ export enum ChartTypeEnum {
SCATTER = 'SCATTER',
VIOLIN_PLOT_TABLE = 'VIOLIN_PLOT_TABLE',
MUTATED_GENES_TABLE = 'MUTATED_GENES_TABLE',
MUTATION_TYPE_COUNTS_TABLE = 'MUTATION_TYPE_COUNTS_TABLE',
STRUCTURAL_VARIANT_GENES_TABLE = 'STRUCTURAL_VARIANT_GENES_TABLE',
STRUCTURAL_VARIANTS_TABLE = 'STRUCTURAL_VARIANTS_TABLE',
CNA_GENES_TABLE = 'CNA_GENES_TABLE',
Expand All @@ -92,6 +93,7 @@ export enum ChartTypeNameEnum {
SCATTER = 'density plot',
VIOLIN_PLOT_TABLE = 'table',
MUTATED_GENES_TABLE = 'table',
MUTATION_TYPE_COUNTS_TABLE = 'table',
STRUCTURAL_VARIANT_GENES_TABLE = 'table',
STRUCTURAL_VARIANTS_TABLE = 'table',
CNA_GENES_TABLE = 'table',
Expand Down Expand Up @@ -207,6 +209,11 @@ const studyViewFrontEnd = {
h: 2,
minW: 2,
},
[ChartTypeEnum.MUTATION_TYPE_COUNTS_TABLE]: {
w: 2,
h: 2,
minW: 2,
},
[ChartTypeEnum.STRUCTURAL_VARIANT_GENES_TABLE]: {
w: 2,
h: 2,
Expand Down
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