@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/GSEA-Y5R2THIJ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/gsea/model/GseaParams.ts", "../plots/gsea/model/GSEAModel.ts", "../plots/gsea/view/GSEAControls.ts", "../plots/gsea/viewModel/GSEAViewModel.ts", "../plots/gsea/view/GSEAView.ts", "../plots/gsea/GSEA.ts"],
+  "sourcesContent": ["type DefaultGseaParams = {\n\tgenome: string\n}\n\ntype DapParams = {\n\torganism: string\n\tassay: string\n\tcohort: string\n}\n\nexport type ProteomeDAPGseaParams = DefaultGseaParams & {\n\tdapParams: DapParams\n\tdslabel: string\n}\n\nexport type ScctGseaParams = DefaultGseaParams & {\n\tgenes: string[]\n\tfold_change: number[]\n\tgenes_length: number\n}\n\nexport type OtherTermTypesGseaParams = DefaultGseaParams & {\n\tcacheId: string\n\tdaRequest: any\n\tgenes_length: number\n\tdslabel: string\n}\n\nexport type GseaParams = ProteomeDAPGseaParams | ScctGseaParams | OtherTermTypesGseaParams\n\nexport function isValidGseaParams(value: any): value is GseaParams {\n\treturn isProteomeDAPGseaParams(value) || isScctGseaParams(value) || isOtherTermTypesGseaParams(value)\n}\n\nexport function isProteomeDAPGseaParams(value: unknown): value is ProteomeDAPGseaParams {\n\tif (!value || typeof value !== 'object') return false\n\tconst p = value as Record<string, unknown>\n \tconst d: any = p.dapParams as DapParams\n \treturn (\n \t\ttypeof p.genome === 'string' &&\n \t\ttypeof p.dslabel === 'string' &&\n \t\td &&\n \t\ttypeof d.organism === 'string' &&\n \t\ttypeof d.assay === 'string' &&\n \t\ttypeof d.cohort === 'string'\n \t)\n}\n\nexport function isScctGseaParams(value: unknown): value is ScctGseaParams {\n\tif (!value || typeof value !== 'object') return false\n\tconst p = value as Record<string, unknown>\n\treturn (\n\t\ttypeof p.genome === 'string' &&\n\t\tArray.isArray(p.genes) &&\n\t\tp.genes.every(g => typeof g === 'string') &&\n\t\tArray.isArray(p.fold_change) &&\n\t\tp.fold_change.every(fc => typeof fc === 'number') &&\n\t\ttypeof p.genes_length === 'number'\n\t)\n}\n\nexport function isOtherTermTypesGseaParams(value: unknown): value is OtherTermTypesGseaParams {\n\tif (!value || typeof value !== 'object') return false\n\tconst p = value as Record<string, unknown>\n\treturn (\n\t\ttypeof p.genome === 'string' &&\n\t\ttypeof p.cacheId === 'string' &&\n\t\t'daRequest' in p &&\n\t\ttypeof p.genes_length === 'number' &&\n\t\ttypeof p.dslabel === 'string'\n\t)\n}\n", "import type { GSEA } from '../GSEA'\nimport { type GseaParams, isProteomeDAPGseaParams, isScctGseaParams, isOtherTermTypesGseaParams } from './GseaParams'\nimport { PROTEOME_DAP, SINGLECELL_CELLTYPE } from '#types'\nimport type { AppApi } from '#rx'\nimport { dofetch3 } from '#common/dofetch'\nimport { VolcanoModel } from '#plots/volcano/model/VolcanoModel.ts'\nimport { getDefaultVolcanoSettings } from '#plots/volcano/settings/defaults.ts'\nimport type { GenesetEnrichmentRequest } from '#types'\n\nexport class GSEAModel {\n\tgsea: GSEA\n\tapp: AppApi\n\ttermType!: string\n\n\tconstructor(gsea: GSEA) {\n\t\tthis.gsea = gsea\n\t\tthis.app = gsea.app\n\t}\n\n\tasync getGseaParams(_params: any, state: any, config: any): Promise<GseaParams> {\n\t\tif (!this.termType) this.termType = config.termType\n\t\tconst params = structuredClone(_params)\n\t\tif (!params.genome) params.genome = state.genome\n\t\tif (!params.dslabel) params.dslabel = state.dslabel\n\n\t\tif (this.termType === PROTEOME_DAP) this.getProteomeDAPParams(params)\n\t\telse if (this.termType === SINGLECELL_CELLTYPE) await this.getScctParams(params, state, config)\n\t\telse await this.getOtherTermTypesParams(params, config)\n\t\treturn params\n\t}\n\n\tgetProteomeDAPParams(params: any): void {\n\t\tif (isProteomeDAPGseaParams(params)) return\n\t\tif (!params.dapParams) params.dapParams = this.gsea.state.config.proteomeDetails\n\t}\n\n\tasync getScctParams(params: any, state, config): Promise<void> {\n\t\tif (isScctGseaParams(params)) return\n\n\t\t// SCCT has no DA cache \u2014 fetch the full DE gene list for the\n\t\t// chosen cluster (omit volcanoRender so the route returns the\n\t\t// raw gene array, not the threshold-passing `dots` subset)\n\t\t// and pass genes + fold_change inline. `render_gsea` takes\n\t\t// this path when neither cacheId nor dapParams is set.\n\n\t\tlet response\n\t\ttry {\n\t\t\tresponse = await this.getDEGenes(state, config)\n\t\t\tif (response.error) throw new Error(response.error)\n\t\t\tif (!Array.isArray(response.data) || response.data.length === 0) {\n\t\t\t\tthrow new Error('No DE genes returned for this cluster')\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(e.message || e)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tthrow new Error(e.message || e)\n\t\t}\n\n\t\t//Process returned response into params\n\t\tconst genes: string[] = []\n\t\tconst fold_change: number[] = []\n\t\tfor (const g of response.data) {\n\t\t\tgenes.push(g.gene_name)\n\t\t\tfold_change.push(g.fold_change)\n\t\t}\n\t\tparams.genes = genes\n\t\tparams.fold_change = fold_change\n\t\tparams.genes_length = genes.length\n\t}\n\n\tasync getDEGenes(state, config): Promise<any> {\n\t\tconst body = {\n\t\t\tgenome: state.genome,\n\t\t\tdslabel: state.dslabel,\n\t\t\tsample: config.sample,\n\t\t\ttermId: config.termId,\n\t\t\tcategoryName: config.categoryName\n\t\t}\n\t\treturn await dofetch3('termdb/singlecellDEgenes', { body })\n\t}\n\n\tasync getOtherTermTypesParams(params: any, config): Promise<void> {\n\t\tif (isOtherTermTypesGseaParams(params)) return\n\t\tlet response\n\t\ttry {\n\t\t\tresponse = await this.getCachedResponse(config)\n\t\t\tif (!response?.data?.cacheId || response.error) {\n\t\t\t\tthrow new Error(response.error || 'No DE cacheId returned from volcano model')\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(e.message || e)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tthrow new Error(e.message || e)\n\t\t}\n\n\t\tparams.cacheId = response.data.cacheId\n\t\tparams.daRequest = response.daRequest\n\t\tparams.genes_length = response.data.totalRows\n\t}\n\n\tasync getCachedResponse(config): Promise<any> {\n\t\tconst volcanoSettings = config.settings?.volcano || getDefaultVolcanoSettings({}, { termType: config.termType })\n\t\tconst model = new VolcanoModel(this.gsea, config.termType)\n\t\treturn await model.getData(config, volcanoSettings)\n\t}\n\n\tasync runEnrichment(body: GenesetEnrichmentRequest): Promise<any> {\n\t\tthis.toggleLoading(true)\n\t\ttry {\n\t\t\treturn await dofetch3('genesetEnrichment', { body })\n\t\t} finally {\n\t\t\tthis.toggleLoading(false)\n\t\t}\n\t}\n\n\ttoggleLoading(isLoading: boolean): void {\n\t\tthis.gsea.dom.actionsDiv.style('display', isLoading ? 'none' : 'block')\n\t\tthis.gsea.dom.loadingDiv.style('display', isLoading ? 'block' : 'none')\n\t}\n}\n", "import type { GSEA } from '../GSEA'\nimport { controlsInit } from '#plots/controls.js'\n\nexport async function setControls(controlsDiv, gsea: GSEA) {\n\tconst inputs: any = [\n\t\t{\n\t\t\tlabel: 'Minimum Gene Set Size Filter Cutoff',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'min_gene_set_size_cutoff',\n\t\t\ttitle: 'Minimum Gene set size cutoff. Helps in filtering out small gene sets',\n\t\t\tmin: 0\n\t\t},\n\t\t{\n\t\t\tlabel: 'Maximum Gene Set Size Filter Cutoff',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'max_gene_set_size_cutoff',\n\t\t\ttitle: 'Maximum Gene set size cutoff. Helps in filtering out large gene sets',\n\t\t\tmax: 25000\n\t\t},\n\t\t{\n\t\t\tlabel: 'Filter Non-coding Genes',\n\t\t\ttype: 'checkbox',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'filter_non_coding_genes',\n\t\t\ttitle: 'Filter non-coding genes',\n\t\t\tboxLabel: ''\n\t\t},\n\t\t{\n\t\t\tlabel: 'FDR or Top Gene Sets',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'fdr_or_top',\n\t\t\ttitle: 'Toggle between FDR cutoff and top gene sets in ascending order of FDR',\n\t\t\toptions: [\n\t\t\t\t{ label: 'FDR', value: 'fdr' },\n\t\t\t\t{ label: 'Top Gene Sets', value: 'top' }\n\t\t\t]\n\t\t},\n\t\t{\n\t\t\tlabel: 'GSEA method',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'gsea_method',\n\t\t\ttitle: 'Toggle between blitzgsea and CERNO method',\n\t\t\toptions: [\n\t\t\t\t{ label: 'blitzgsea', value: 'blitzgsea' },\n\t\t\t\t{ label: 'CERNO', value: 'cerno' }\n\t\t\t],\n\t\t\tgetDisplayStyle: () => {\n\t\t\t\treturn gsea.testEnabled ? '' : 'none'\n\t\t\t}\n\t\t},\n\n\t\t{\n\t\t\tlabel: 'Number of Permutations',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'num_permutations',\n\t\t\ttitle: 'Number of permutations to be used for GSEA. Higher number increases accuracy but also compute time.',\n\t\t\tmin: 0,\n\t\t\tmax: 40000, // Setting it to pretty lenient limit for testing\n\t\t\tgetDisplayStyle: plot => {\n\t\t\t\tconst settings = plot.settings.gsea\n\t\t\t\treturn settings.gsea_method === 'blitzgsea' ? '' : 'none'\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'FDR Filter Cutoff (Linear Scale)',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'fdr_cutoff',\n\t\t\ttitle: 'P-value significance',\n\t\t\tmin: 0,\n\t\t\tmax: 1,\n\t\t\tgetDisplayStyle: plot => {\n\t\t\t\tconst settings = plot.settings.gsea\n\t\t\t\treturn settings.fdr_or_top == 'fdr' ? '' : 'none'\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Number of top Gene Sets by FDR',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'gsea',\n\t\t\tsettingsKey: 'top_genesets',\n\t\t\ttitle: 'Number of top gene sets to be displayed in ascending order of FDR',\n\t\t\tmin: 0,\n\t\t\tmax: 5000,\n\t\t\tgetDisplayStyle: plot => {\n\t\t\t\tconst settings = plot.settings.gsea\n\t\t\t\treturn settings.fdr_or_top == 'top' ? '' : 'none'\n\t\t\t}\n\t\t}\n\t]\n\n\tgsea.components.controls = await controlsInit({\n\t\tapp: gsea.app,\n\t\tid: gsea.id,\n\t\tholder: controlsDiv,\n\t\tinputs: inputs\n\t})\n\n\tgsea.components.controls.on('downloadClick.gsea', () => {\n\t\tif (!gsea.imageUrl) return alert('No image to download')\n\t\tconst dataUrl = gsea.imageUrl\n\t\tconst downloadImgName = `${gsea.state.config.gsea_params.geneset_name || ''}_GSEA_IMG`\n\t\tconst a = document.createElement('a')\n\t\tdocument.body.appendChild(a)\n\n\t\ta.addEventListener(\n\t\t\t'click',\n\t\t\t() => {\n\t\t\t\t// Download the image\n\t\t\t\ta.download = downloadImgName + '.png'\n\t\t\t\ta.href = dataUrl\n\t\t\t\tdocument.body.removeChild(a)\n\t\t\t},\n\t\t\tfalse\n\t\t)\n\t\ta.click()\n\t})\n}\n", "import type { GSEA } from '../GSEA'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\ntype PathwayOpt = { label: string; value: string; selected?: boolean }\n\ntype GseaResultEntry = {\n\tgeneset_size: number\n\tleading_edge: string\n\tfdr?: number\n\tpvalue?: number\n\tnes?: number\n\tauc?: number\n\tes?: number\n}\n\ntype RankedDE = {\n\tgenes: string[]\n\tfold_change: number[]\n}\n\nexport class GSEAViewModel {\n\tgsea: GSEA\n\t//Initial pathway opts from ds. Do not mutate this directly\n\tinitPathwayOpts: PathwayOpt[]\n\trankedDE: RankedDE | null = null\n\trankedDEKey = ''\n\tviewData!: any\n\n\tconstructor(gsea: GSEA) {\n\t\tthis.gsea = gsea\n\t\tthis.initPathwayOpts = structuredClone(gsea.app.opts.genome.termdbs.msigdb.analysisGenesetGroups)\n\t}\n\n\tasync processData() {\n\t\tconst settings = this.gsea.state.config.settings.gsea\n\t\tconst viewData: any = {\n\t\t\tpathwayOpts: this.getPathwayOpts(settings)\n\t\t}\n\n\t\tif (!settings.pathway || settings.pathway == '-') {\n\t\t\tthis.viewData = viewData\n\t\t\treturn\n\t\t}\n\n\t\tlet outputMap: Record<string, GseaResultEntry>\n\t\ttry {\n\t\t\tconst output = await this.gsea.model.runEnrichment(this.getRequestBody(settings))\n\t\t\tif (output?.error) throw Object.assign(new Error(output.error), { code: output.code })\n\t\t\toutputMap = this.getOutputMap(output, settings.gsea_method)\n\t\t} catch (e: any) {\n\t\t\tconst msg = String(e?.message || e)\n\t\t\tif (e?.code === 'CACHE_BUSY') {\n\t\t\t\tif (window.confirm(msg)) {\n\t\t\t\t\tawait this.processData()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.viewData = viewData\n\t\t\t\treturn\n\t\t\t}\n\t\t\tviewData.error = /daCacheMissing|ENOENT|no such file/i.test(msg)\n\t\t\t\t? 'The differential-analysis cache for this GSEA is no longer available. Reopen the volcano plot to regenerate it.'\n\t\t\t\t: msg\n\t\t\tthis.viewData = viewData\n\t\t\treturn\n\t\t}\n\n\t\tviewData.statsData = this.getStatsData(outputMap)\n\t\tviewData.tableData = this.getTableData(outputMap, settings)\n\t\tviewData.selectedRows = this.getSelectedRows(viewData.tableData.rowItems)\n\t\tviewData.showHighlightButton =\n\t\t\tthis.gsea.state.config.chartType == 'differentialAnalysis' &&\n\t\t\tthis.gsea.state.config.gsea_params?.geneset_name != null\n\n\t\tconst selectedGeneset = this.gsea.state.config.gsea_params?.geneset_name\n\t\tif (selectedGeneset) {\n\t\t\tif (settings.gsea_method == 'blitzgsea') {\n\t\t\t\ttry {\n\t\t\t\t\tviewData.detailImage = await this.getDetailImage(settings, selectedGeneset)\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tconst msg = String(e?.message || e)\n\t\t\t\t\tif (e?.code === 'CACHE_BUSY') {\n\t\t\t\t\t\tif (window.confirm(msg)) {\n\t\t\t\t\t\t\tawait this.processData()\n\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t}\n\t\t\t\t\t} else {\n\t\t\t\t\t\tviewData.detailError = /daCacheMissing|ENOENT|no such file/i.test(msg)\n\t\t\t\t\t\t\t? 'The differential-analysis cache for this GSEA is no longer available. Reopen the volcano plot to regenerate it.'\n\t\t\t\t\t\t\t: msg\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tviewData.cernoPlotData = await this.getCernoPlotData(outputMap, selectedGeneset)\n\t\t\t}\n\t\t}\n\n\t\tthis.viewData = viewData\n\t}\n\n\tgetPathwayOpts(settings) {\n\t\t//Do not mutate the initial array\n\t\tconst pathwayOpts = structuredClone(this.initPathwayOpts)\n\t\tif (this.gsea.testEnabled && settings.gsea_method == 'blitzgsea') {\n\t\t\tpathwayOpts.push(\n\t\t\t\t{ label: 'REACTOME (blitzgsea)', value: 'REACTOME--blitzgsea' },\n\t\t\t\t{ label: 'KEGG (blitzgsea)', value: 'KEGG--blitzgsea' },\n\t\t\t\t{ label: 'WikiPathways (blitzgsea)', value: 'WikiPathways--blitzgsea' }\n\t\t\t)\n\t\t}\n\t\tif (settings.pathway) {\n\t\t\t//Note: in the ds file, `{ label: '-', value: '-' }` is analysisGenesetGroups[0]\n\t\t\tpathwayOpts.shift()\n\t\t\tconst opt = pathwayOpts.find(opt => opt.value == settings.pathway)\n\t\t\tif (!opt) console.warn(`Selected pathway ${settings.pathway} not found in pathway options.`)\n\t\t\telse opt.selected = true\n\t\t}\n\t\treturn pathwayOpts\n\t}\n\n\tgetRequestBody(settings, geneset_name?: string) {\n\t\tconst p = this.gsea.gsea_params\n\t\tconst body: any = {\n\t\t\tgenome: p.genome,\n\t\t\tgeneSetGroup: settings.pathway,\n\t\t\tfilter_non_coding_genes: settings.filter_non_coding_genes,\n\t\t\tmethod: settings.gsea_method\n\t\t}\n\t\tif (p.cacheId) {\n\t\t\tbody.cacheId = p.cacheId\n\t\t\tif (p.daRequest) body.daRequest = p.daRequest\n\t\t\tif (p.dslabel) body.dslabel = p.dslabel\n\t\t} else if (p.dapParams) {\n\t\t\tbody.dapParams = p.dapParams\n\t\t\tbody.dslabel = p.dslabel\n\t\t} else {\n\t\t\tbody.genes = p.genes\n\t\t\tbody.fold_change = p.fold_change\n\t\t}\n\n\t\tif (settings.gsea_method == 'blitzgsea') {\n\t\t\tbody.num_permutations = settings.num_permutations\n\t\t}\n\t\tif (geneset_name) body.geneset_name = geneset_name\n\t\treturn body\n\t}\n\n\tgetOutputMap(output: any, method: string): Record<string, GseaResultEntry> {\n\t\tif (method == 'blitzgsea') {\n\t\t\tif (!output?.data || typeof output.data != 'object') throw new Error('Invalid blitzgsea response')\n\t\t\treturn output.data\n\t\t}\n\n\t\tif (output?.data && !Array.isArray(output.data) && !output.data.genes && !output.data.fold_change) {\n\t\t\treturn output.data\n\t\t}\n\t\tif (output && typeof output == 'object' && !Array.isArray(output)) return output\n\t\tthrow new Error('Invalid cerno response')\n\t}\n\n\tgetStatsData(outputMap: Record<string, GseaResultEntry>) {\n\t\treturn [{ label: 'Gene sets analyzed', value: Object.keys(outputMap).length }]\n\t}\n\n\tgetTableData(outputMap: Record<string, GseaResultEntry>, settings) {\n\t\tconst entries = Object.entries(outputMap).map(([genesetName, result]) => ({ genesetName, result }))\n\t\tconst rowItems: any[] = []\n\n\t\tif (settings.fdr_or_top == 'top') {\n\t\t\tentries.sort((a, b) => Number(a.result.fdr ?? Infinity) - Number(b.result.fdr ?? Infinity))\n\t\t\tfor (let index = 0; index < Math.min(settings.top_genesets, entries.length); index++) {\n\t\t\t\tconst item = entries[index]\n\t\t\t\tif (this.withinSizeCutoff(item.result, settings)) rowItems.push(this.makeRowItem(item, settings.gsea_method))\n\t\t\t}\n\t\t} else {\n\t\t\tfor (const item of entries) {\n\t\t\t\tif (!this.withinSizeCutoff(item.result, settings)) continue\n\t\t\t\tif (Number(item.result.fdr ?? Infinity) > settings.fdr_cutoff) continue\n\t\t\t\trowItems.push(this.makeRowItem(item, settings.gsea_method))\n\t\t\t}\n\t\t}\n\n\t\treturn {\n\t\t\tcolumns: this.getTableColumns(settings.gsea_method),\n\t\t\trows: rowItems.map(item => item.row),\n\t\t\trowItems\n\t\t}\n\t}\n\n\twithinSizeCutoff(result: GseaResultEntry, settings) {\n\t\treturn (\n\t\t\tsettings.max_gene_set_size_cutoff >= result.geneset_size &&\n\t\t\tsettings.min_gene_set_size_cutoff <= result.geneset_size\n\t\t)\n\t}\n\n\tmakeRowItem(item: { genesetName: string; result: GseaResultEntry }, method: string) {\n\t\tconst pvalue = item.result.pvalue != null ? roundValueAuto(item.result.pvalue) : item.result.pvalue\n\t\tconst fdr = item.result.fdr != null ? roundValueAuto(item.result.fdr) : item.result.fdr\n\t\tconst leadingEdge = item.result.leading_edge\n\t\tconst genes = leadingEdge ? leadingEdge.split(',').map(gene => gene.trim()).filter(Boolean) : []\n\n\t\tif (method == 'blitzgsea') {\n\t\t\tconst nes = item.result.nes != null ? roundValueAuto(item.result.nes) : item.result.nes\n\t\t\treturn {\n\t\t\t\tgenesetName: item.genesetName,\n\t\t\t\tgenes,\n\t\t\t\trow: [\n\t\t\t\t\t{ value: item.genesetName },\n\t\t\t\t\t{ value: nes },\n\t\t\t\t\t{ value: item.result.geneset_size },\n\t\t\t\t\t{ value: pvalue },\n\t\t\t\t\t{ value: fdr },\n\t\t\t\t\t{ value: leadingEdge }\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\n\t\tconst auc = item.result.auc != null ? roundValueAuto(item.result.auc) : item.result.auc\n\t\tconst es = item.result.es != null ? roundValueAuto(item.result.es) : item.result.es\n\t\treturn {\n\t\t\tgenesetName: item.genesetName,\n\t\t\tgenes,\n\t\t\trow: [\n\t\t\t\t{ value: item.genesetName },\n\t\t\t\t{ value: auc },\n\t\t\t\t{ value: es },\n\t\t\t\t{ value: item.result.geneset_size },\n\t\t\t\t{ value: pvalue },\n\t\t\t\t{ value: fdr },\n\t\t\t\t{ value: leadingEdge }\n\t\t\t]\n\t\t}\n\t}\n\n\tgetTableColumns(method: string) {\n\t\tif (method == 'blitzgsea') {\n\t\t\treturn [\n\t\t\t\t{ label: 'Gene Set', sortable: true },\n\t\t\t\t{ label: 'Normalized Enrichment Score', barplot: { axisWidth: 200 }, sortable: true },\n\t\t\t\t{ label: 'Gene Set Size', sortable: true },\n\t\t\t\t{ label: 'P value', sortable: true },\n\t\t\t\t{ label: 'FDR', sortable: true },\n\t\t\t\t{ label: 'Leading Edge' }\n\t\t\t]\n\t\t}\n\n\t\treturn [\n\t\t\t{ label: 'Gene Set', sortable: true },\n\t\t\t{ label: 'Area Under Curve', barplot: { axisWidth: 200 }, sortable: true },\n\t\t\t{ label: 'Enrichment Score', barplot: { axisWidth: 200 }, sortable: true },\n\t\t\t{ label: 'Total Gene Set Size', sortable: true },\n\t\t\t{ label: 'P value', sortable: true },\n\t\t\t{ label: 'FDR', sortable: true },\n\t\t\t{ label: 'Gene Set Hits' }\n\t\t]\n\t}\n\n\tgetSelectedRows(rowItems: any[]) {\n\t\tconst selectedGeneset = this.gsea.state.config.gsea_params?.geneset_name\n\t\tconst selectedIndex = rowItems.findIndex(item => item.genesetName == selectedGeneset)\n\t\treturn selectedIndex > -1 ? [selectedIndex] : []\n\t}\n\n\tasync getDetailImage(settings, genesetName: string) {\n\t\tconst image = await this.gsea.model.runEnrichment(this.getRequestBody(settings, genesetName))\n\t\tif (image?.error) throw Object.assign(new Error(image.error), { code: image.code })\n\n\t\tif (this.gsea.imageUrl) URL.revokeObjectURL(this.gsea.imageUrl)\n\t\tthis.gsea.imageUrl = URL.createObjectURL(image)\n\t\treturn {\n\t\t\tsrc: this.gsea.imageUrl,\n\t\t\twidth: 600,\n\t\t\theight: 400\n\t\t}\n\t}\n\n\tasync getCernoPlotData(outputMap: Record<string, GseaResultEntry>, genesetName: string) {\n\t\tconst selected = outputMap[genesetName]\n\t\tif (!selected) throw new Error(`${genesetName} not found`)\n\n\t\tconst rankedDE = await this.getRankedDE()\n\t\tconst rankedGenes = rankedDE.genes.map((gene, index) => ({ gene, fold_change: rankedDE.fold_change[index] }))\n\t\trankedGenes.sort((a, b) => b.fold_change - a.fold_change)\n\n\t\treturn {\n\t\t\tauc: selected.auc,\n\t\t\tgenesetName,\n\t\t\tleadingEdgeGenes: selected.leading_edge.split(',').map(gene => gene.trim()).filter(Boolean),\n\t\t\trankedGenes\n\t\t}\n\t}\n\n\tasync getRankedDE(): Promise<RankedDE> {\n\t\tconst cacheKey = this.getRankedDECacheKey()\n\t\tif (this.rankedDE && this.rankedDEKey == cacheKey) return this.rankedDE\n\n\t\tif (!this.gsea.gsea_params.cacheId && !this.gsea.gsea_params.dapParams) {\n\t\t\tconst rankedDE = {\n\t\t\t\tgenes: this.gsea.gsea_params.genes,\n\t\t\t\tfold_change: this.gsea.gsea_params.fold_change\n\t\t\t}\n\t\t\tthis.rankedDE = rankedDE\n\t\t\tthis.rankedDEKey = cacheKey\n\t\t\treturn rankedDE\n\t\t}\n\n\t\tconst response = await this.gsea.model.runEnrichment({\n\t\t\tgenome: this.gsea.gsea_params.genome,\n\t\t\tdslabel: this.gsea.gsea_params.dslabel,\n\t\t\tfetchDE: true,\n\t\t\tgeneSetGroup: '-',\n\t\t\tfilter_non_coding_genes: false,\n\t\t\tmethod: 'cerno',\n\t\t\t...(this.gsea.gsea_params.cacheId\n\t\t\t\t? {\n\t\t\t\t\tcacheId: this.gsea.gsea_params.cacheId,\n\t\t\t\t\tdaRequest: this.gsea.gsea_params.daRequest\n\t\t\t\t}\n\t\t\t\t: { dapParams: this.gsea.gsea_params.dapParams })\n\t\t})\n\t\tif (response?.error) throw Object.assign(new Error(response.error), { code: response.code })\n\n\t\tconst rankedDE = response.data as RankedDE\n\t\tthis.rankedDE = rankedDE\n\t\tthis.rankedDEKey = cacheKey\n\t\treturn rankedDE\n\t}\n\n\tgetRankedDECacheKey() {\n\t\tif (this.gsea.gsea_params.cacheId) return `cache:${this.gsea.gsea_params.cacheId}`\n\t\tif (this.gsea.gsea_params.dapParams) return `dap:${JSON.stringify(this.gsea.gsea_params.dapParams)}`\n\t\tconst genes = this.gsea.gsea_params.genes || []\n\t\treturn `inline:${genes.length}:${genes[0] || ''}:${genes[genes.length - 1] || ''}`\n\t}\n}\n", "import type { GSEA } from '../GSEA'\nimport * as d3axis from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\nimport { renderTable, table2col, axisstyle, sayerror } from '#dom'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\nexport class GSEAView {\n\tgsea: GSEA\n\tdom: any\n\tpathwayDropDown: any\n\n\tconstructor(gsea: GSEA) {\n\t\tthis.gsea = gsea\n\t\tthis.dom = gsea.dom\n\t}\n\n\tinitRender() {\n\t\tthis.renderActions()\n\t}\n\n\trenderActions() {\n\t\tthis.dom.actionsDiv\n\t\t\t.append('span')\n\t\t\t.attr('data-testid', 'sjpp-gsea-pathway')\n\t\t\t.style('margin-right', '10px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.text('Select a gene set group:')\n\n\t\tthis.pathwayDropDown = this.dom.actionsDiv\n\t\t\t.append('select')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.on('change', async () => {\n\t\t\t\tconst value = this.pathwayDropDown.node().value\n\t\t\t\tconst settings = structuredClone(this.gsea.state.config.settings.gsea)\n\t\t\t\tsettings.pathway = value\n\t\t\t\tawait this.gsea.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.gsea.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\t//Need to clear the gsea_params completely\n\t\t\t\t\t\tgsea_params: {\n\t\t\t\t\t\t\tgeneset_name: null,\n\t\t\t\t\t\t\tpathway: value\n\t\t\t\t\t\t},\n\t\t\t\t\t\thighlightGenes: [],\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tgsea: settings\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\tupdate() {\n\t\tconst viewData = this.gsea.viewModel.viewData\n\t\tthis.renderPathwayOptions(viewData.pathwayOpts)\n\n\t\tthis.dom.detailsDiv.selectAll('*').remove()\n\t\tthis.dom.holder.selectAll('*').remove()\n\t\tthis.dom.tableDiv.selectAll('*').remove()\n\n\t\tif (viewData.error) {\n\t\t\tsayerror(this.dom.holder, viewData.error)\n\t\t\treturn\n\t\t}\n\n\t\tif (!viewData.tableData) return\n\n\t\tthis.renderStats(viewData.statsData)\n\t\tif (viewData.detailImage) this.renderImage(viewData.detailImage)\n\t\tif (viewData.cernoPlotData) this.renderCernoPlot(viewData.cernoPlotData)\n\t\tif (viewData.detailError) sayerror(this.dom.holder, viewData.detailError)\n\t\tif (viewData.showHighlightButton) this.renderHighlightButton()\n\t\tthis.renderResultsTable(viewData)\n\t}\n\n\trenderPathwayOptions(pathwayOpts) {\n\t\tthis.pathwayDropDown.selectAll('option').remove()\n\t\tthis.pathwayDropDown\n\t\t\t.selectAll('option')\n\t\t\t.data(pathwayOpts)\n\t\t\t.enter()\n\t\t\t.append('option')\n\t\t\t.text(d => d.label)\n\t\t\t.property('value', d => d.value)\n\t\t\t.property('selected', d => d.selected)\n\t}\n\n\trenderStats(statsData) {\n\t\tconst tableStats = table2col({ holder: this.dom.detailsDiv.attr('data-testid', 'sjpp-gsea-stats') })\n\t\tconst [, countHeader] = tableStats.addRow()\n\t\tcountHeader.style('text-align', 'center').style('font-size', '0.8em').style('opacity', '0.8').text('COUNT')\n\n\t\tfor (const row of statsData) {\n\t\t\tconst [labelCell, valueCell] = tableStats.addRow()\n\t\t\tlabelCell.text(row.label)\n\t\t\tvalueCell.style('text-align', 'end').text(row.value)\n\t\t}\n\t}\n\n\trenderImage(detailImage) {\n\t\tthis.dom.holder.append('img').attr('width', detailImage.width).attr('height', detailImage.height).attr('src', detailImage.src)\n\t}\n\n\trenderHighlightButton() {\n\t\tthis.dom.detailsDiv\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('display', 'block')\n\t\t\t.attr('aria-label', 'Highlight genes in the volcano plot')\n\t\t\t.text('Highlight genes')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.gsea.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.gsea.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tchildType: 'volcano',\n\t\t\t\t\t\thighlightedData: this.gsea.state.config.highlightGenes\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\trenderResultsTable(viewData) {\n\t\tconst tableDiv = this.dom.tableDiv.append('div')\n\t\trenderTable({\n\t\t\tdownload: {\n\t\t\t\tfileName: this.gsea.state.config.downloadFilename || ''\n\t\t\t},\n\t\t\tcolumns: viewData.tableData.columns,\n\t\t\trows: viewData.tableData.rows,\n\t\t\tdiv: tableDiv,\n\t\t\tshowLines: true,\n\t\t\tmaxHeight: '30vh',\n\t\t\tsingleMode: true,\n\t\t\tresize: true,\n\t\t\theader: { allowSort: true },\n\t\t\tselectedRows: viewData.selectedRows,\n\t\t\tnoButtonCallback: async index => {\n\t\t\t\tconst rowItem = viewData.tableData.rowItems[index]\n\t\t\t\tconst config: any = {\n\t\t\t\t\tgsea_params: {\n\t\t\t\t\t\tgeneset_name: rowItem.genesetName\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (this.gsea.state.config.chartType == 'differentialAnalysis' && rowItem.genes.length) {\n\t\t\t\t\tconfig.highlightGenes = rowItem.genes\n\t\t\t\t}\n\t\t\t\tawait this.gsea.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.gsea.id,\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\trenderCernoPlot(cernoPlotData) {\n\t\tconst holder = this.dom.holder\n\t\tconst svgWidth = 400\n\t\tconst svgHeight = 400\n\t\tconst svg = holder.append('svg').attr('width', svgWidth).attr('height', svgHeight)\n\t\tconst topPad = 20\n\t\tconst rightPad = 5\n\t\tconst xPad = 50\n\t\tconst yPad = 100\n\t\tconst yAxis = svg.append('g')\n\t\tconst xAxis = svg.append('g')\n\n\t\tconst xScale = scaleLinear().domain([0, cernoPlotData.rankedGenes.length]).range([xPad, svgWidth - rightPad])\n\t\tconst yScale = scaleLinear().domain([100, 0]).range([topPad, svgHeight - yPad])\n\n\t\tyAxis.attr('transform', `translate(${xPad},0)`)\n\t\txAxis.attr('transform', `translate(0,${svgHeight - yPad})`)\n\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.text('Gene list')\n\t\t\t.attr('fill', 'black')\n\t\t\t.attr('text-anchor', 'start')\n\t\t\t.attr('transform', `translate(${xScale(cernoPlotData.rankedGenes.length / 3)},${svgHeight - yPad + 2 * topPad})`)\n\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.text('Percentage of gene set')\n\t\t\t.attr('fill', 'black')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('y', xPad / 2)\n\t\t\t.attr('x', -svgWidth / 2.5)\n\t\t\t.attr('transform', 'rotate(-90)')\n\n\t\tlet fontSize = 30\n\t\tconst title = svg\n\t\t\t.append('text')\n\t\t\t.text(cernoPlotData.genesetName)\n\t\t\t.attr('fill', 'black')\n\t\t\t.attr('text-anchor', 'start')\n\t\t\t.attr('font-size', `${fontSize}px`)\n\t\t\t.attr('transform', `translate(${xPad},${topPad / 2})`)\n\n\t\tlet titleBox = title.node().getBBox()\n\t\twhile (titleBox.width > svgWidth - xPad || titleBox.height > (topPad * 3.5) / 5) {\n\t\t\tfontSize -= 1\n\t\t\ttitle.node().setAttribute('font-size', `${fontSize}px`)\n\t\t\ttitleBox = title.node().getBBox()\n\t\t}\n\n\t\tif (typeof cernoPlotData.auc === 'number') {\n\t\t\tconst aucPos =\n\t\t\t\tcernoPlotData.auc >= 0.5\n\t\t\t\t\t? `${xScale((cernoPlotData.rankedGenes.length * 3) / 3.5)},${svgHeight - yPad * 1.5}`\n\t\t\t\t\t: `${xScale((cernoPlotData.rankedGenes.length * 0.8) / 4.5)},${svgHeight - yPad * 3}`\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.text(`AUC=${roundValueAuto(cernoPlotData.auc)}`)\n\t\t\t\t.attr('fill', 'black')\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('transform', `translate(${aucPos})`)\n\t\t}\n\n\t\taxisstyle({\n\t\t\taxis: yAxis.call(d3axis.axisLeft(yScale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true,\n\t\t\tfontsize: '10'\n\t\t})\n\t\taxisstyle({\n\t\t\taxis: xAxis.call(d3axis.axisBottom(xScale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true,\n\t\t\tfontsize: '10'\n\t\t})\n\n\t\tconst hitGenes = new Set(cernoPlotData.leadingEdgeGenes)\n\t\tconst yIncrement = 100 / Math.max(hitGenes.size, 1)\n\t\tconst lines = svg.append('g')\n\t\tlet yIter = 100\n\t\tfor (let index = 0; index < cernoPlotData.rankedGenes.length; index++) {\n\t\t\tconst rankedGene = cernoPlotData.rankedGenes[index]\n\t\t\tconst yOld = yIter\n\t\t\tif (hitGenes.has(rankedGene.gene)) {\n\t\t\t\tyIter -= yIncrement\n\t\t\t\tlines\n\t\t\t\t\t.append('line')\n\t\t\t\t\t.style('stroke', 'red')\n\t\t\t\t\t.attr('x1', xScale(index))\n\t\t\t\t\t.attr('y1', svgHeight)\n\t\t\t\t\t.attr('x2', xScale(index))\n\t\t\t\t\t.attr('y2', svgHeight - yPad + 2.5 * topPad)\n\t\t\t}\n\t\t\tlines\n\t\t\t\t.append('line')\n\t\t\t\t.style('stroke', 'red')\n\t\t\t\t.attr('x1', xScale(index))\n\t\t\t\t.attr('y1', yScale(100 - yOld))\n\t\t\t\t.attr('x2', xScale(index + 1))\n\t\t\t\t.attr('y2', yScale(100 - yIter))\n\t\t}\n\t}\n}\n", "import { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { PlotBase } from '#plots/PlotBase.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PROTEOME_DAP, SINGLECELL_CELLTYPE } from '#types'\nimport { getDefaultGseaSettings } from './settings/defaults'\nimport { GSEAModel } from './model/GSEAModel'\nimport { isValidGseaParams } from './model/GseaParams'\nimport { setControls } from './view/GSEAControls'\nimport { GSEAViewModel } from './viewModel/GSEAViewModel'\nimport { GSEAView } from './view/GSEAView'\n\nexport class GSEA extends PlotBase implements RxComponent {\n\tstatic type = 'gsea'\n\n\ttype: string\n\tsettings!: any\n\tcomponents!: { controls: any }\n\timageUrl: any\n\tconfig!: any\n\ttestEnabled: boolean\n\tgsea_params!: any\n\tmodel!: GSEAModel\n\tviewModel!: GSEAViewModel\n\tview!: GSEAView\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = GSEA.type\n\t\tthis.opts = opts\n\t\tthis.components = {\n\t\t\tcontrols: {}\n\t\t}\n\t\t//Either allow a node to be passed or create a new div\n\t\tconst controlsDiv =\n\t\t\ttypeof opts.controls == 'object' ? opts.controls : opts.holder.append('div').style('display', 'inline-block')\n\t\tconst main = opts.holder.append('div').style('display', 'inline-block')\n\t\tconst actionsDiv = main\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-gsea-actions')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('text-align', 'left')\n\n\t\t//TODO: implement toggleLoadingDiv from parent\n\t\tconst loadingDiv = main\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-gsea-loading')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('text-align', 'left')\n\t\t\t.text('Loading...')\n\t\tconst holder = main\n\t\t\t.append('div')\n\t\t\t.style('margin-left', '50px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.attr('data-testid', 'sjpp-gsea-holder')\n\t\tconst detailsDiv = main\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-gsea-details')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin-top', '50px')\n\n\t\tconst tableDiv = main.append('div').style('margin', '10px').attr('data-testid', 'sjpp-gsea-results-table')\n\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\theader: opts.header,\n\t\t\tactionsDiv,\n\t\t\tloadingDiv,\n\t\t\tcontrolsDiv,\n\t\t\tdetailsDiv,\n\t\t\ttableDiv\n\t\t}\n\n\t\tthis.testEnabled = JSON.parse(sessionStorage.getItem('optionalFeatures') || '{}')?.gsea_test\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw new Error(`No plot with id='${this.id}' found`)\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermfilter,\n\t\t\tgenome: appState.vocab.genome,\n\t\t\tdslabel: appState.vocab.dslabel\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tconst config = structuredClone(state.config)\n\n\t\tthis.model = new GSEAModel(this)\n\t\t/** Ensures plots init'ed from session are properly vetted and\n\t\t * mutated as necessary. */\n\t\tvalidateConfigByTermType(config)\n\n\t\tif (!isValidGseaParams(config.gsea_params)) {\n\t\t\tthis.gsea_params = await this.model.getGseaParams(config.gsea_params, state, config)\n\t\t} else {\n\t\t\tthis.gsea_params = config.gsea_params\n\t\t}\n\n\t\tawait setControls(this.dom.controlsDiv, this)\n\t\tthis.viewModel = new GSEAViewModel(this)\n\t\tthis.view = new GSEAView(this)\n\n\t\tthis.view.initRender()\n\t}\n\n\tasync main() {\n\t\tconst state = structuredClone(this.state)\n\t\t//TODO: Fix this to use parentId instead\n\t\tif (state.config.chartType != this.type && state.config.childType != this.type) return\n\n\t\tif (this.dom.header) {\n\t\t\tconst geneCount = this.gsea_params.genes_length ?? this.gsea_params.genes?.length ?? 0\n\t\t\tthis.dom.header.html(\n\t\t\t\tgeneCount + ' genes <span style=\"font-size:.8em;opacity:.7\">GENE SET ENRICHMENT ANALYSIS</span>'\n\t\t\t)\n\t\t}\n\t\tif (this.imageUrl) URL.revokeObjectURL(this.imageUrl)\n\t\tthis.imageUrl = null\n\n\t\tawait this.viewModel.processData()\n\t\tthis.view.update()\n\t\t// render_gsea(this)\n\t}\n}\n\nexport const gseaInit = getCompInit(GSEA)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = gseaInit\n\n/************* \n * TODO: \n * The config object contains the same data over and over. \n * ex. samplelst:{groups} is the same thing as tw.q.groups. \n * ex. gsea_params contain duplicate information in settings.gsea \n * and in the state. \n * ex. the plot state is added to the config unnecessarily.\n * \n * This poorly constructed object increases the complexity of the code \n * and makes it harder to maintain.\n * Need to reduce the overall redundancy and simplify the structure.\n ************/\nexport async function getPlotConfig(opts, app) {\n\t// if (!opts.gsea_params) throw 'No gsea_params provided [gsea getPlotConfig()]'\n\tif (!opts.termType) throw new Error('No termType provided [gsea getPlotConfig()]')\n\ttry {\n\t\tconst config = {\n\t\t\tgsea_params: {\n\t\t\t\tgenome: app.opts.state.vocab.genome\n\t\t\t},\n\t\t\t//idea for fixing nav button\n\t\t\t//samplelst: { groups: app.opts.state.groups}\n\t\t\tsettings: {\n\t\t\t\tgsea: getDefaultGseaSettings(opts.overrides, opts)\n\t\t\t}\n\t\t}\n\n\t\tcopyMerge(config, opts)\n\t\tvalidateConfigByTermType(config)\n\t\treturn config\n\t} catch (e) {\n\t\tthrow `${e} [gsea getPlotConfig()]`\n\t}\n}\n\nfunction validateConfigByTermType(config) {\n\tif (!config.gsea_params) config.gsea_params = {}\n\tif (config.termType === PROTEOME_DAP) {\n\t\tif (!config.proteomeDetails) throw new Error('No proteomeDetails provided for DAP GSEA')\n\t\tconfig.gsea_params.dapParams = config.proteomeDetails\n\t} else if (config.termType === SINGLECELL_CELLTYPE) {\n\t\tif (!config.sample || !config.termId || !config.categoryName)\n\t\t\tthrow new Error('Missing sample, termId, or categoryName for single cell cluster GSEA')\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\n\t// to fill in menu, create options in \"holder\"\n\t// to hide menu, call chartsInstance.dom.tip.hide()\n\t// upon clicking an option, generate plot:\n\tchartsInstance.prepPlot({\n\t\tconfig: {\n\t\t\tchartType: 'gsea'\n\t\t}\n\t})\n}\n"],
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+  "names": ["opt", "rankedDE"]
+}

package/dist/GeneExpInput-JDU6EI7K.js

@@ -0,0 +1,367 @@
+import {
+  GeneSetEditUI,
+  PlotBase,
+  addGeneSearchbox,
+  getCurrentCohortChartTypes,
+  getGEunit,
+  getSCGEunit,
+  sayerror
+} from "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import {
+  importPlot
+} from "./chunk-Z5U6HOE4.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  Tabs
+} from "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import {
+  GENE_EXPRESSION,
+  SINGLECELL_GENE_EXPRESSION,
+  SSGSEA,
+  typeGroup
+} from "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/GeneExpInput.ts
+var GeneExpInput = class _GeneExpInput extends PlotBase {
+  static {
+    this.type = "GeneExpInput";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _GeneExpInput.type;
+    this.opts = opts;
+    this.components = {
+      plots: {}
+    };
+  }
+  makeTerm(_term) {
+    const termProperties = this.state.config?.termProperties || {};
+    const term = { ..._term, ...termProperties, type: this.termType, unit: this.unit };
+    return term;
+  }
+  makeConfig(_config) {
+    const spawnConfig = this.state.config?.spawnConfig || {};
+    const tmp = { ..._config, ...spawnConfig };
+    return tmp;
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    const subplots = appState.plots.filter((p) => p.parentId === this.id);
+    return {
+      config,
+      termdbConfig: appState.termdbConfig,
+      subplots
+    };
+  }
+  async init(appState) {
+    const state = this.getState(appState);
+    this.genome = this.app.opts.genome;
+    this.termType = state.config.termType;
+    this.unit = this.getUnit();
+    this.dom = this.initDom();
+    const chartTypes = new Set(getCurrentCohortChartTypes(appState));
+    this.tabs = [
+      {
+        label: "One gene",
+        isVisible: () => true,
+        callback: (event, tab) => {
+          this.renderGeneSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Two genes",
+        isVisible: () => true,
+        callback: (event, tab) => {
+          this.renderTwoGeneSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Hierarchical clustering",
+        isVisible: () => chartTypes.has("matrix"),
+        callback: (event, tab) => {
+          this.renderGeneMultiSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: `Differential ${typeGroup[this.termType].toLowerCase()} analysis`,
+        //Only enabling for gene expression for now
+        chartType: "DEinput",
+        isVisible: () => chartTypes.has("DA") && this.termType === GENE_EXPRESSION,
+        callback: async (event, tab) => {
+          await this.app.dispatch({
+            type: "plot_create",
+            parentId: this.id,
+            config: {
+              chartType: "DEinput",
+              parentId: this.id,
+              /** ' ' overrides the default 'hide_search' mode in DEInput.
+               * 'hide_search' by default expands all terms. */
+              header_mode: " "
+            }
+          });
+          delete tab.callback;
+        }
+      },
+      {
+        label: typeGroup[SSGSEA],
+        isVisible: () => {
+          return this.termType === GENE_EXPRESSION && state.termdbConfig?.allowedTermTypes?.includes(SSGSEA);
+        },
+        callback: async (event, tab) => {
+          await this.renderSSGSEA(tab);
+          delete tab.callback;
+        }
+      }
+    ];
+    const chartTabs = new Tabs({
+      holder: this.dom.tabs,
+      tabs: this.tabs,
+      tabsPosition: "vertical"
+    });
+    await chartTabs.main();
+  }
+  getUnit() {
+    return this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi);
+  }
+  initDom() {
+    const headerText = this.opts.headerText ? `${this.opts.headerText} ` : "";
+    const dom = {
+      header: {
+        title: this.opts.header.append("span").style("padding-right", "5px").text(headerText).attr("data-testid", "sjpp-gene-exp-input-headerText"),
+        plot: this.opts.header.append("span").text(typeGroup[this.termType].toUpperCase()).style("font-size", "0.7em").style("opacity", "0.6").attr("data-testid", "sjpp-gene-exp-input-termType")
+      },
+      tabs: this.opts.holder.append("div").style("margin", "10px").attr("data-testid", "sjpp-gene-exp-input-tabs-wrapper")
+    };
+    return dom;
+  }
+  async main() {
+    const state = this.getState(this.app.getState());
+    for (const subplot of state.subplots || []) {
+      if (!this.components.plots[subplot.id]) await this.initSubplotInTab(subplot);
+    }
+  }
+  renderGeneSelect(tab) {
+    const row = tab.contentHolder.style("padding", "15px");
+    row.append("span").style("padding", "5px").text("Select a gene:");
+    const geneSearch = addGeneSearchbox({
+      row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        const tw = {
+          term: this.makeTerm({
+            gene: geneSearch.geneSymbol,
+            name: `${geneSearch.geneSymbol} ${this.unit}`
+          })
+        };
+        const config = this.makeConfig({
+          chartType: "summary",
+          term: tw
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  /** Guide the user to select the first gene then
+   * a second to launch the summary plot on submit.*/
+  renderTwoGeneSelect(tab) {
+    const term = {};
+    const term2 = {};
+    const holder = tab.contentHolder.style("padding", "10px");
+    const gene1row = holder.append("div").style("padding", "5px");
+    const gene2row = holder.append("div").style("padding", "5px").style("display", "none");
+    const submitButton = holder.append("button").attr("type", "button").attr("disabled", true);
+    gene1row.append("span").text("Select the first gene:");
+    const geneSearch1 = addGeneSearchbox({
+      row: gene1row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        gene2row.style("display", "block");
+        if (!geneSearch1.geneSymbol) throw new Error("First gene result is required");
+        term.gene = geneSearch1.geneSymbol;
+        term.name = `${geneSearch1.geneSymbol} ${this.unit}`;
+      }
+    });
+    gene2row.append("span").text("Select the second gene:");
+    const geneSearch2 = addGeneSearchbox({
+      row: gene2row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        if (!geneSearch2.geneSymbol) throw new Error("Second gene result is required");
+        term2.gene = geneSearch2.geneSymbol;
+        term2.name = `${geneSearch2.geneSymbol} ${this.unit}`;
+        submitButton.attr("disabled", null);
+      }
+    });
+    submitButton.text("Submit").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").on("click", async () => {
+      if (!term.name || !term.gene) {
+        sayerror(holder, "Missing first gene. Please provide a valid gene.");
+        return;
+      }
+      if (!term2.name || !term2.gene) {
+        sayerror(holder, "Missing second gene. Please provide a valid gene.");
+        return;
+      }
+      const config = this.makeConfig({
+        chartType: "summary",
+        term: { term: this.makeTerm(term) },
+        term2: { term: this.makeTerm(term2) }
+      });
+      await this.dispatchEdits(config);
+    });
+  }
+  // /** Render the GeneSetEdit UI for selection and then
+  //  * launch the hierarchical clustering on submit.*/
+  renderGeneMultiSelect(tab) {
+    const holder = tab.contentHolder.style("padding", "10px");
+    const grpWrapper = holder.append("div").style("padding", "10px");
+    grpWrapper.append("span").style("font-weight", "bold").text("Group name:");
+    let customName = "New custom group";
+    const input = grpWrapper.append("input").style("margin", "2px 5px").style("width", "210px").attr("placeholder", "Group Name").on("input", () => {
+      customName = input.property("value");
+    });
+    new GeneSetEditUI({
+      holder: holder.append("div"),
+      /** running hier clustering and the editing group
+       * is the group used for clustering pass this mode
+       * value to inform ui to support the optional button
+       * "top variably exp gene" this is hardcoded for
+       * the purpose of gene expression and should be improved. */
+      genome: this.genome,
+      mode: "geneExpression",
+      vocabApi: this.app.vocabApi,
+      callback: async ({ geneList, name }) => {
+        if (geneList.length <= 2) {
+          return alert("At least three genes are required for hierarchical clustering. Please select more genes.");
+        }
+        const group = {
+          name: name || customName,
+          lst: [],
+          type: "hierCluster"
+        };
+        const tws = await Promise.all(
+          geneList.map((d) => {
+            const gene = d.symbol || d.gene;
+            const name2 = `${gene} ${this.unit}`;
+            const term = this.makeTerm({ gene, name: name2 });
+            return { term, q: {} };
+          })
+        );
+        group.lst = [...tws];
+        const config = this.makeConfig({
+          chartType: "hierCluster",
+          termgroups: [group],
+          //TODO: Need to allow singleCellGeneExpression as well
+          dataType: GENE_EXPRESSION
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  async renderSSGSEA(tab) {
+    const holder = tab.contentHolder.style("padding", "10px");
+    const _ = await import("./ssGSEA-THW4WFMI.js");
+    const searchHandler = new _.SearchHandler();
+    await searchHandler.init({
+      holder,
+      app: this.app,
+      genomeObj: this.genome,
+      callback: async (term) => {
+        const config = this.makeConfig({
+          chartType: "summary",
+          term: { term }
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  async initSubplotInTab(subplot) {
+    const holder = this.tabs.find((tab) => tab.chartType === subplot.chartType)?.contentHolder;
+    if (!holder) throw new Error(`No tab found for chart type ${subplot.chartType}`);
+    const opts = Object.assign({}, subplot, {
+      holder,
+      app: this.app,
+      parentId: this.id,
+      id: subplot.id
+    });
+    const { componentInit: componentInit2 } = await importPlot(opts.chartType);
+    this.components.plots[subplot.id] = await componentInit2(opts);
+  }
+  async dispatchEdits(config) {
+    await this.app.dispatch({
+      type: "app_refresh",
+      subactions: [
+        {
+          type: "plot_create",
+          config
+        },
+        {
+          type: "plot_delete",
+          id: this.id
+        }
+      ]
+    });
+  }
+};
+var geneExpInputInit = getCompInit(GeneExpInput);
+var componentInit = geneExpInputInit;
+var enabledTermTypes = /* @__PURE__ */ new Set([GENE_EXPRESSION, SINGLECELL_GENE_EXPRESSION]);
+function getPlotConfig(opts) {
+  if (!opts?.termType) throw new Error("termType is required in opts");
+  if (!enabledTermTypes.has(opts.termType)) throw new Error(`Invalid termType: ${opts.termType}`);
+  const config = {
+    chartType: "GeneExpInput",
+    termType: opts.termType,
+    hidePlotFilter: true
+  };
+  return copyMerge(config, opts);
+}
+export {
+  GeneExpInput,
+  componentInit,
+  geneExpInputInit,
+  getPlotConfig
+};
+//# sourceMappingURL=GeneExpInput-JDU6EI7K.js.map

package/dist/Geomap-J763OK2F.js

@@ -0,0 +1,89 @@
+import {
+  renderGeomap
+} from "./chunk-ZNEJUKJW.js";
+import {
+  PlotBase
+} from "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/geomap/Geomap.ts
+var Geomap = class _Geomap extends PlotBase {
+  static {
+    this.type = "geomap";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _Geomap.type;
+    const holder = opts.holder.append("div").style("padding", "10px");
+    this.dom = {
+      holder,
+      header: opts.header,
+      controls: opts.controls,
+      tip: new Menu({ padding: "9px 11px" })
+    };
+    if (this.dom.header) this.dom.header.html("Site Map");
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw `No plot with id='${this.id}' found`;
+    return { config };
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("plot_")) return action.id === this.id;
+    return true;
+  }
+  async main() {
+    const geomap = this.state.config.geomap;
+    renderGeomap(this.dom.holder, geomap, this.dom.tip);
+  }
+};
+var componentInit = getCompInit(Geomap);
+async function getPlotConfig(opts, app) {
+  const fromDs = app?.vocabApi?.termdbConfig?.geomap;
+  const config = {
+    chartType: "geomap",
+    // the map is not filtered by dictionary terms, so hide the per-plot filter UI
+    hidePlotFilter: true,
+    geomap: fromDs ? structuredClone(fromDs) : { sites: [] }
+  };
+  return copyMerge(config, opts);
+}
+export {
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=Geomap-J763OK2F.js.map

package/dist/Geomap-J763OK2F.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/geomap/Geomap.ts"],
+  "sourcesContent": ["import type { MassState, BasePlotConfig, MassAppApi } from '#mass/types/mass'\nimport type { GeomapConfig } from '#types'\nimport type { Elem, Div } from '../../types/d3.d'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from '../PlotBase'\nimport { Menu } from '#dom'\nimport { renderGeomap } from './render'\n\ntype GeomapDom = {\n\tholder: Div\n\theader?: Elem\n\tcontrols?: Elem\n\ttip: Menu\n}\n\nclass Geomap extends PlotBase implements RxComponent {\n\tstatic type = 'geomap'\n\ttype: string\n\tdom: GeomapDom\n\n\tconstructor(opts: { holder: Div; header?: Elem; controls?: Elem }, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = Geomap.type\n\t\tconst holder = opts.holder.append('div').style('padding', '10px')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\theader: opts.header,\n\t\t\tcontrols: opts.controls,\n\t\t\ttip: new Menu({ padding: '9px 11px' })\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Site Map')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\treactsTo(action: { type: string; id?: string }) {\n\t\tif (action.type.startsWith('plot_')) return action.id === this.id\n\t\treturn true\n\t}\n\n\tasync main() {\n\t\tconst geomap: GeomapConfig | undefined = this.state.config.geomap\n\t\trenderGeomap(this.dom.holder, geomap, this.dom.tip)\n\t}\n}\n\nexport const componentInit = getCompInit(Geomap)\n\nexport async function getPlotConfig(opts: { geomap?: GeomapConfig }, app: MassAppApi) {\n\t// seed locations from the dataset-provided termdbConfig.geomap when the launcher\n\t// (chart catalog) passes only { chartType:'geomap' }\n\tconst fromDs: GeomapConfig | undefined = app?.vocabApi?.termdbConfig?.geomap\n\tconst config = {\n\t\tchartType: 'geomap',\n\t\t// the map is not filtered by dictionary terms, so hide the per-plot filter UI\n\t\thidePlotFilter: true,\n\t\tgeomap: fromDs ? structuredClone(fromDs) : { sites: [] }\n\t}\n\treturn copyMerge(config, opts)\n}\n"],
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+  "names": []
+}