@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/GSEA-KOXOVC5V.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, DMR_SCAN_ELEMENT_TYPE } 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\t/* A scan's rows are DMRs, and GSEA ranks genes by gene-body delta-beta instead, so totalRows\n\t\twould put the DMR count in a header that says \"genes\". The ranked list comes back from the\n\t\troute's fetchDE mode, off the same cached gene-body deltas the enrichment runs on. */\n\t\tif (response.daRequest?.element_type === DMR_SCAN_ELEMENT_TYPE) {\n\t\t\tconst ranked = await dofetch3('genesetEnrichment', {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: params.genome,\n\t\t\t\t\tdslabel: params.dslabel,\n\t\t\t\t\tcacheId: params.cacheId,\n\t\t\t\t\tdaRequest: params.daRequest,\n\t\t\t\t\tfetchDE: true,\n\t\t\t\t\tmethod: 'blitzgsea',\n\t\t\t\t\tgeneSetGroup: '',\n\t\t\t\t\tfilter_non_coding_genes: false\n\t\t\t\t}\n\t\t\t})\n\t\t\tif (ranked?.error) throw new Error(ranked.error)\n\t\t\tparams.genes_length = ranked?.data?.genes?.length ?? 0\n\t\t}\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\n/* field names are the engines' own, passed through unchanged: blitzgsea's dataframe columns\n(python/src/gsea.py) and cerno's output_struct (rust/src/cerno.rs). Both spell it `pval`.\nnes may be the string 'Infinity'/'-Infinity' -- see formatStat() below. */\ntype GseaResultEntry = {\n\tgeneset_size: number\n\tleading_edge: string\n\tfdr?: number\n\tpval?: number\n\tnes?: number | string\n\tauc?: number\n\tes?: number\n}\n\n/* a stat as the table should show it. Three cases the engines actually produce:\n  - a number -> rounded\n  - 'Infinity'/'-Infinity' -> blitzgsea's nes when the permutation p-value underflowed its gamma\n    fit, i.e. more extreme than the null model can score. Real information, and the accompanying\n    pval is exactly 0 for the same reason; both used to render as an empty cell\n  - null/undefined -> genuinely not computed (NaN upstream), left blank */\nfunction formatStat(v: number | string | null | undefined) {\n\tif (v == null) return v\n\tif (v === 'Infinity') return '\u221E'\n\tif (v === '-Infinity') return '\u2212\u221E' // minus sign, not hyphen, to match the axis labels\n\treturn typeof v == 'number' ? roundValueAuto(v) : v\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 = formatStat(item.result.pval)\n\t\tconst fdr = formatStat(item.result.fdr)\n\t\tconst leadingEdge = item.result.leading_edge\n\t\tconst genes = leadingEdge\n\t\t\t? leadingEdge\n\t\t\t\t\t.split(',')\n\t\t\t\t\t.map(gene => gene.trim())\n\t\t\t\t\t.filter(Boolean)\n\t\t\t: []\n\n\t\tif (method == 'blitzgsea') {\n\t\t\tconst nes = formatStat(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 = formatStat(item.result.auc)\n\t\tconst es = formatStat(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{\n\t\t\t\t\tlabel: 'Normalized Enrichment Score',\n\t\t\t\t\tbarplot: { axisWidth: 200 },\n\t\t\t\t\tsortable: true,\n\t\t\t\t\ttooltip:\n\t\t\t\t\t\t'Normal quantile of the permutation p-value. \u00B1\u221E means the p-value underflowed the permutation model, so the enrichment is beyond what the null distribution can score \u2014 the P value column reads 0 for the same reason. Rank these by enrichment score, not by how far off the scale they are.'\n\t\t\t\t},\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\n\t\t\t\t.split(',')\n\t\t\t\t.map(gene => gene.trim())\n\t\t\t\t.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\t\tcacheId: this.gsea.gsea_params.cacheId,\n\t\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 { DMR_SCAN_ELEMENT_TYPE } from '#types'\nimport 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\t/* A DMR scan has no gene-level rows, so the server ranks every gene by the mean delta-beta\n\t\tover its body instead (genesetEnrichment.ts). Said here because the plot looks identical to\n\t\tone ranked by promoter delta-beta and means something different. */\n\t\tthis.dom.actionsDiv.selectAll('.sjpp-gsea-ranking-note').remove()\n\t\tconst da = this.gsea.gsea_params?.daRequest\n\t\tif (da?.element_type === DMR_SCAN_ELEMENT_TYPE) {\n\t\t\tthis.dom.actionsDiv\n\t\t\t\t.append('span')\n\t\t\t\t.attr('class', 'sjpp-gsea-ranking-note')\n\t\t\t\t.style('margin-left', '14px')\n\t\t\t\t.style('font-size', '.9em')\n\t\t\t\t.style('color', '#555')\n\t\t\t\t.text(\n\t\t\t\t\tda.scan?.backgroundCorrection\n\t\t\t\t\t\t? 'Genes ranked by gene-body \u0394\u03B2 in excess of matched intergenic background (case \u2212 control); negative is gene-body methylation loss'\n\t\t\t\t\t\t: 'Genes ranked by gene-body \u0394\u03B2 (case \u2212 control); negative is gene-body methylation loss'\n\t\t\t\t)\n\t\t}\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\n\t\t\t.append('img')\n\t\t\t.attr('width', detailImage.width)\n\t\t\t.attr('height', detailImage.height)\n\t\t\t.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()\n\t\t\t.domain([0, cernoPlotData.rankedGenes.length])\n\t\t\t.range([xPad, svgWidth - rightPad])\n\t\tconst yScale = scaleLinear()\n\t\t\t.domain([100, 0])\n\t\t\t.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 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'#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\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: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = GSEA.type\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}\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 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+  "names": ["opt", "rankedDE"]
+}

package/dist/GeneExpInput-DYBK54HC.js

@@ -0,0 +1,42 @@
+import {
+  GeneExpInput,
+  componentInit2 as componentInit,
+  geneExpInputInit,
+  getPlotConfig2 as getPlotConfig,
+  getSelectableGETermTypes,
+  getUnit
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import "./chunk-SB36AUG7.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  GeneExpInput,
+  componentInit,
+  geneExpInputInit,
+  getPlotConfig,
+  getSelectableGETermTypes,
+  getUnit
+};
+//# sourceMappingURL=GeneExpInput-DYBK54HC.js.map

package/dist/Geomap-QRD2WZVL.js

@@ -0,0 +1,84 @@
+import {
+  renderGeomap
+} from "./chunk-M367Y7ML.js";
+import {
+  PlotBase
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import "./chunk-SB36AUG7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.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-QRD2WZVL.js.map