@sjcrh/proteinpaint-client 2.196.0 → 2.197.0

package/dist/chunk-JFRSVFWO.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/gsea.js"],
-  "sourcesContent": ["import * as d3axis from 'd3-axis'\nimport { Menu, renderTable, table2col, axisstyle, sayerror } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { controlsInit } from './controls'\nimport { getCompInit, copyMerge } from '#rx'\nimport { scaleLinear } from 'd3-scale'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { VolcanoModel } from '#plots/volcano/model/VolcanoModel.ts'\nimport { getDefaultVolcanoSettings } from '#plots/volcano/settings/defaults.ts'\nimport { PlotBase } from '#plots/PlotBase.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PROTEOME_DAP, SINGLECELL_CELLTYPE } from '#types'\n\nconst tip = new Menu()\n\nclass gsea extends PlotBase {\n\tstatic type = 'gsea'\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\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\t}\n\n\tasync setControls() {\n\t\tthis.dom.controlsDiv.selectAll('*').remove()\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Minimum Gene Set Size Filter Cutoff',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'min_gene_set_size_cutoff',\n\t\t\t\ttitle: 'Minimum Gene set size cutoff. Helps in filtering out small gene sets',\n\t\t\t\tmin: 0\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Maximum Gene Set Size Filter Cutoff',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'max_gene_set_size_cutoff',\n\t\t\t\ttitle: 'Maximum Gene set size cutoff. Helps in filtering out large gene sets',\n\t\t\t\tmax: 25000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Filter Non-coding Genes',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'filter_non_coding_genes',\n\t\t\t\ttitle: 'Filter non-coding genes',\n\t\t\t\tboxLabel: ''\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'FDR or Top Gene Sets',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'fdr_or_top',\n\t\t\t\ttitle: 'Toggle between FDR cutoff and top gene sets in ascending order of FDR',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'FDR', value: 'fdr' },\n\t\t\t\t\t{ label: 'Top Gene Sets', value: 'top' }\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\n\t\tif (JSON.parse(sessionStorage.getItem('optionalFeatures')).gsea_test) {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'GSEA method',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'gsea_method',\n\t\t\t\ttitle: 'Toggle between blitzgsea and CERNO method',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'blitzgsea', value: 'blitzgsea' },\n\t\t\t\t\t{ label: 'CERNO', value: 'cerno' }\n\t\t\t\t]\n\t\t\t})\n\t\t}\n\t\tif (this.settings.gsea_method == 'blitzgsea') {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Number of Permutations',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'num_permutations',\n\t\t\t\ttitle: 'Number of permutations to be used for GSEA. Higher number increases accuracy but also compute time.',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 40000 // Setting it to pretty lenient limit for testing\n\t\t\t})\n\t\t}\n\t\tif (this.settings.fdr_or_top == 'fdr') {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'FDR Filter Cutoff (Linear Scale)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'fdr_cutoff',\n\t\t\t\ttitle: 'P-value significance',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 1\n\t\t\t})\n\t\t} else if (this.settings.fdr_or_top == 'top') {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Number of top Gene Sets by FDR',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'gsea',\n\t\t\t\tsettingsKey: 'top_genesets',\n\t\t\t\ttitle: 'Number of top gene sets to be displayed in ascending order of FDR',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 5000\n\t\t\t})\n\t\t} else {\n\t\t\tthrow 'unknown FDR/top option'\n\t\t}\n\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.controlsDiv,\n\t\t\tinputs: inputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.gsea', () => {\n\t\t\tif (!this.imageUrl) return alert('No image to download')\n\t\t\tconst dataUrl = this.imageUrl\n\t\t\tconst downloadImgName = `${this.state.config.gsea_params.geneset_name || ''}_GSEA_IMG`\n\t\t\tconst a = document.createElement('a')\n\t\t\tdocument.body.appendChild(a)\n\n\t\t\ta.addEventListener(\n\t\t\t\t'click',\n\t\t\t\t() => {\n\t\t\t\t\t// Download the image\n\t\t\t\t\ta.download = downloadImgName + '.png'\n\t\t\t\t\ta.href = dataUrl\n\t\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\t},\n\t\t\t\tfalse\n\t\t\t)\n\t\t\ta.click()\n\t\t})\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${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}\n\t}\n\n\t/** This allows the gsea to run independently. If the DE data\n\t * was already requested (e.g. in the DA from the volcano plot),\n\t * the cached response returns rather than running the DE\n\t * route again.\n\t *\n\t * Also allows loading the gsea from a mass session file without\n\t * error. */\n\tasync init(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config.gsea_params) {\n\t\t\ttry {\n\t\t\t\tif (config.termType === PROTEOME_DAP) {\n\t\t\t\t\tawait this.app.save({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tgsea_params: {\n\t\t\t\t\t\t\t\tdapParams: config.proteomeDetails,\n\t\t\t\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome,\n\t\t\t\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t} else if (config.termType === SINGLECELL_CELLTYPE) {\n\t\t\t\t\t// SCCT has no DA cache \u2014 fetch the full DE gene list for the\n\t\t\t\t\t// chosen cluster (omit volcanoRender so the route returns the\n\t\t\t\t\t// raw gene array, not the threshold-passing `dots` subset)\n\t\t\t\t\t// and pass genes + fold_change inline. `render_gsea` takes\n\t\t\t\t\t// this path when neither cacheId nor dapParams is set.\n\t\t\t\t\tconst body = {\n\t\t\t\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\t\t\tsample: config.sample,\n\t\t\t\t\t\ttermId: config.termId,\n\t\t\t\t\t\tcategoryName: config.categoryName\n\t\t\t\t\t}\n\t\t\t\t\tconst response = await dofetch3('termdb/singlecellDEgenes', { body, signal: this.api?.getAbortSignal() })\n\t\t\t\t\tif (response.error) throw response.error\n\t\t\t\t\tif (!Array.isArray(response.data) || response.data.length === 0) throw 'No DE genes returned for this cluster'\n\t\t\t\t\tconst genes = []\n\t\t\t\t\tconst fold_change = []\n\t\t\t\t\tfor (const g of response.data) {\n\t\t\t\t\t\tgenes.push(g.gene_name)\n\t\t\t\t\t\tfold_change.push(g.fold_change)\n\t\t\t\t\t}\n\t\t\t\t\tawait this.app.save({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tgsea_params: {\n\t\t\t\t\t\t\t\tgenes,\n\t\t\t\t\t\t\t\tfold_change,\n\t\t\t\t\t\t\t\tgenes_length: genes.length,\n\t\t\t\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t} else {\n\t\t\t\t\tconst volcanoSettings =\n\t\t\t\t\t\tconfig.settings?.volcano || getDefaultVolcanoSettings({}, { termType: 'geneExpression' })\n\t\t\t\t\tconst model = new VolcanoModel(this, config.termType)\n\t\t\t\t\tconst response = await model.getData(config, volcanoSettings)\n\t\t\t\t\tif (!response?.data?.cacheId || response.error) {\n\t\t\t\t\t\tthrow response.error || 'No DE cacheId returned from volcano model'\n\t\t\t\t\t}\n\t\t\t\t\tawait this.app.save({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tgsea_params: {\n\t\t\t\t\t\t\t\tcacheId: response.data.cacheId,\n\t\t\t\t\t\t\t\t// Snapshot of the DE request so the server can regenerate\n\t\t\t\t\t\t\t\t// the cache if this GSEA request lands on a peer node or\n\t\t\t\t\t\t\t\t// arrives after the cache TTL has expired.\n\t\t\t\t\t\t\t\tdaRequest: response.daRequest,\n\t\t\t\t\t\t\t\tgenes_length: response.data.totalRows,\n\t\t\t\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome,\n\t\t\t\t\t\t\t\t// Sending dslabel at the top level makes the global\n\t\t\t\t\t\t\t\t// auth middleware populate clientAuthResult on this\n\t\t\t\t\t\t\t\t// request the same way it did for the volcano\n\t\t\t\t\t\t\t\t// request, so the server can re-apply the same\n\t\t\t\t\t\t\t\t// auth-filter injection to daRequest before hashing.\n\t\t\t\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t} catch (e) {\n\t\t\t\tif (e instanceof Error) console.error(e.message || e)\n\t\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\t\tthrow e\n\t\t\t}\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t}\n\n\tasync main() {\n\t\t//Not not use structuredClone(this.state.config)\n\t\t//Does not include the plot config changes in init()\n\t\tconst config = this.app.getState().plots.find(p => p.id === this.id)\n\t\tthis.config = structuredClone(config)\n\t\tif (this.config.chartType != this.type && this.config.childType != this.type) return\n\t\tthis.settings = this.config.settings.gsea\n\n\t\tthis.imageUrl = null // Reset the image URL\n\t\tawait this.setControls()\n\t\tif (this.dom.header) {\n\t\t\tconst geneCount = this.config.gsea_params.genes_length ?? this.config.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\trender_gsea(this)\n\t}\n}\n\nasync function renderPathwayDropdown(self) {\n\tconst settings = structuredClone(self.settings)\n\tconst pathwayOpts = structuredClone(self.app.opts.genome.termdbs.msigdb.analysisGenesetGroups) // duplicate to avoid repeated insertion on each app launch\n\n\tif (JSON.parse(sessionStorage.getItem('optionalFeatures')).gsea_test && self.settings.gsea_method == 'blitzgsea') {\n\t\t// This contains geneset groups that are specific to blitzgsea itself\n\t\t// TEMPORARY FIX to test this library that will trigger auto download support files in python\n\t\t// NEVER ENABLE ON PROD especially gdc prod, where container has firewall and it crashes..\n\t\t// delete this if library is replaced\n\t\tpathwayOpts.push(\n\t\t\t{ label: 'REACTOME (blitzgsea)', value: 'REACTOME--blitzgsea' },\n\t\t\t{ label: 'KEGG (blitzgsea)', value: 'KEGG--blitzgsea' },\n\t\t\t{ label: 'WikiPathways (blitzgsea)', value: 'WikiPathways--blitzgsea' }\n\t\t)\n\t}\n\n\tif (settings.pathway) {\n\t\tpathwayOpts.shift()\n\t\tpathwayOpts.find(opt => opt.value == settings.pathway).selected = true\n\t}\n\n\tself.dom.actionsDiv\n\t\t.append('span')\n\t\t.attr('data-testid', 'sjpp-gsea-pathway')\n\t\t.style('margin-right', '10px')\n\t\t.text('Select a gene set group:')\n\n\tconst dropdown = self.dom.actionsDiv.append('select').on('change', event => {\n\t\tif (!settings.pathway) {\n\t\t\t//Remove placeholder from dropdown on first change\n\t\t\tconst placeholder = dropdown.select('option[value=\"-\"]')\n\t\t\tplaceholder.remove()\n\t\t\tpathwayOpts.shift()\n\t\t}\n\n\t\tconst idx = event.target.selectedIndex\n\t\tsettings.pathway = pathwayOpts[idx].value\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: {\n\t\t\t\t//Need to clear the gsea_params completely\n\t\t\t\tgsea_params: {\n\t\t\t\t\tgeneset_name: null,\n\t\t\t\t\tpathway: pathwayOpts[idx].value\n\t\t\t\t},\n\t\t\t\thighlightGenes: [],\n\t\t\t\tsettings: {\n\t\t\t\t\tgsea: settings\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t})\n\tfor (const opt of pathwayOpts) {\n\t\tdropdown\n\t\t\t.append('option')\n\t\t\t.text(opt.label)\n\t\t\t.attr('value', opt.value)\n\t\t\t.attr('selected', opt.selected ? true : null)\n\t}\n}\n\nasync function render_gsea(self) {\n\t/*\nm {}\n- gene\n- logfoldchange\n- averagevalue\n- pvalue\n\nadd:\n- vo_circle\n\t*/\n\n\t//Render the dropdown if launched from state\n\t//Otherwise will persist on load\n\tself.dom.actionsDiv.selectAll('*').remove()\n\trenderPathwayDropdown(self)\n\tif (self.settings.pathway == '-' || self.settings.pathway == undefined) return\n\tself.dom.detailsDiv.selectAll('*').remove()\n\tself.dom.holder.selectAll('*').remove()\n\tself.dom.tableDiv.selectAll('*').remove()\n\tself.config.gsea_params.geneSetGroup = self.settings.pathway\n\tself.config.gsea_params.filter_non_coding_genes = self.settings.filter_non_coding_genes\n\tself.config.gsea_params.num_permutations = self.settings.num_permutations\n\n\tlet output\n\ttry {\n\t\tconst p = self.config.gsea_params\n\t\tconst body = {\n\t\t\tgenome: p.genome,\n\t\t\tgeneSetGroup: self.settings.pathway,\n\t\t\tfilter_non_coding_genes: self.settings.filter_non_coding_genes,\n\t\t\tmethod: self.settings.gsea_method\n\t\t}\n\t\tif (p.cacheId) {\n\t\t\tbody.cacheId = p.cacheId\n\t\t\t// Sending the DE request snapshot lets the server regenerate the\n\t\t\t// cache on miss (farm node without the file, TTL-expired).\n\t\t\tif (p.daRequest) body.daRequest = p.daRequest\n\t\t\t// Top-level dslabel makes the global auth middleware populate\n\t\t\t// clientAuthResult so the server can re-apply the same\n\t\t\t// auth-filter injection to daRequest before hashing.\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 (self.settings.gsea_method == 'blitzgsea') {\n\t\t\tbody.num_permutations = self.settings.num_permutations\n\t\t}\n\t\toutput = await rungsea(body, self.dom)\n\t\tif (output.error) {\n\t\t\tthrow Object.assign(new Error(output.error), { code: output.code })\n\t\t}\n\t} catch (e) {\n\t\t// Inline error block instead of alert(). Mirror the detail-plot\n\t\t// branch below so the GSEA pane shows the failure in-context (e.g.\n\t\t// blitzgsea calibration failures on small/degenerate signatures\n\t\t// from gsea.py's _safe_blitz_gsea, or daCacheMissing on a\n\t\t// stale-session cache regen).\n\t\tself.dom.holder.selectAll('*').remove()\n\t\tconst msg = String(e?.message || e)\n\t\tif (e?.code === 'CACHE_BUSY') {\n\t\t\tif (window.confirm(msg)) render_gsea(self)\n\t\t\treturn\n\t\t}\n\t\tconst userMsg = /daCacheMissing|ENOENT|no such file/i.test(msg)\n\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: msg\n\t\tsayerror(self.dom.holder, userMsg)\n\t\treturn\n\t}\n\n\t//Ensure the image renders when toggling between tabs\n\tif (self.config.gsea_params.geneset_name != null) {\n\t\ttry {\n\t\t\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\t\t\tself.config.gsea_params.method = self.settings.gsea_method\n\t\t\t\tconst image = await rungsea(self.config.gsea_params, self.dom)\n\t\t\t\t// //render_gsea_plot(self, plot_data)\n\t\t\t\tif (image.error) throw image.error\n\t\t\t\tself.imageUrl = URL.createObjectURL(image)\n\t\t\t\tconst png_width = 600\n\t\t\t\tconst png_height = 400\n\t\t\t\tself.dom.holder.append('img').attr('width', png_width).attr('height', png_height).attr('src', self.imageUrl)\n\t\t\t} else if (self.settings.gsea_method == 'cerno') {\n\t\t\t\tif (!self.rankedDE && (self.config.gsea_params.cacheId || self.config.gsea_params.dapParams)) {\n\t\t\t\t\tconst fetchBody = {\n\t\t\t\t\t\tgenome: self.config.gsea_params.genome,\n\t\t\t\t\t\tdslabel: self.config.gsea_params.dslabel,\n\t\t\t\t\t\tfetchDE: true,\n\t\t\t\t\t\tgeneSetGroup: '-',\n\t\t\t\t\t\tfilter_non_coding_genes: false,\n\t\t\t\t\t\tmethod: 'cerno'\n\t\t\t\t\t}\n\t\t\t\t\tif (self.config.gsea_params.cacheId) {\n\t\t\t\t\t\tfetchBody.cacheId = self.config.gsea_params.cacheId\n\t\t\t\t\t\tfetchBody.daRequest = self.config.gsea_params.daRequest\n\t\t\t\t\t} else if (self.config.gsea_params.dapParams) {\n\t\t\t\t\t\tfetchBody.dapParams = self.config.gsea_params.dapParams\n\t\t\t\t\t}\n\t\t\t\t\tconst deResp = await dofetch3('genesetEnrichment', {\n\t\t\t\t\t\tbody: fetchBody\n\t\t\t\t\t})\n\t\t\t\t\tif (deResp.error) throw Object.assign(new Error(deResp.error), { code: deResp.code })\n\t\t\t\t\tself.rankedDE = deResp.data\n\t\t\t\t}\n\t\t\t\trender_cerno_plot(self, output)\n\t\t\t} else {\n\t\t\t\tthrow 'Unknown method:' + self.settings.gsea_method\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tself.dom.holder.selectAll('*').remove()\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)) render_gsea(self)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst userMsg = /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\tsayerror(self.dom.holder, userMsg)\n\t\t\treturn\n\t\t}\n\t}\n\n\tconst table_stats = table2col({ holder: self.dom.detailsDiv.attr('data-testid', 'sjpp-gsea-stats') })\n\tconst [t1, t2] = table_stats.addRow()\n\tt2.style('text-align', 'center').style('font-size', '0.8em').style('opacity', '0.8').text('COUNT')\n\tlet addStats\n\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\taddStats = [\n\t\t\t{\n\t\t\t\tlabel: 'Gene sets analyzed',\n\t\t\t\tvalues: Object.keys(output.data).length\n\t\t\t}\n\t\t]\n\t} else if (self.settings.gsea_method == 'cerno') {\n\t\taddStats = [\n\t\t\t{\n\t\t\t\tlabel: 'Gene sets analyzed',\n\t\t\t\tvalues: Object.keys(output).length\n\t\t\t}\n\t\t]\n\t} else {\n\t\tthrow 'Unknown method:' + self.settings.gsea_method\n\t}\n\n\tfor (const dataRow of addStats) {\n\t\tconst [td1, td2] = table_stats.addRow()\n\t\ttd1.text(dataRow.label)\n\t\ttd2.style('text-align', 'end').text(dataRow.values)\n\t}\n\n\t// Generating the table\n\tself.gsea_table_rows = []\n\tlet output_keys\n\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\toutput_keys = Object.entries(output.data).map(([key, value]) => {\n\t\t\treturn { key, value } // Convert to an array of objects\n\t\t})\n\t} else if (self.settings.gsea_method == 'cerno') {\n\t\toutput_keys = Object.entries(output).map(([key, value]) => {\n\t\t\treturn { key, value } // Convert to an array of objects\n\t\t})\n\t} else {\n\t\tthrow 'Unknown method:' + self.settings.gsea_method\n\t}\n\n\tif (self.settings.fdr_or_top == 'top') {\n\t\t// Sorting the top (top_genesets) genesets in decreasing order\n\t\toutput_keys.sort((i, j) => Number(i.value.fdr) - Number(j.value.fdr))\n\t\tconst top_genesets = Math.min(self.settings.top_genesets, output_keys.length) // If the length of the table is less than the top cutoff, only iterate till the end of the table\n\t\tfor (let iter = 0; iter < top_genesets; iter++) {\n\t\t\tif (\n\t\t\t\tself.settings.max_gene_set_size_cutoff >= output_keys[iter].value.geneset_size &&\n\t\t\t\tself.settings.min_gene_set_size_cutoff <= output_keys[iter].value.geneset_size\n\t\t\t) {\n\t\t\t\tsetResultsRows(output_keys, iter, self)\n\t\t\t}\n\t\t}\n\t} else if (self.settings.fdr_or_top == 'fdr') {\n\t\tfor (let iter = 0; iter < output_keys.length; iter++) {\n\t\t\tif (\n\t\t\t\tself.settings.fdr_cutoff >= output_keys[iter].value.fdr &&\n\t\t\t\tself.settings.max_gene_set_size_cutoff >= output_keys[iter].value.geneset_size &&\n\t\t\t\tself.settings.min_gene_set_size_cutoff <= output_keys[iter].value.geneset_size\n\t\t\t) {\n\t\t\t\tsetResultsRows(output_keys, iter, self)\n\t\t\t}\n\t\t}\n\t}\n\n\tself.dom.tableDiv.selectAll('*').remove()\n\tconst d_gsea = self.dom.tableDiv.append('div')\n\t// table columns showing analysis results for each gene set\n\tself.gsea_table_cols = []\n\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\tself.gsea_table_cols = [\n\t\t\t{ label: 'Gene Set', sortable: true },\n\t\t\t//{ label: 'Enrichment Score' },\n\t\t\t{ label: 'Normalized Enrichment Score', barplot: { axisWidth: 200 }, sortable: true },\n\t\t\t{ label: 'Gene Set Size', sortable: true },\n\t\t\t{ label: 'P value', sortable: true },\n\t\t\t//{ label: 'Sidak' },\n\t\t\t{ label: 'FDR', sortable: true },\n\t\t\t{ label: 'Leading Edge' }\n\t\t]\n\t} else if (self.settings.gsea_method == 'cerno') {\n\t\tself.gsea_table_cols = [\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} else {\n\t\tthrow 'Unknown method:' + self.settings.gsea_method\n\t}\n\tlet download = {}\n\n\tif (self.config.chartType == 'differentialAnalysis') {\n\t\t//Highlight genes button\n\t\tself.dom.detailsDiv\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style(\n\t\t\t\t'display',\n\t\t\t\tself.config.chartType == 'differentialAnalysis' && self.config.gsea_params.geneset_name == null\n\t\t\t\t\t? 'none'\n\t\t\t\t\t: 'block'\n\t\t\t)\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\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tchildType: 'volcano',\n\t\t\t\t\t\thighlightedData: self.config.highlightGenes\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\tif (self.state.config.downloadFilename) download.fileName = self.state.config.downloadFilename\n\n\t//Table rerenders when main is called\n\t//Fix to show which gene set is selected after rerender\n\tconst geneSetIdx = self.gsea_table_rows.findIndex(row => row[0].value == self.config.gsea_params.geneset_name)\n\tconst selectedRows = geneSetIdx > -1 ? [geneSetIdx] : []\n\n\trenderTable({\n\t\tdownload,\n\t\tcolumns: self.gsea_table_cols,\n\t\trows: self.gsea_table_rows,\n\t\tdiv: d_gsea,\n\t\tshowLines: true,\n\t\tmaxHeight: '30vh',\n\t\tsingleMode: true,\n\t\tresize: true,\n\t\theader: { allowSort: true },\n\t\tselectedRows: selectedRows,\n\t\tnoButtonCallback: async index => {\n\t\t\tconst config = {\n\t\t\t\tgsea_params: {\n\t\t\t\t\tgeneset_name: self.gsea_table_rows[index][0].value\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (self.config.chartType == 'differentialAnalysis') {\n\t\t\t\t//Saves the data to highlight in the volcano plot\n\t\t\t\tlet genes\n\t\t\t\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\t\t\t\tgenes = [...self.gsea_table_rows[index][5].value.split(',')]\n\t\t\t\t} else if (self.settings.gsea_method == 'cerno') {\n\t\t\t\t\tgenes = [...self.gsea_table_rows[index][6].value.split(',')]\n\t\t\t\t} else {\n\t\t\t\t\tthrow 'Unknown method:' + self.settings.gsea_method\n\t\t\t\t}\n\t\t\t\tif (genes) config.highlightGenes = genes\n\t\t\t}\n\t\t\tawait self.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig\n\t\t\t})\n\t\t}\n\t})\n}\n\nfunction setResultsRows(output_keys, iter, self) {\n\tconst pathway_name = output_keys[iter].key\n\tconst pval = output_keys[iter].value.pval\n\t\t? roundValueAuto(output_keys[iter].value.pval)\n\t\t: output_keys[iter].value.pval\n\tconst fdr = output_keys[iter].value.fdr ? roundValueAuto(output_keys[iter].value.fdr) : output_keys[iter].value.fdr\n\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\tconst nes = output_keys[iter].value.nes ? roundValueAuto(output_keys[iter].value.nes) : output_keys[iter].value.nes\n\t\t// const sidak = output_keys[iter].value.sidak\n\t\t// \t? roundValueAuto(output_keys[iter].value.sidak)\n\t\t// \t: output_keys[iter].value.sidak\n\t\tself.gsea_table_rows.push([\n\t\t\t{ value: pathway_name },\n\t\t\t{ value: nes },\n\t\t\t{ value: output_keys[iter].value.geneset_size },\n\t\t\t{ value: pval },\n\t\t\t//{ value: sidak },\n\t\t\t{ value: fdr },\n\t\t\t{ value: output_keys[iter].value.leading_edge }\n\t\t])\n\t} else if (self.settings.gsea_method == 'cerno') {\n\t\tconst auc = output_keys[iter].value.auc ? roundValueAuto(output_keys[iter].value.auc) : output_keys[iter].value.auc\n\t\tconst es = output_keys[iter].value.es ? roundValueAuto(output_keys[iter].value.es) : output_keys[iter].value.es\n\t\tself.gsea_table_rows.push([\n\t\t\t{ value: pathway_name },\n\t\t\t{ value: auc },\n\t\t\t{ value: es },\n\t\t\t{ value: output_keys[iter].value.geneset_size },\n\t\t\t{ value: pval },\n\t\t\t{ value: fdr },\n\t\t\t{ value: output_keys[iter].value.leading_edge }\n\t\t])\n\t} else {\n\t\tthrow 'Unknown method:' + self.settings.gsea_method\n\t}\n}\n\nfunction render_cerno_plot(self, cerno_output) {\n\tconst holder = self.dom.holder\n\tholder.selectAll('*').remove()\n\tconst svg_width = 400\n\tconst svg_height = 400\n\tconst svg = holder.append('svg').attr('width', svg_width).attr('height', svg_height)\n\tconst toppad = 20\n\tconst rightpad = 5\n\tconst yaxisw = 50 //Math.max(50, svg_width / 8)\n\tconst xaxish = 50 //Math.max(50, svg_height / 8)\n\tconst yaxisg = svg.append('g')\n\tconst xaxisg = svg.append('g')\n\tconst xpad = 50\n\tconst ypad = 100\n\n\tconst rankedDE = self.rankedDE || self.config.gsea_params\n\tconst DE_output = []\n\tfor (let i = 0; i < rankedDE.genes.length; i++) {\n\t\tconst item = { gene: rankedDE.genes[i], fold_change: rankedDE.fold_change[i] }\n\t\tDE_output.push(item)\n\t}\n\tDE_output.sort((i, j) => j.fold_change - i.fold_change) // Sorting genes in descending order of fold change\n\n\tconst xscale = scaleLinear()\n\t\t.domain([0, DE_output.length])\n\t\t.range([xpad, svg_width - rightpad])\n\tconst yscale = scaleLinear()\n\t\t.domain([100, 0])\n\t\t.range([toppad, svg_height - ypad])\n\n\tyaxisg.attr('transform', 'translate(' + xpad + ',' + 0 + ')')\n\txaxisg.attr('transform', 'translate(' + 0 + ',' + (svg_height - ypad) + ')')\n\tconst xlab = svg\n\t\t.append('text')\n\t\t.text('Gene list')\n\t\t.attr('fill', 'black')\n\t\t.attr('text-anchor', 'start')\n\t\t.attr('transform', 'translate(' + xscale(DE_output.length / 3) + ',' + (svg_height - ypad + 2 * toppad) + ')')\n\tconst ylab = svg\n\t\t.append('text')\n\t\t.text('Percentage of gene set')\n\t\t.attr('fill', 'black')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('y', xpad / 2)\n\t\t.attr('x', -svg_width / 2.5)\n\t\t.attr('transform', 'rotate(-90)')\n\tlet fontSize = 30\n\tconst title = svg\n\t\t.append('text')\n\t\t.text(self.config.gsea_params.geneset_name)\n\t\t.attr('fill', 'black')\n\t\t.attr('text-anchor', 'start')\n\t\t.attr('font-size', fontSize + 'px')\n\t\t.attr('transform', 'translate(' + xpad + ',' + toppad / 2 + ')')\n\n\t// Check to see if the text fits into the svg width and toppad dimensions. If not, decrease the font size until the text fits into these dimensions\n\tlet title_bbox = title.node().getBBox()\n\twhile (title_bbox.width > svg_width - xpad || title_bbox.height > (toppad * 3.5) / 5) {\n\t\tfontSize -= 1 // Decrease font size\n\t\ttitle.node().setAttribute('font-size', fontSize + 'px')\n\t\ttitle_bbox = title.node().getBBox() // Measure again\n\t}\n\n\tconst auc = cerno_output[self.config.gsea_params.geneset_name].auc\n\tif (typeof auc === 'number') {\n\t\tlet auc_pos\n\t\tif (auc >= 0.5) {\n\t\t\t// The position of the text changes depending upon the value of auc so as to avoid the auc curve overlapping with the text\n\t\t\tauc_pos = xscale((DE_output.length * 3) / 3.5) + ',' + (svg_height - ypad * 1.5)\n\t\t} else {\n\t\t\tauc_pos = xscale((DE_output.length * 0.8) / 4.5) + ',' + (svg_height - ypad * 3)\n\t\t}\n\t\tconst auc_text = svg\n\t\t\t.append('text')\n\t\t\t.text('AUC=' + roundValueAuto(auc))\n\t\t\t.attr('fill', 'black')\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('transform', 'translate(' + auc_pos + ')')\n\t} else {\n\t\t// Should not happen\n\t\tthrow 'AUC not a number:' + auc\n\t}\n\n\taxisstyle({\n\t\taxis: yaxisg.call(d3axis.axisLeft().scale(yscale)),\n\t\tcolor: 'black',\n\t\tshowline: true,\n\t\tfontsize: '10'\n\t})\n\taxisstyle({\n\t\taxis: xaxisg.call(d3axis.axisBottom().scale(xscale)),\n\t\tcolor: 'black',\n\t\tshowline: true,\n\t\tfontsize: '10'\n\t})\n\n\t// Find genes that were found from cerno output\n\tif (Object.keys(cerno_output).includes(self.config.gsea_params.geneset_name)) {\n\t\tconst hit_genes = cerno_output[self.config.gsea_params.geneset_name].leading_edge.split(',')\n\t\tconst y_increment = 100 / hit_genes.length\n\t\tconst lines = svg.append('g')\n\n\t\tlet y_iter = 100\n\t\tfor (let i = 0; i < DE_output.length; i++) {\n\t\t\tconst y_old = y_iter\n\t\t\t// Increment y only when gene is found in geneset\n\t\t\tif (hit_genes.includes(DE_output[i].gene)) {\n\t\t\t\ty_iter = y_iter - y_increment\n\t\t\t\tlines\n\t\t\t\t\t.append('line') // attach a line\n\t\t\t\t\t.style('stroke', 'red') // colour the line\n\t\t\t\t\t.attr('x1', xscale(i)) // x position of the first end of the line\n\t\t\t\t\t.attr('y1', svg_height) // y position of the first end of the line\n\t\t\t\t\t.attr('x2', xscale(i)) // x position of the second end of the line\n\t\t\t\t\t.attr('y2', svg_height - ypad + 2.5 * toppad) // y position of the second end of the line\n\t\t\t}\n\t\t\tlines\n\t\t\t\t.append('line') // attach a line\n\t\t\t\t.style('stroke', 'red') // colour the line\n\t\t\t\t.attr('x1', xscale(i)) // x position of the first end of the line\n\t\t\t\t.attr('y1', yscale(100 - y_old)) // y position of the first end of the line\n\t\t\t\t.attr('x2', xscale(i + 1)) // x position of the second end of the line\n\t\t\t\t.attr('y2', yscale(100 - y_iter)) // y position of the second end of the line\n\t\t}\n\t} else {\n\t\t// Should not happen\n\t\tthrow '${self.config.gsea_params.geneset_name} not found'\n\t}\n\n\t//console.log('cerno_output:', cerno_output)\n\n\t// Find the genes that were found in the clicked geneset\n\t//const genes_found\n}\n\n// function render_gsea_plot(self, plot_data) {\n// \t// This function is for client side rendering of the gsea plot. This is not currently used. 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-  "names": []
-}

package/dist/chunk-JNBJG57F.js

@@ -1,448 +0,0 @@
-import {
-  getDefaultViolinSettings
-} from "./chunk-ROJ3LJLE.js";
-import {
-  getDefaultScatterSettings
-} from "./chunk-3LYZMOLO.js";
-import {
-  getDefaultBoxplotSettings
-} from "./chunk-5QTJUPFS.js";
-import {
-  PlotBase,
-  defaultUiLabels,
-  fillTermWrapper,
-  filterRxCompInit,
-  getDefaultBarSettings,
-  term0_term2_defaultQ
-} from "./chunk-WY2PGUVX.js";
-import {
-  importPlot
-} from "./chunk-MBUQ34CF.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  isNumericTerm
-} from "./chunk-NNFAUP2I.js";
-
-// plots/summary.ts
-var SummaryPlot = class _SummaryPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    // expected class-specific props
-    this.chartsByType = {};
-    this.configTermKeys = ["term", "term0", "term2"];
-    this.type = _SummaryPlot.type;
-    this.dom = this.getDom(opts);
-    this.tabsData = this.getTabsData();
-    this.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true });
-    this.components = {
-      plots: {}
-    };
-  }
-  static {
-    this.type = "summary";
-  }
-  preApiFreeze(api) {
-    api.getError = () => {
-      return this.error;
-    };
-  }
-  getDom(opts) {
-    const holder = opts.holder;
-    holder.header.style("padding", 0);
-    const paneTitleDiv = holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px");
-    return {
-      tip: new Menu({ padding: "0px" }),
-      holder,
-      body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-      // will hold no data notice or the page title in multichart views
-      errdiv: holder.body.append("div").attr("class", "sja_errorbar").style("display", "none").style("padding", "5px"),
-      loading: holder.body.append("div").style("display", "none").style("padding", "5px").html("Loading ..."),
-      // dom.viz will hold the rendered view
-      viz: holder.body.append("div"),
-      plotDivs: {},
-      paneTitleDiv,
-      paneTitleText: paneTitleDiv.append("div").classed("sjpp-term-header", true).style("display", "inline-block").style("vertical-align", "sub"),
-      chartToggles: paneTitleDiv.append("div").style("display", "inline-block").style("margin-left", "10px"),
-      localRecoverDiv: paneTitleDiv.append("div").style("display", "inline-block"),
-      filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9)
-    };
-  }
-  getTabsData() {
-    const callback = (event, tab) => this.tabClickCallback(event, tab);
-    return [
-      {
-        childType: "barchart",
-        label: "Barchart",
-        isVisible: () => true,
-        disabled: () => false,
-        getConfig: async () => {
-          if (!this.config) return;
-          const config = { id: this.id, childType: "barchart" };
-          const { term, term2 } = this.config || {};
-          if (term) {
-            const mode = isNumericTerm(term?.term) ? "discrete" : term?.q.mode || "discrete";
-            config.term = await this.getWrappedTermCopy(term, mode);
-          }
-          if (term2) {
-            const mode = isNumericTerm(term2.term) ? "discrete" : term2.q.mode || "discrete";
-            config.term2 = await this.getWrappedTermCopy(term2, mode);
-          }
-          return config;
-        },
-        active: true,
-        callback
-      },
-      {
-        childType: "violin",
-        label: "Violin",
-        disabled: () => false,
-        isVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),
-        getConfig: async () => {
-          const term = this.config?.term;
-          const term2 = this.config.term2;
-          let _term, _term2;
-          this.violinContTerm = isNumericTerm(term?.term) ? "term" : "term2";
-          if (this.violinContTerm && this.violinContTerm === "term" || term.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          } else if (this.violinContTerm && this.violinContTerm === "term2" || term2?.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else if (term2?.q?.mode == "discrete") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          }
-          const config = { childType: "violin", term: _term, term2: _term2 };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "boxplot",
-        label: "Boxplot",
-        disabled: () => false,
-        isVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),
-        getConfig: async () => {
-          const _term = this.config?.term;
-          const _term2 = this.config.term2;
-          let termMode = "continuous", term2Mode = "discrete";
-          this.boxContTerm = isNumericTerm(_term?.term) ? "term" : "term2";
-          if (this.boxContTerm && this.boxContTerm === "term" || _term.q?.mode == "continuous") {
-            termMode = "continuous";
-            term2Mode = "discrete";
-            this.boxContTerm = "term";
-          } else if (this.boxContTerm && this.boxContTerm === "term2" || _term2?.q?.mode == "continuous") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          } else if (_term2?.q?.mode == "discrete") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          }
-          const term = await this.getWrappedTermCopy(_term, termMode);
-          const term2 = await this.getWrappedTermCopy(_term2, term2Mode);
-          const config = {
-            childType: "boxplot",
-            term,
-            term2
-          };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "sampleScatter",
-        label: "Scatter",
-        disabled: () => false,
-        isVisible: () => {
-          return isNumericTerm(this.config?.term.term) && isNumericTerm(this.config?.term2?.term);
-        },
-        getConfig: async () => {
-          const _term = await this.getWrappedTermCopy(this.config?.term, "continuous");
-          const _term2 = await this.getWrappedTermCopy(this.config?.term2, "continuous");
-          const config = {
-            childType: "sampleScatter",
-            term: _term,
-            term2: _term2,
-            groups: [],
-            term0: this.config.term0
-          };
-          return config;
-        },
-        active: false,
-        callback
-      }
-    ];
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.initUi(this.opts, config);
-    if (config?.hidePlotFilter) return;
-    this.components.filter = await filterRxCompInit({
-      app: this.app,
-      vocabApi: this.app.vocabApi,
-      parentId: this.id,
-      holder: this.dom.filterDiv,
-      hideLabel: true,
-      emptyLabel: "+Add new filter",
-      callback: (filter) => {
-        this.app.dispatch({
-          id: this.id,
-          type: "plot_edit",
-          config: { filter }
-        });
-      }
-    });
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.startsWith("plot_")) {
-      if (action.type.startsWith("plot_")) {
-        return action.id === this.id || action.id == this.parentId;
-      }
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    return false;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    delete this.error;
-    this.dom.errdiv.style("display", "none").html("");
-    this.dom.loading.style("display", "");
-    this.config = await this.getMutableConfig();
-    this.maySetSandboxHeader();
-    if (!this.components.plots[this.config.childType]) {
-      await this.setComponent(this.config);
-    }
-    this.dom.loading.style("display", "none");
-    this.render();
-    const activeTabIndex = this.tabsData.findIndex((tab) => tab.childType == this.config.childType);
-    this.chartToggles.update(activeTabIndex);
-    const numVisTabs = this.tabsData.filter((d) => d.isVisible()).length;
-    if (numVisTabs > 1) this.dom.chartToggles.style("display", "inline-block");
-    else this.dom.chartToggles.style("display", "none");
-  }
-  maySetSandboxHeader() {
-    const { term, term2, headerText, assayCohortTitle } = this.config;
-    const mainTerm = term.getTitleText?.() || term.term.name;
-    const _headerPretext = headerText ? `${headerText} ` : "";
-    const _headerSuffix = assayCohortTitle ? ` (${assayCohortTitle})` : "";
-    const titleBase = mainTerm + _headerSuffix;
-    if (term2?.type) {
-      this.dom.paneTitleText.html(`${_headerPretext}${term2.getTitleText?.() || term2.term.name} vs ${titleBase}`);
-    } else {
-      this.dom.paneTitleText.html(`${_headerPretext}${titleBase}`);
-    }
-  }
-  async setComponent(config) {
-    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
-    this.dom.plotDivs[config.childType] = this.dom.viz.append("div");
-    const componentOpts = {
-      app: this.app,
-      holder: this.dom.plotDivs[config.childType],
-      id: this.id,
-      parent: this.api
-    };
-    if (config.parentId) componentOpts.parentId = config.parentId;
-    this.components.plots[config.childType] = await _.componentInit(componentOpts);
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-  initUi(opts, config) {
-    this.dom.paneTitleText.html(config.term.term.name);
-    this.chartToggles.main();
-  }
-  async tabClickCallback(event, tab) {
-    if (!tab || !tab.getConfig) return;
-    let config;
-    try {
-      this.dom.viz.style("display", "none");
-      this.dom.loading.style("display", "");
-      config = await tab.getConfig();
-      this.dom.loading.style("display", "none");
-      this.dom.viz.style("display", "");
-      if (config)
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config
-        });
-    } catch (e) {
-      this.dom.loading.style("display", "none");
-      this.error = e;
-      this.dom.errdiv.style("display", "").html(`Error: ${e.message || e.error || e}`);
-    }
-  }
-  async getWrappedTermCopy(term, mode) {
-    if (!term) return;
-    const tw = structuredClone(term);
-    tw.q.mode = mode;
-    await fillTermWrapper(tw, this.app.vocabApi);
-    return tw;
-  }
-  render() {
-    for (const childType of Object.keys(this.components.plots)) {
-      const chart = this.components.plots[childType];
-      if (chart.type != this.config.childType) {
-        this.dom.plotDivs[chart.type].style("display", "none");
-      }
-    }
-    this.dom.plotDivs[this.config.childType].style("display", "");
-  }
-  getChartImages() {
-    const chart = this.components.plots[this.config.childType];
-    if (chart?.getChartImages) {
-      return chart.getChartImages();
-    }
-    return null;
-  }
-};
-var summaryInit = getCompInit(SummaryPlot);
-var componentInit = summaryInit;
-async function getPlotConfig(opts, app) {
-  if (!opts.term) throw "summary getPlotConfig: opts.term{} missing";
-  try {
-    opts.term = await fillTermWrapper(
-      opts.term,
-      app.vocabApi,
-      opts.term.q || { geneVariant: { type: "predefined-groupset" } }
-    );
-    if (opts.term2)
-      opts.term2 = await fillTermWrapper(
-        opts.term2,
-        app.vocabApi,
-        opts.term2.bins || opts.term2.q ? void 0 : term0_term2_defaultQ
-      );
-    if (opts.term0)
-      opts.term0 = await fillTermWrapper(
-        opts.term0,
-        app.vocabApi,
-        opts.term0.bins || opts.term0.q ? void 0 : term0_term2_defaultQ
-      );
-    if (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi);
-    if (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi);
-    if (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi);
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    throw `${e} [summary getPlotConfig()]`;
-  }
-  const config = {
-    chartType: "summary",
-    childType: "barchart",
-    term: opts.term,
-    groups: [],
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    //Allow hiding the plot filter when appropriate (e.g. single cell summary plots)
-    hidePlotFilter: opts.hidePlotFilter || false,
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      common: {
-        use_logscale: false,
-        // flag for y-axis scale type, 0=linear, 1=log
-        use_percentage: false
-        // Move to barchart settings
-        // barheight: 300, // maximum bar length
-        // barwidth: 20, // bar thickness
-        // barspace: 2 // space between two bars
-      },
-      barchart: getDefaultBarSettings(app),
-      violin: getDefaultViolinSettings(app),
-      boxplot: getDefaultBoxplotSettings(app),
-      sampleScatter: getDefaultScatterSettings(opts)
-    },
-    mayAdjustConfig(config2, edits = {}) {
-      return mayAdjustConfig(config2, opts, edits);
-    }
-  };
-  if (config.term.term.type == "geneVariant") config.settings.barchart.colorBars = true;
-  copyMerge(config, opts);
-  Object.assign(config.controlLabels, app.vocabApi.termdbConfig.uiLabels || {});
-  return config;
-}
-var discreteByContinuousPlots = /* @__PURE__ */ new Set(["violin", "boxplot"]);
-function mayAdjustConfig(config, opts, edits = {}) {
-  if (edits.childType) {
-    if (config.childType != edits.childType) throw `action.config.childType was not applied in mass store.plot_edit()`;
-    return;
-  }
-  if (config.term?.q?.mode == "continuous" && config.term2?.q?.mode == "continuous") {
-    config.childType = "sampleScatter";
-  } else if (config.term?.term?.type == "termCollection") {
-    if (config.term.term.memberType == "categorical") {
-      config.childType = "barchart";
-    } else if (config.term.term.memberType == "numeric") {
-      if (config.childType) {
-        if (config.childType == "barchart") {
-          config.childType = "violin";
-        } else {
-        }
-      } else {
-        config.childType = "violin";
-      }
-    } else {
-      throw new Error("config.term.term.memberType not categorical or numeric");
-    }
-  } else if (config.term?.q?.mode == "continuous" || config.term2?.q?.mode == "continuous") {
-    if (!discreteByContinuousPlots.has(config.childType)) {
-      if (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {
-        console.warn(
-          `ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`
-        );
-        config.childType = "violin";
-      } else {
-        config.childType = opts.childType || "violin";
-      }
-    }
-  } else {
-    config.childType = "barchart";
-  }
-}
-
-export {
-  summaryInit,
-  componentInit,
-  getPlotConfig,
-  mayAdjustConfig
-};
-//# sourceMappingURL=chunk-JNBJG57F.js.map