@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-56AN5PPQ.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'\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\tconst volcanoSettings =\n\t\t\t\t\tconfig.settings?.volcano || getDefaultVolcanoSettings({}, { termType: 'geneExpression' })\n\t\t\t\tconst model = new VolcanoModel(this.app, config.termType)\n\t\t\t\tconst response = await model.getData(config, volcanoSettings)\n\t\t\t\tif (!response?.data?.cacheId || response.error) {\n\t\t\t\t\tthrow response.error || 'No DE cacheId returned from volcano model'\n\t\t\t\t}\n\t\t\t\tawait this.app.save({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tgsea_params: {\n\t\t\t\t\t\t\tcacheId: response.data.cacheId,\n\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// the cache if this GSEA request lands on a peer node or\n\t\t\t\t\t\t\t// arrives after the cache TTL has expired.\n\t\t\t\t\t\t\tdaRequest: response.daRequest,\n\t\t\t\t\t\t\tgenes_length: response.data.totalRows,\n\t\t\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome,\n\t\t\t\t\t\t\t// Sending dslabel at the top level makes the global\n\t\t\t\t\t\t\t// auth middleware populate clientAuthResult on this\n\t\t\t\t\t\t\t// request the same way it did for the volcano\n\t\t\t\t\t\t\t// request, so the server can re-apply the same\n\t\t\t\t\t\t\t// auth-filter injection to daRequest before hashing.\n\t\t\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel\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 {\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 output.error\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\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) {\n\t\t\t\t\tconst deResp = await dofetch3('genesetEnrichment', {\n\t\t\t\t\t\tbody: {\n\t\t\t\t\t\t\tgenome: self.config.gsea_params.genome,\n\t\t\t\t\t\t\tcacheId: self.config.gsea_params.cacheId,\n\t\t\t\t\t\t\t// Also send daRequest so the server can recompute\n\t\t\t\t\t\t\t// the cache on miss (same farm-safety reason as\n\t\t\t\t\t\t\t// the primary enrichment call).\n\t\t\t\t\t\t\tdaRequest: self.config.gsea_params.daRequest,\n\t\t\t\t\t\t\t// Top-level dslabel so the auth middleware populates\n\t\t\t\t\t\t\t// clientAuthResult for the server's auth-filter\n\t\t\t\t\t\t\t// adjustment of daRequest.\n\t\t\t\t\t\t\tdslabel: self.config.gsea_params.dslabel,\n\t\t\t\t\t\t\tfetchDE: true,\n\t\t\t\t\t\t\tgeneSetGroup: '-',\n\t\t\t\t\t\t\tfilter_non_coding_genes: false,\n\t\t\t\t\t\t\tmethod: 'cerno'\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\tif (deResp.error) throw deResp.error\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\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-5FO3NKA4.js

@@ -1,155 +0,0 @@
-import {
-  dofetch3
-} from "./chunk-YC6ZJ7RP.js";
-import {
-  DNA_METHYLATION,
-  GENE_EXPRESSION,
-  SINGLECELL_CELLTYPE
-} from "./chunk-EGWVYY7K.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-
-// plots/volcano/colors.ts
-function getGroupColors(config) {
-  const groups = config?.samplelst?.groups;
-  const termValues = config?.tw?.term?.values;
-  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
-  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
-  return {
-    controlColor: toHex(rawDown, "red"),
-    caseColor: toHex(rawUp, "blue")
-  };
-}
-function toHex(color, fallback) {
-  const c = rgb(color || fallback);
-  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
-}
-
-// plots/volcano/model/VolcanoModel.ts
-var VolcanoModel = class {
-  constructor(app, termType) {
-    this.app = app;
-    this.termType = termType;
-  }
-  /** May use mapper instead as more termTypes are added */
-  async getData(config, settings) {
-    this.config = config;
-    this.settings = settings;
-    if (this.termType === GENE_EXPRESSION) {
-      const body = await this.getGERequestBody();
-      const response = await dofetch3("termdb/DE", { body });
-      if (response && !response.error) response.daRequest = body;
-      return response;
-    }
-    if (this.termType === DNA_METHYLATION) {
-      const body = await this.getDMRequestBody();
-      const response = await dofetch3("termdb/diffMeth", { body });
-      if (response && !response.error) response.daRequest = body;
-      return response;
-    }
-    if (this.termType === SINGLECELL_CELLTYPE) {
-      const body = await this.getSCCTRequestBody();
-      return await dofetch3("termdb/singlecellDEgenes", { body });
-    } else {
-      throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
-    }
-  }
-  //Gene expression
-  async getGERequestBody() {
-    await this.getOtherSamples(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      method: this.settings.method,
-      min_count: this.settings.minCount,
-      min_total_count: this.settings.minTotalCount,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      cpm_cutoff: this.settings.cpmCutoff,
-      volcanoRender: this.getVolcanoRender()
-    };
-    this.addConfounderTw(body);
-    return body;
-  }
-  //DNA methylation
-  async getDMRequestBody() {
-    await this.getOtherSamples(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      min_samples_per_group: this.settings.minSamplesPerGroup,
-      volcanoRender: this.getVolcanoRender()
-    };
-    this.addConfounderTw(body);
-    return body;
-  }
-  /** Parameters telling the server to run the `volcano` Rust renderer and return a
-   * volcano PNG + top-significant rows instead of the full dot list. */
-  getVolcanoRender() {
-    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
-    const { caseColor, controlColor } = getGroupColors(this.config);
-    return {
-      significanceThresholds: {
-        pValueCutoff: this.settings.pValue,
-        pValueType: this.settings.pValueType,
-        foldChangeCutoff: this.settings.foldChangeCutoff
-      },
-      pixelWidth: this.settings.width,
-      pixelHeight: this.settings.height,
-      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
-      colorSignificantUp: caseColor,
-      colorSignificantDown: controlColor,
-      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
-      dotRadius,
-      maxInteractiveDots: this.settings.maxInteractiveDots
-    };
-  }
-  //This is a workaround until the server can accept an arr of confounder tws
-  addConfounderTw(body) {
-    const confounders = this.config?.confounderTws;
-    if (confounders?.length) {
-      body.tw = this.config.confounderTws[0];
-      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
-    }
-  }
-  //Single cell cell type
-  getSCCTRequestBody() {
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      sample: this.config.sample,
-      termId: this.config.termId,
-      categoryName: this.config.categoryName,
-      volcanoRender: this.getVolcanoRender()
-    };
-    return body;
-  }
-  /** retrieve the sampleId/sampleName for samples in
-   * the "others" group instead of using {in: false} */
-  async getOtherSamples(samplelst) {
-    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
-    if (!othersSamplesGroup) return;
-    const state = this.app.getState();
-    const samplesGroup = samplelst.groups.find((g) => g.in);
-    othersSamplesGroup.values = [];
-    for (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
-      if (samplesGroup.values.indexOf((i) => i.sampleId == s.id) == -1) {
-        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
-      }
-    }
-    othersSamplesGroup.in = true;
-  }
-};
-
-export {
-  getGroupColors,
-  VolcanoModel
-};
-//# sourceMappingURL=chunk-5FO3NKA4.js.map

package/dist/chunk-5FO3NKA4.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/volcano/colors.ts", "../plots/volcano/model/VolcanoModel.ts"],
-  "sourcesContent": ["import { rgb } from 'd3-color'\n\n/** Resolve the case/control dot colors for a volcano plot in one place so the\n * interactive SVG overlay (VolcanoViewModel) and the server-rendered PNG\n * (VolcanoModel \u2192 Rust) paint each dot the same color.\n *\n * `caseColor` maps to points with `fold_change > 0` (group 2 in samplelst),\n * `controlColor` to `fold_change < 0` (group 1). Every returned color is a\n * `#rrggbb` hex string \u2014 CSS names like `'red'` are normalized via d3-color\n * so the Rust renderer's hex-only parser doesn't fall back to a muted tuple.\n */\nexport function getGroupColors(config: any): { caseColor: string; controlColor: string } {\n\tconst groups = config?.samplelst?.groups\n\tconst termValues = config?.tw?.term?.values\n\tconst rawDown = termValues?.[groups?.[0]?.name]?.color || 'red'\n\tconst rawUp = termValues?.[groups?.[1]?.name]?.color || 'blue'\n\treturn {\n\t\tcontrolColor: toHex(rawDown, 'red'),\n\t\tcaseColor: toHex(rawUp, 'blue')\n\t}\n}\n\n/** Normalize any CSS-accepted color string into `#rrggbb`. */\nexport function toHex(color: string | undefined, fallback: string): string {\n\tconst c = rgb(color || fallback)\n\treturn c.displayable() ? c.formatHex() : rgb(fallback).formatHex()\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { dofetch3 } from '#common/dofetch'\nimport type { DERequest, DiffMethRequest, TermdbSingleCellDEgenesRequest, VolcanoRenderRequest } from '#types'\nimport { DNA_METHYLATION, GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#shared/terms.js'\nimport { getGroupColors, toHex } from '../colors'\n\nexport class VolcanoModel {\n\tapp: MassAppApi\n\tconfig!: any\n\tsettings!: any\n\ttermType: string\n\n\tconstructor(app: MassAppApi, termType: string) {\n\t\tthis.app = app\n\t\tthis.termType = termType\n\t}\n\n\t/** May use mapper instead as more termTypes are added */\n\tasync getData(config: any, settings: any) {\n\t\tthis.config = config\n\t\tthis.settings = settings\n\n\t\tif (this.termType === GENE_EXPRESSION) {\n\t\t\tconst body = await this.getGERequestBody()\n\t\t\tconst response = await dofetch3('termdb/DE', { body })\n\t\t\t// Surface the DE request so downstream plots (GSEA) can snapshot\n\t\t\t// it and later ask the server to recompute the DA cache if the\n\t\t\t// file is missing on a peer node or after TTL eviction.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === DNA_METHYLATION) {\n\t\t\tconst body = await this.getDMRequestBody()\n\t\t\tconst response = await dofetch3('termdb/diffMeth', { body })\n\t\t\t// Surface the DM request the same way the GE branch above does so\n\t\t\t// the GSEA tab can snapshot it and the server can recompute the DM\n\t\t\t// cache if the file is missing on a peer node or after TTL.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === SINGLECELL_CELLTYPE) {\n\t\t\tconst body = await this.getSCCTRequestBody()\n\t\t\treturn await dofetch3('termdb/singlecellDEgenes', { body })\n\t\t} else {\n\t\t\tthrow new Error(`Volcano plot does not support route for termType='${this.termType}'`)\n\t\t}\n\t}\n\n\t//Gene expression\n\tasync getGERequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tmethod: this.settings.method,\n\t\t\tmin_count: this.settings.minCount,\n\t\t\tmin_total_count: this.settings.minTotalCount,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tcpm_cutoff: this.settings.cpmCutoff,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DERequest> //remove Partial when storage_type is removed from DERequest\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//DNA methylation\n\tasync getDMRequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmin_samples_per_group: this.settings.minSamplesPerGroup,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DiffMethRequest>\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t/** Parameters telling the server to run the `volcano` Rust renderer and return a\n\t * volcano PNG + top-significant rows instead of the full dot list. */\n\tgetVolcanoRender(): VolcanoRenderRequest {\n\t\t// Match the client overlay's radius (see VolcanoViewModel.setPointData)\n\t\t// so the PNG rings and the interactive overlay rings line up; otherwise\n\t\t// a smaller PNG ring sits inside the larger overlay ring and looks like\n\t\t// a stray dot at the center.\n\t\tconst dotRadius = Math.max(this.settings.width, this.settings.height) / 80\n\t\t// Resolve case/control colors via the shared helper (see colors.ts) so the\n\t\t// PNG and the SVG overlay paint each side with the exact same hex string.\n\t\tconst { caseColor, controlColor } = getGroupColors(this.config)\n\t\treturn {\n\t\t\tsignificanceThresholds: {\n\t\t\t\tpValueCutoff: this.settings.pValue,\n\t\t\t\tpValueType: this.settings.pValueType,\n\t\t\t\tfoldChangeCutoff: this.settings.foldChangeCutoff\n\t\t\t},\n\t\t\tpixelWidth: this.settings.width,\n\t\t\tpixelHeight: this.settings.height,\n\t\t\tcolorSignificant: toHex(this.settings.defaultSignColor, 'red'),\n\t\t\tcolorSignificantUp: caseColor,\n\t\t\tcolorSignificantDown: controlColor,\n\t\t\tcolorNonsignificant: toHex(this.settings.defaultNonSignColor, 'black'),\n\t\t\tdotRadius,\n\t\t\tmaxInteractiveDots: this.settings.maxInteractiveDots\n\t\t}\n\t}\n\n\t//This is a workaround until the server can accept an arr of confounder tws\n\taddConfounderTw(body) {\n\t\tconst confounders = this.config?.confounderTws\n\t\tif (confounders?.length) {\n\t\t\tbody.tw = this.config.confounderTws[0]\n\t\t\tif (confounders.length > 1) body.tw2 = this.config.confounderTws[1]\n\t\t}\n\t}\n\n\t//Single cell cell type\n\tgetSCCTRequestBody(): TermdbSingleCellDEgenesRequest {\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsample: this.config.sample,\n\t\t\ttermId: this.config.termId,\n\t\t\tcategoryName: this.config.categoryName,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t\treturn body\n\t}\n\n\t/** retrieve the sampleId/sampleName for samples in\n\t * the \"others\" group instead of using {in: false} */\n\tasync getOtherSamples(samplelst) {\n\t\tconst othersSamplesGroup = samplelst.groups.find(g => !g.in)\n\t\tif (!othersSamplesGroup) return\n\n\t\tconst state = this.app.getState()\n\t\tconst samplesGroup = samplelst.groups.find(g => g.in)\n\t\tothersSamplesGroup.values = []\n\t\t// retrieve full list of samples based on current filter. put samples not in samplesGroup in \"others\" group\n\t\tfor (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {\n\t\t\t// s={id,name}, samplelst.groups[].values[]={sampleId,sample}\n\t\t\tif (samplesGroup.values.indexOf(i => i.sampleId == s.id) == -1) {\n\t\t\t\tothersSamplesGroup.values.push({ sampleId: s.id, sample: s.name })\n\t\t\t}\n\t\t}\n\t\tothersSamplesGroup.in = true\n\t}\n}\n"],
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package/dist/chunk-5HOR6JQ2.js

@@ -1,100 +0,0 @@
-import {
-  SearchHandler,
-  fillTermWrapper,
-  table2col,
-  termsettingInit
-} from "./chunk-LN3QYBGI.js";
-
-// plots/summarizeMutationDiagnosis.ts
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let dictTw;
-  {
-    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
-    if (!t) throw "defaultTw4correlationPlot missing";
-    dictTw = structuredClone(t);
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-  }
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "0px 10px 10px 10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Mutation Variable");
-    const searchDiv = td2.append("div");
-    const geneSearchInst = new SearchHandler();
-    geneSearchInst.init({
-      holder: searchDiv,
-      app: chartsInstance.app,
-      // required to supply "opts.app.vocabApi" for the search ui
-      genomeObj: chartsInstance.app.opts.genome,
-      msg: "Hit ENTER to launch plot.",
-      callback: async (geneTw) => {
-        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
-        launchPlot({
-          tw1: dictTw,
-          tw2: geneTw,
-          chartsInstance,
-          holder
-        });
-      }
-    });
-    searchDiv.style("padding", "0px 0px 5px 0px");
-  }
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Compare Mutations Against");
-    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
-    const pill = await termsettingInit({
-      menuOptions: "{edit,replace}",
-      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
-      target="filter" works for gdc since in gdc ds it is overriding filter to dict
-      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
-      maybe this is okay for non-gdc ds as the default dictTw is meaningful
-      */
-      usecase: { target: "filter" },
-      vocabApi: chartsInstance.app.vocabApi,
-      holder: pillDiv,
-      callback: async (tw) => {
-        waitDiv.text("LOADING ...");
-        try {
-          await pill.main(tw);
-          dictTw = tw;
-          waitDiv.text("Click to edit/replace the variable before searching gene.");
-        } catch (e) {
-          waitDiv.text("Error: " + (e.message || e));
-        }
-      }
-    });
-    try {
-      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-      await pill.main(dictTw);
-      waitDiv.text("Click to edit/replace the variable before searching gene.");
-    } catch (e) {
-      waitDiv.text("Error: " + (e.message || e));
-    }
-  }
-}
-function launchPlot({ tw1, tw2, chartsInstance, holder }) {
-  const chart = {
-    config: {
-      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
-      // TODO define sandbox header with gene+term name
-      term: tw1,
-      term2: tw2
-    }
-  };
-  chartsInstance.plotCreate(chart);
-  holder.selectAll("*").remove();
-  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
-  setTimeout(() => {
-    holder.style("display", "none");
-  }, 1e3);
-}
-
-export {
-  makeChartBtnMenu,
-  launchPlot
-};
-//# sourceMappingURL=chunk-5HOR6JQ2.js.map

package/dist/chunk-5LZKQFLO.js

@@ -1,180 +0,0 @@
-import {
-  NumericModes
-} from "./chunk-EGWVYY7K.js";
-
-// plots/proteomeAbundance.ts
-function renderAssayAndCohortRadios({
-  holder,
-  organisms,
-  selectedProteomeDetails,
-  onChange,
-  organismTitle = "Organism",
-  assayTitle = "Assay Type",
-  cohortTitle = "Sample Set"
-}) {
-  const organismEntries = Object.entries(organisms || {});
-  if (!organismEntries.length) {
-    holder.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No proteome organisms available.");
-    return {
-      getSelected: () => ({ organism: void 0, assay: void 0, cohort: void 0 })
-    };
-  }
-  const initialProteomeDetails = selectedProteomeDetails || {};
-  const organismRadioName = `sjpp-proteome-organism-${Math.random().toString().slice(-6)}`;
-  const assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`;
-  const cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`;
-  let selectedOrganism = organisms[initialProteomeDetails.organism || ""] ? initialProteomeDetails.organism : organismEntries[0][0];
-  let selectedAssay = initialProteomeDetails.assay;
-  let selectedCohort = initialProteomeDetails.cohort;
-  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(organismTitle);
-  const organismListDiv = holder.append("div").style("margin-bottom", "10px");
-  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(assayTitle);
-  const assayListDiv = holder.append("div").style("margin-bottom", "10px");
-  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(cohortTitle);
-  const cohortListDiv = holder.append("div").style("max-height", "300px").style("overflow-y", "auto").style("border", "1px solid #ddd").style("border-radius", "4px").style("padding", "5px");
-  for (const [organismKey] of organismEntries) {
-    const organismLabel = organismListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
-    organismLabel.append("input").attr("type", "radio").attr("name", organismRadioName).attr("value", organismKey).property("checked", organismKey === selectedOrganism).style("margin-right", "6px").on("change", () => {
-      selectedOrganism = organismKey;
-      selectedAssay = void 0;
-      selectedCohort = void 0;
-      renderAssayOptions();
-      renderCohortOptions();
-      onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
-    });
-    organismLabel.append("span").text(organismKey);
-  }
-  renderAssayOptions();
-  renderCohortOptions();
-  onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
-  return {
-    getSelected: () => ({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })
-  };
-  function renderAssayOptions() {
-    assayListDiv.selectAll("*").remove();
-    const assays = organisms[selectedOrganism || ""]?.assays || {};
-    const assayEntries = Object.entries(assays);
-    if (!assayEntries.length) {
-      selectedAssay = void 0;
-      selectedCohort = void 0;
-      assayListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No assays available.");
-      return;
-    }
-    if (!selectedAssay || !assays[selectedAssay]) {
-      selectedAssay = assayEntries.some(([k]) => k === initialProteomeDetails.assay) ? initialProteomeDetails.assay : assayEntries[0][0];
-    }
-    for (const [assayKey] of assayEntries) {
-      const assayLabel = assayListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
-      assayLabel.append("input").attr("type", "radio").attr("name", assayRadioName).attr("value", assayKey).property("checked", assayKey === selectedAssay).style("margin-right", "6px").on("change", () => {
-        selectedAssay = assayKey;
-        selectedCohort = void 0;
-        renderCohortOptions();
-        onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
-      });
-      assayLabel.append("span").text(assayKey);
-    }
-  }
-  function renderCohortOptions() {
-    cohortListDiv.selectAll("*").remove();
-    const cohorts = Object.keys(organisms[selectedOrganism || ""]?.assays?.[selectedAssay || ""]?.cohorts || {});
-    if (!cohorts.length) {
-      selectedCohort = void 0;
-      cohortListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No cohorts available.");
-      return;
-    }
-    if (!selectedCohort || !organisms[selectedOrganism || ""]?.assays?.[selectedAssay || ""]?.cohorts?.[selectedCohort]) {
-      selectedCohort = cohorts.includes(initialProteomeDetails.cohort || "") ? initialProteomeDetails.cohort : cohorts[0];
-    }
-    for (const cohortKey of cohorts) {
-      const cohortLabel = cohortListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
-      cohortLabel.append("input").attr("type", "radio").attr("name", cohortRadioName).attr("value", cohortKey).property("checked", cohortKey === selectedCohort).style("margin-right", "6px").on("change", () => {
-        selectedCohort = cohortKey;
-        onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
-      });
-      cohortLabel.append("span").text(cohortKey);
-    }
-  }
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const organisms = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms || {};
-  const menuDiv = holder.append("div");
-  let selectedProteomeDetails;
-  const launchOption = menuDiv.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").style("display", "block").style("margin", "10px auto 10px").text("Select Protein").on("click", () => {
-    const current = selectedProteomeDetails;
-    if (!current?.organism || !current.assay || !current.cohort) return;
-    const { organism, assay, cohort } = current;
-    const assayCohortTitle = `${organism} ${assay}: ${cohort}`;
-    const chart = {
-      label: "Protein Abundance",
-      chartType: "proteomeAbundance",
-      usecase: {
-        target: "proteomeAbundance",
-        detail: "term",
-        proteomeDetails: { organism, assay, cohort },
-        label: `Organism: ${organism}; Assay: ${assay}; Sample set: ${cohort}`
-      },
-      processSelection: (termlst) => termlst,
-      updateActionBySelectedTerms: (action, termlst) => {
-        action.config.assayCohortTitle = assayCohortTitle;
-        const currentDetails = selectedProteomeDetails;
-        if (!currentDetails?.organism || !currentDetails.assay || !currentDetails.cohort) return;
-        const { organism: organism2, assay: assay2, cohort: cohort2 } = currentDetails;
-        action.config.proteomeDetails = { organism: organism2, assay: assay2, cohort: cohort2 };
-        const twlst = termlst.map((term) => {
-          const t = structuredClone(term);
-          t.proteomeDetails = { organism: organism2, assay: assay2, cohort: cohort2 };
-          return { term: t, q: { mode: NumericModes.continuous } };
-        });
-        if (twlst.length == 1) {
-          action.config.chartType = "summary";
-          action.config.term = twlst[0];
-          const proteomeOverlayTerm = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms?.[organism2]?.overlayTerm;
-          if (proteomeOverlayTerm) action.config.term2 = { term: structuredClone(proteomeOverlayTerm), q: {} };
-          return;
-        }
-        if (twlst.length == 2) {
-          action.config.chartType = "summary";
-          action.config.term = twlst[0];
-          action.config.term2 = twlst[1];
-          return;
-        }
-        action.config.chartType = "hierCluster";
-        action.config.dataType = "proteomeAbundance";
-        action.config.termgroups = [{ name: "Protein Abundance Cluster", lst: twlst, type: "hierCluster" }];
-      }
-    };
-    chartsInstance.dom.tip.clear();
-    chartsInstance.showTree_selectlst(chart);
-  });
-  const syncLaunchButtonState = () => {
-    if (!launchOption) return;
-    if (selectedProteomeDetails?.cohort) launchOption.style("opacity", 1).style("pointer-events", "auto");
-    else launchOption.style("opacity", 0.5).style("pointer-events", "none");
-  };
-  renderAssayAndCohortRadios({
-    holder: menuDiv,
-    organisms,
-    onChange: (proteomeDetails) => {
-      selectedProteomeDetails = proteomeDetails;
-      syncLaunchButtonState();
-    }
-  });
-  syncLaunchButtonState();
-}
-function toTvslstFilter(filterConfig) {
-  if (filterConfig && Array.isArray(filterConfig) && filterConfig.length)
-    return {
-      type: "tvslst",
-      in: true,
-      join: filterConfig.length > 1 ? "and" : "",
-      lst: filterConfig.map((tvs) => ({ type: "tvs", tvs }))
-    };
-}
-
-export {
-  renderAssayAndCohortRadios,
-  makeChartBtnMenu,
-  toTvslstFilter
-};
-//# sourceMappingURL=chunk-5LZKQFLO.js.map