@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-THUXB7EE.js.map

@@ -0,0 +1,7 @@
+{
+  "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 } from '#shared/terms.js'\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 {\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.app, 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 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 || 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 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-TVXVP4M6.js

@@ -0,0 +1,215 @@
+import {
+  make_radios
+} from "./chunk-2XPDA6NL.js";
+import {
+  initBinConfig
+} from "./chunk-MYWJQRTD.js";
+import {
+  format
+} from "./chunk-OAWQ6LOO.js";
+
+// termsetting/handlers/NumRegularBinEditor.ts
+var NumRegularBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  render(div) {
+    if (this.q?.type != "regular-bin") this.q = this.getDefaultQ();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (this.dom.binsTable) {
+      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return;
+      else {
+        this.dom.binsTable.remove();
+        delete this.dom.binsTable;
+      }
+    }
+    const binsTable = div.append("table");
+    this.dom.binsTable = binsTable;
+    this.renderBinSizeInput(binsTable.append("tr"));
+    this.renderFirstBinInput(binsTable.append("tr"));
+    this.renderLastBinInputs(binsTable.append("tr"));
+  }
+  getDefaultQ() {
+    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
+    const t = this.tw.term;
+    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
+    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
+    const binConfig = initBinConfig(this.editHandler.handler.density_data);
+    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
+  }
+  renderBinSizeInput(tr) {
+    const handler = this.editHandler.handler;
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
+    const { min, max } = handler.density_data;
+    const q = this.q;
+    const origBinSize = q.bin_size;
+    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr("value", "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : q.bin_size).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
+      const newValue = Number(event.target.value);
+      if (newValue <= 0) {
+        window.alert("Please enter non-negative bin size.");
+        event.target.value = origBinSize;
+        return;
+      }
+      if ((max - min) / newValue > 100) {
+        window.alert("Bin size too small. Try setting a bigger value.");
+        event.target.value = origBinSize;
+        return;
+      }
+      q.bin_size = newValue;
+      this.dom.bin_size_input.style("color", q.bin_size > max - min ? "red" : newValue != origBinSize ? "green" : "");
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+  }
+  renderFirstBinInput(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    if (!q.first_bin) throw "missing q.first_bin";
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
+    const { min, max } = handler.density_data;
+    const origValue = q.first_bin.stop;
+    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
+      const newValue = Number(event.target.value);
+      if (newValue < min || newValue > max) {
+        window.alert("First bin stop value out of bound.");
+        event.target.value = origValue;
+        return;
+      }
+      this.q.first_bin.stop = newValue;
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
+  }
+  renderLastBinInputs(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
+    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
+    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
+    const radio_div = td1.append("div");
+    const radios = make_radios({
+      holder: radio_div,
+      options: [
+        { label: "Automatic", value: "auto", checked: isAuto },
+        { label: "Fixed", value: "fixed", checked: !isAuto }
+      ],
+      callback: (v) => {
+        if (v == "auto") {
+          delete q.last_bin;
+          edit_div.style("display", "none");
+          handler.density.setBinLines(this.getBoundaryOpts());
+          return;
+        }
+        edit_div.style("display", "inline-block");
+        if (this.dom.last_start_input.property("value") == "") {
+          this.dom.last_start_input.property("value", this.tw.q.last_bin?.start || handler.density_data.max);
+        }
+        this.setLastBinStart();
+      }
+    });
+    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
+    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
+    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", q.last_bin?.start || "").style("width", "100px").on("change", () => this.setLastBinStart());
+    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
+  }
+  setLastBinStart() {
+    const q = this.q;
+    const { max } = this.editHandler.handler.density_data;
+    const strInput = this.dom.last_start_input.property("value");
+    if (strInput === "") return;
+    const inputValue = Number(strInput);
+    if (q.first_bin && inputValue <= q.first_bin.stop) {
+      window.alert("Last bin start cannot be smaller than first bin stop.");
+      this.dom.last_start_input.property("value", max);
+      return;
+    }
+    if (inputValue > max) {
+      window.alert("Last bin start value out of bound.");
+      this.dom.last_start_input.property("value", max);
+      return;
+    }
+    if (q.last_bin) q.last_bin.start = inputValue;
+    else
+      q.last_bin = {
+        start: inputValue,
+        stopunbounded: true,
+        stopinclusive: false
+      };
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  getBoundaryOpts() {
+    const { min, max } = this.editHandler.handler.density_data;
+    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
+    const boundaryValues = [];
+    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
+      if (this.q.last_bin?.start === i) break;
+      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
+      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
+      boundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
+    }
+    if (this.q.last_bin) {
+      boundaryValues.push({
+        x: this.q.last_bin.start,
+        isDraggable: true,
+        isLastVisibleLine: true,
+        movesWithLineIndex: -1
+      });
+    }
+    return {
+      values: boundaryValues,
+      callback: (d, value) => {
+        if (d.index === 0) {
+          this.dom.first_stop_input.property("value", value);
+          this.q.first_bin.stop = value;
+        } else {
+          this.editHandler.handler.dom.last_start_input.property("value", value);
+          if (this.q.last_bin) this.q.last_bin.start = value;
+        }
+      }
+    };
+  }
+  getEditedQ(destroyDom = true) {
+    const bin_size = this.dom.bin_size_input.property("value");
+    const config = {
+      mode: "discrete",
+      type: "regular-bin",
+      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
+      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
+      bin_size: Number(bin_size),
+      first_bin: {
+        startunbounded: true,
+        stop: Number(this.dom.first_stop_input.property("value"))
+      },
+      rounding: bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
+    };
+    if (this.dom.fixed_radio.property("checked")) {
+      config.last_bin = {
+        start: Number(this.dom.last_start_input.property("value")),
+        stopunbounded: true
+      };
+    }
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return config;
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.binsTable.selectAll("*").remove();
+    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
+    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
+    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumRegularBinEditor
+};
+//# sourceMappingURL=chunk-TVXVP4M6.js.map