@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-TBLWSWGI.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/gsea.js"],
-  "sourcesContent": ["import * as d3axis from 'd3-axis'\nimport { Menu, renderTable, table2col, axisstyle } 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 || !response.data || response.error) {\n\t\t\t\t\tthrow response.error || 'No data returned from volcano model'\n\t\t\t\t}\n\t\t\t\tconst inputGenes = response.data.map(g => g.gene_name)\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\tgenes: inputGenes,\n\t\t\t\t\t\t\tfold_change: response.data.map(g => g.fold_change),\n\t\t\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome,\n\t\t\t\t\t\t\tgenes_length: inputGenes.length\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\tthis.dom.header.html(\n\t\t\t\tthis.config.gsea_params.genes.length +\n\t\t\t\t\t' genes <span style=\"font-size:.8em;opacity:.7\">GENE SET ENRICHMENT ANALYSIS</span>'\n\t\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\tpickle_file: 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 body = {\n\t\t\tgenome: self.config.gsea_params.genome,\n\t\t\tgenes: self.config.gsea_params.genes,\n\t\t\tfold_change: self.config.gsea_params.fold_change,\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\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\talert('Error: ' + e)\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\tif (self.settings.gsea_method == 'blitzgsea') {\n\t\t\tself.config.gsea_params.method = self.settings.gsea_method\n\t\t\tconst image = await rungsea(self.config.gsea_params, self.dom)\n\t\t\t// //render_gsea_plot(self, plot_data)\n\t\t\tif (image.error) throw image.error\n\t\t\tself.imageUrl = URL.createObjectURL(image)\n\t\t\tconst png_width = 600\n\t\t\tconst png_height = 400\n\t\t\tself.dom.holder.append('img').attr('width', png_width).attr('height', png_height).attr('src', self.imageUrl)\n\t\t} else if (self.settings.gsea_method == 'cerno') {\n\t\t\trender_cerno_plot(self, output)\n\t\t} else {\n\t\t\tthrow 'Unknown method:' + self.settings.gsea_method\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\tpickle_file: output.pickle_file,\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 DE_output = []\n\tfor (let i = 0; i < self.config.gsea_params.genes.length; i++) {\n\t\tconst item = { gene: self.config.gsea_params.genes[i], fold_change: self.config.gsea_params.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. May be used later if client side rendering is later desired.\n// \tconsole.log('self.dom.holder:', self.dom.holder)\n// \tconst holder = self.dom.holder\n// \tconsole.log('plot_data:', plot_data)\n// \tholder.selectAll('*').remove()\n// \tconst running_sum = plot_data.running_sum.split(',').map(x => parseFloat(x))\n// \tconst es = parseFloat(plot_data.es)\n// \tconsole.log('running_sum:', running_sum)\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 = 50\n// \tconst rightpad = 50\n// \tconst yaxisw = Math.max(50, svg_width / 8)\n// \tconst xaxish = Math.max(50, svg_height / 8)\n// \tconst yaxisg = svg.append('g')\n// \tconst xaxisg = svg.append('g')\n// \tconst xpad = svg_width / 50\n// \tconst ypad = svg_height / 50\n// \tyaxisg.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + (toppad - ypad) + ')')\n// \txaxisg.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + (svg_height - ypad) + ')')\n// \tconst xlab = xaxisg.append('text').text('Rank').attr('fill', 'black').attr('text-anchor', 'middle') //.attr('transform', 'translate(' + 200 + ',' + 200 + ')')\n// \tconst ylab = yaxisg\n// \t\t.append('text')\n// \t\t.text('ES')\n// \t\t.attr('fill', 'black')\n// \t\t.attr('text-anchor', 'middle')\n// \t\t.attr('transform', 'rotate(-90)')\n// \tconst xscale = scaleLinear().domain(running_sum).range([0, svg_width])\n// \tconst yscale = scaleLinear().domain([0, 100]).range([0, svg_height])\n// \t//const xscale = scaleLinear().domain([Math.min(running_sum), Math.max(running_sum)]).range([0, 100])\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// \t//xscale.range([0, svg_width])\n// \t//yscale.range([svg_height, 0])\n// \tconst lines = svg.append('g')\n// \t//svg.selectAll(\".axis text\").style(\"font-size\", \"100px\")\n// \tlet gene_number = 0\n// \tlet y1 = 0\n// \tfor (const rs of running_sum) {\n// \t\tlines\n// \t\t\t.append('line') // attach a line\n// \t\t\t.style('stroke', 'green') // colour the line\n// \t\t\t.attr('x1', xscale(gene_number)) // x position of the first end of the line\n// \t\t\t.attr('y1', yscale(y1)) // y position of the first end of the line\n// \t\t\t.attr('x2', xscale(gene_number)) // x position of the second end of the line\n// \t\t\t.attr('y2', yscale(Math.abs(rs))) // y position of the second end of the line\n// \t\tgene_number += 1\n// \t\ty1 = Math.abs(rs)\n// \t}\n// }\n\nexport function getDefaultGseaSettings(overrides = {}) {\n\tconst defaults = {\n\t\tfdr_cutoff: 0.05,\n\t\tnum_permutations: 1000,\n\t\ttop_genesets: 40,\n\t\tpathway: undefined,\n\t\tgeneset_name: null,\n\t\tmin_gene_set_size_cutoff: 0,\n\t\tmax_gene_set_size_cutoff: 20000,\n\t\tfilter_non_coding_genes: true,\n\t\tfdr_or_top: 'top',\n\t\tgsea_method: 'blitzgsea'\n\t}\n\tif (JSON.parse(sessionStorage.getItem('optionalFeatures')).gsea_test) {\n\t\t// set default method to CERNO when serverconfig flag gsea_test is defined\n\t\tdefaults.gsea_method = 'cerno'\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n\nexport async function getPlotConfig(opts, app) {\n\t// if (!opts.gsea_params) throw 'No gsea_params provided [gsea getPlotConfig()]'\n\ttry {\n\t\tconst config = {\n\t\t\t//idea for fixing nav button\n\t\t\t//samplelst: { groups: app.opts.state.groups}\n\t\t\tsettings: {\n\t\t\t\tgsea: getDefaultGseaSettings(opts.overrides)\n\t\t\t}\n\t\t}\n\t\treturn copyMerge(config, opts)\n\t} catch (e) {\n\t\tthrow `${e} [gsea getPlotConfig()]`\n\t}\n}\n\nexport const gseaInit = getCompInit(gsea)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = gseaInit\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\n\t// to fill in menu, create options in \"holder\"\n\t// to hide menu, call chartsInstance.dom.tip.hide()\n\t// upon clicking an option, generate plot:\n\tchartsInstance.prepPlot({\n\t\tconfig: {\n\t\t\tchartType: 'gsea'\n\t\t}\n\t})\n}\n\nasync function rungsea(body, dom) {\n\t//Only show the loading div as the gsea is running\n\tdom.actionsDiv.style('display', 'none')\n\tdom.loadingDiv.style('display', 'block')\n\tconst data = await dofetch3('genesetEnrichment', { body })\n\tdom.loadingDiv.style('display', 'none')\n\tdom.actionsDiv.style('display', 'block')\n\treturn data\n}\n"],
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-  "names": []
-}

package/dist/chunk-TE3DK3A6.js

@@ -1,147 +0,0 @@
-import {
-  violinRenderer
-} from "./chunk-F6V4AYWP.js";
-import {
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import {
-  drag_default
-} from "./chunk-SEEYV6P2.js";
-import {
-  pointer_default,
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// termsetting/handlers/NumericDensity.ts
-var NumericDensity = class {
-  constructor(opts) {
-    this.dom = {};
-    // WeakMap allows deletion of value when the object/DOM key is deleted,
-    // so better for avoiding memory leak
-    this.vrByDiv = /* @__PURE__ */ new WeakMap();
-    this.ranges = [];
-    this.no_density_data = false;
-    this.brushes = [];
-    this.plot_size = {
-      width: 500,
-      height: 100,
-      xpad: 10,
-      ypad: 20,
-      radius: 8
-    };
-    this.opts = opts;
-    this.termsetting = opts.termsetting;
-    this.tw = opts.termsetting.tw;
-  }
-  async setData() {
-    if (this.density_data) return this.density_data;
-    const self = this.termsetting;
-    const d = await self.vocabApi.getViolinBox(
-      {
-        plotType: "violin",
-        tw: { term: self.term, q: self.q },
-        svgw: this.plot_size.width,
-        radius: this.plot_size.radius,
-        filter: self.filter
-      },
-      self.opts.getBodyParams?.()
-    );
-    if (d.error) throw d;
-    this.density_data = d;
-    return this.density_data;
-  }
-  async showViolin(div, boundaryOpts) {
-    await this.setData();
-    if (!this.vrByDiv.has(div)) {
-      div.style("padding", "5px").selectAll("*").remove();
-      const loadingDiv = div.append("div").style("padding", "10px").style("text-align", "center").html("Getting distribution data ...<br/>");
-      const densityDiv = div.append("div");
-      loadingDiv.remove();
-      const vr = new violinRenderer({
-        holder: densityDiv,
-        rd: this.density_data,
-        width: this.plot_size.width,
-        height: this.plot_size.height,
-        radius: this.plot_size.radius
-      });
-      this.vrByDiv.set(div, vr);
-    }
-    this.vr = this.vrByDiv.get(div);
-    this.dom.svg = this.vr.svg;
-    this.vr.render();
-    if (boundaryOpts) await this.setBinLines(boundaryOpts);
-    return this.density_data;
-  }
-  async setBinLines(boundaryOpts) {
-    if (this.density_data.max == this.density_data.min) {
-      this.handleNoDensity();
-    } else {
-      if (this.dom.binsize_g) this.dom.binsize_g.selectAll("*").remove();
-      this.dom.binsize_g = this.dom.svg.append("g").attr("transform", `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`).attr("class", "binsize_g");
-      const maxvalue = this.density_data.max;
-      const minvalue = this.density_data.min;
-      this.xscale = linear().domain([minvalue, maxvalue]).range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad]);
-      this.ranges = [];
-      this.brushes = [];
-      this.renderBinLines(boundaryOpts);
-    }
-  }
-  handleNoDensity() {
-    this.no_density_data = true;
-    this.ranges = [];
-    this.brushes = [];
-  }
-  renderBinLines(boundaryOpts) {
-    const { density_data, plot_size, tw, xscale } = this;
-    if (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`;
-    const scaledMinX = Math.round(this.xscale(density_data.min));
-    const scaledMaxX = Math.round(this.xscale(density_data.max));
-    const lines = [];
-    for (const [index, v] of boundaryOpts.values.entries()) {
-      lines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) });
-    }
-    const lastVisibleLine = lines.find((l) => l.isLastVisibleLine);
-    const lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX;
-    const dragger = drag_default().on("drag", onDrag).on("end", onDrag);
-    this.dom.binsize_g.selectAll("line").remove();
-    this.dom.binsize_g.selectAll("line").data(lines).enter().append("line").style("stroke", (d) => d.isDraggable ? "#cc0000" : "#555").style("stroke-width", 1).attr("x1", (d) => d.scaledX).attr("y1", 0).attr("x2", (d) => d.scaledX).attr("y2", plot_size.height).style("cursor", (d) => d.isDraggable ? "ew-resize" : "").attr("display", (d) => !d.isDraggable && d.scaledX > lastVisibleScaledX ? "none" : "").on("mouseover", function(_, d) {
-      if (d.isDraggable) select_default(this).style("stroke-width", 3);
-    }).on("mouseout", function() {
-      select_default(this).style("stroke-width", 1);
-    }).each(function(d) {
-      if (d.isDraggable) select_default(this).call(dragger);
-    });
-    const lineElems = this.dom.binsize_g.node().querySelectorAll("line");
-    function onDrag(event, _d) {
-      const draggedX = pointer_default(event, this)[0];
-      if (draggedX <= scaledMinX || draggedX >= scaledMaxX) return;
-      const d = _d;
-      d.draggedX = draggedX;
-      select_default(this).attr("x1", d.draggedX).attr("y1", 0).attr("x2", d.draggedX).attr("y2", plot_size.height);
-      const lastVisibleScaledX2 = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX;
-      const xOffset = d.draggedX - d.scaledX;
-      if (xOffset) {
-        for (const elem of lineElems) {
-          const c = elem.__data__;
-          if (c.movesWithLineIndex !== d.index) continue;
-          c.draggedX = c.scaledX + xOffset;
-          select_default(elem).attr("x1", c.draggedX).attr("x2", c.draggedX).style("display", c.draggedX >= lastVisibleScaledX2 ? "none" : "");
-        }
-        const inverted = xscale.invert(d.draggedX);
-        const value = tw.term.type == "integer" ? Math.round(inverted) : inverted.toFixed(3);
-        boundaryOpts.callback(d, Number(value));
-      }
-    }
-  }
-  destroy() {
-    for (const [k, v] of Object.entries(this.dom)) {
-      delete this.dom[k];
-      if (typeof v.remove == "function") v.remove();
-    }
-  }
-};
-
-export {
-  NumericDensity
-};
-//# sourceMappingURL=chunk-TE3DK3A6.js.map