@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/Volcano-X4ZWK644.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/volcano/viewModel/VolcanoViewModel.ts", "../plots/volcano/interactions/VolcanoInteractions.ts", "../plots/volcano/view/DataPointMouseEvents.ts", "../plots/volcano/view/VolcanoPlotView.ts", "../plots/volcano/VolcanoControlInputs.ts", "../plots/volcano/Volcano.ts"],
+  "sourcesContent": ["import type {\n\tVolcanoPlotDimensions,\n\tVolcanoPlotConfig,\n\tVolcanoPValueTableData,\n\tVolcanoViewData,\n\tDataPointEntry\n} from '../VolcanoTypes'\nimport type { ValidatedVolcanoSettings } from '../settings/Settings'\nimport type { DEFullResponse } from '#types'\nimport { scaleLinear } from 'd3-scale'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { getSampleNum } from '../settings/defaults'\nimport { getGroupColors } from '../colors'\nimport { DNA_METHYLATION, GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#shared/terms.js'\n\nexport class VolcanoViewModel {\n\tconfig: any\n\tdataType: string\n\tresponse: DEFullResponse\n\tpValueTable: VolcanoPValueTableData\n\tsettings: any\n\ttermType: string\n\tviewData: VolcanoViewData\n\tnumSignificant = 0\n\tnumNonSignificant = 0\n\tminLogFoldChange = 0\n\tmaxLogFoldChange = 0\n\t//Used for the y axis domain\n\tminLogPValue = 0\n\tmaxLogPValue = 0\n\t//Unpadded extents \u2014 used for the visible axis labels/ticks (only span real data)\n\tminLogFoldChangeAxis = 0\n\tmaxLogFoldChangeAxis = 0\n\tminLogPValueAxis = 0\n\tmaxLogPValueAxis = 0\n\t//Dot radius in pixels (from server) \u2014 overlay rings size to match the PNG\n\tdotRadiusPx = 2\n\t//Used in place of 0 p values that cannot be log transformed\n\tminNonZeroPValue = 10e-10\n\t//The x coord flush with the left side of the plot\n\tplotX: number\n\treadonly offset = 10\n\treadonly bottomPad = 60\n\treadonly horizPad = 70\n\treadonly topPad = 40\n\t/** Interactive rows returned by the server: threshold-passing dots, sorted by\n\t * significance. The full scatter lives in `response.volcanoPng`. */\n\tdataRows: DataPointEntry[]\n\n\tconstructor(config: VolcanoPlotConfig, response: DEFullResponse, settings: ValidatedVolcanoSettings) {\n\t\tthis.config = config\n\t\tthis.response = response\n\t\tthis.plotX = this.horizPad + this.offset * 2\n\n\t\tthis.dataRows = response.data.dots as DataPointEntry[]\n\n\t\t// Shared helper (colors.ts) so the SVG overlay and the server PNG paint\n\t\t// each side in the exact same hex.\n\t\tconst { caseColor, controlColor } = getGroupColors(this.config)\n\t\tconst barplot = { colorNegative: controlColor, colorPositive: caseColor }\n\n\t\tthis.pValueTable = {\n\t\t\tcolumns: [\n\t\t\t\t{ label: 'log\u2082(fold-change)', barplot, sortable: true },\n\t\t\t\t{ label: 'Original p-value', sortable: true },\n\t\t\t\t{ label: 'Adjusted p-value', sortable: true }\n\t\t\t],\n\t\t\t/** Arr set in setPointData() if settings.showPValueTable is true to\n\t\t\t * prevent unnecessary data processing when the table is not shown */\n\t\t\trows: [],\n\t\t\theight: settings.height + this.topPad\n\t\t}\n\t\tthis.settings = settings\n\t\tthis.termType = config.termType\n\t\tthis.dataType = this.setDataType()\n\n\t\tthis.setMinMaxValues()\n\n\t\tconst plotDim = this.setPlotDimensions()\n\t\tthis.setPTableColumns()\n\t\tconst pointData = this.setPointData(plotDim, controlColor, caseColor)\n\n\t\tif (this.settings.showPValueTable) {\n\t\t\t//Get all rows data for the pValueTable in setPointsData, then sort by fold change\n\t\t\tconst foldChangeIdx = this.pValueTable.columns.findIndex(c => c.label.includes('log\u2082(fold-change)'))\n\t\t\tthis.pValueTable.rows.sort((a: any, b: any) => b[foldChangeIdx].value - a[foldChangeIdx].value)\n\t\t}\n\n\t\tthis.viewData = {\n\t\t\timages: response.images || [],\n\t\t\ttermInfo: this.setTermInfo(plotDim),\n\t\t\tplotDim,\n\t\t\tpointData,\n\t\t\tpValueTableData: this.pValueTable,\n\t\t\tstatsData: this.setStatsData(),\n\t\t\tuserActions: this.setUserActions(),\n\t\t\tvolcanoPng: response.data.volcanoPng,\n\t\t\tplotExtent: response.data.plotExtent\n\t\t}\n\t}\n\n\tsetDataType() {\n\t\tif (this.termType == GENE_EXPRESSION) return 'genes'\n\t\telse if (this.termType == DNA_METHYLATION) return 'promoters'\n\t\telse if (this.termType == SINGLECELL_CELLTYPE) return 'genes' //'cells'??\n\t\telse throw new Error(`Unknown termType: ${this.termType}`)\n\t}\n\n\tsetMinMaxValues() {\n\t\t// The server-drawn PNG owns the axes; we adopt its extents verbatim so\n\t\t// overlay circles land on their counterparts in the PNG. Also adopt the\n\t\t// server's minNonZeroPValue so p=0 rows are capped at the same y position\n\t\t// the PNG used.\n\t\tconst ext = this.response.data.plotExtent\n\t\t// Padded extents \u2014 used for positioning overlay dots & PNG (so dots near\n\t\t// the real-data edge stay fully visible).\n\t\tthis.minLogFoldChange = ext.xMin\n\t\tthis.maxLogFoldChange = ext.xMax\n\t\tthis.minLogPValue = ext.yMin\n\t\tthis.maxLogPValue = ext.yMax\n\t\t// Unpadded extents \u2014 used only for the visible axis ticks/labels.\n\t\tthis.minLogFoldChangeAxis = ext.xMinUnpadded\n\t\tthis.maxLogFoldChangeAxis = ext.xMaxUnpadded\n\t\tthis.minLogPValueAxis = ext.yMinUnpadded\n\t\tthis.maxLogPValueAxis = ext.yMaxUnpadded\n\t\tthis.dotRadiusPx = ext.dotRadiusPx\n\t\tif (ext.minNonZeroPValue > 0) this.minNonZeroPValue = ext.minNonZeroPValue\n\t}\n\n\tsetPlotDimensions() {\n\t\t// Trust the server's authoritative PNG dimensions for the plot rect.\n\t\t// (Recomputing as `settings.width + 2*dotRadiusPx` is wrong when rust's\n\t\t// `pad_px = ceil(2*dot_radius)` rounds up for non-integer dot_radius \u2014\n\t\t// the SVG plot rect would scale the PNG and break pixel_x/pixel_y\n\t\t// alignment with the rasterized dots.)\n\t\tconst ext = this.response.data.plotExtent\n\t\tconst plotW = ext.pixelWidth\n\t\tconst plotH = ext.pixelHeight\n\n\t\t// Positioning scales \u2014 padded data range covers the full plot rect.\n\t\t// Used for overlay dot placement, the PNG image, and the fold-change line.\n\t\tconst xPlotScale = scaleLinear().domain([this.minLogFoldChange, this.maxLogFoldChange]).range([0, plotW])\n\t\tconst yPlotScale = scaleLinear().domain([this.minLogPValue, this.maxLogPValue]).range([plotH, 0])\n\n\t\t// Visible axis scales \u2014 unpadded domain mapped onto the matching pixel\n\t\t// subrange of the padded plot, so axis ticks land exactly at their data\n\t\t// values in the PNG (mirror of manhattan's yAxisScale).\n\t\tconst xScale = scaleLinear()\n\t\t\t.domain([this.minLogFoldChangeAxis, this.maxLogFoldChangeAxis])\n\t\t\t.range([xPlotScale(this.minLogFoldChangeAxis), xPlotScale(this.maxLogFoldChangeAxis)])\n\t\tconst yScale = scaleLinear()\n\t\t\t.domain([this.minLogPValueAxis, this.maxLogPValueAxis])\n\t\t\t.range([yPlotScale(this.minLogPValueAxis), yPlotScale(this.maxLogPValueAxis)])\n\n\t\treturn {\n\t\t\tsvg: {\n\t\t\t\t//20 is for the term info above the plot\n\t\t\t\theight: plotH + this.topPad + this.bottomPad * 2 + this.offset * 3,\n\t\t\t\twidth: plotW + this.horizPad * 2\n\t\t\t},\n\t\t\ttop: {\n\t\t\t\tx: this.plotX,\n\t\t\t\ty: 5\n\t\t\t},\n\t\t\txAxisLabel: {\n\t\t\t\tx: this.horizPad + plotW / 2 + this.offset,\n\t\t\t\ty: this.topPad + plotH + this.bottomPad + this.offset\n\t\t\t},\n\t\t\txScale: {\n\t\t\t\tscale: xScale,\n\t\t\t\tx: this.plotX,\n\t\t\t\ty: plotH + this.topPad + this.offset * 2\n\t\t\t},\n\t\t\tyAxisLabel: {\n\t\t\t\ttext: `-log10(${this.settings.pValueType} P value)`,\n\t\t\t\tx: this.horizPad / 3,\n\t\t\t\ty: this.topPad + plotH / 2\n\t\t\t},\n\t\t\tyScale: {\n\t\t\t\tscale: yScale,\n\t\t\t\tx: this.horizPad,\n\t\t\t\ty: this.topPad\n\t\t\t},\n\t\t\tplot: {\n\t\t\t\theight: plotH,\n\t\t\t\twidth: plotW,\n\t\t\t\tx: this.plotX,\n\t\t\t\ty: this.topPad\n\t\t\t},\n\t\t\tlogFoldChangeLine: {\n\t\t\t\tx: xPlotScale(0) + this.plotX,\n\t\t\t\ty1: this.topPad,\n\t\t\t\ty2: plotH + this.offset * 4\n\t\t\t},\n\t\t\txPlotScale,\n\t\t\tyPlotScale\n\t\t}\n\t}\n\n\tsetTermInfo(\n\t\tplotDim: VolcanoPlotDimensions\n\t\t// caseColor: string,\n\t\t// controlColor: string\n\t) {\n\t\tif (this.termType != GENE_EXPRESSION && this.termType != DNA_METHYLATION) return\n\t\tconst getLabel = (name: string) => {\n\t\t\tif (name.length >= 25) return name.substring(0, 20) + '...'\n\t\t\treturn name\n\t\t}\n\n\t\treturn {\n\t\t\t//Set slightly above the plot\n\t\t\ty: plotDim.top.y + 10,\n\t\t\tfirst: {\n\t\t\t\t// color: controlColor || this.settings.defaultSignColor,\n\t\t\t\tlabel: getLabel(`${this.config.samplelst.groups[0].name} (${this.response.sample_size1})`),\n\t\t\t\tx: 0\n\t\t\t\t// rectX: this.settings.width/2 - 10,\n\t\t\t},\n\t\t\tsecond: {\n\t\t\t\t// color: caseColor || this.settings.defaultSignColor,\n\t\t\t\tlabel: getLabel(`${this.config.samplelst.groups[1].name} (${this.response.sample_size2})`),\n\t\t\t\tx: this.settings.width\n\t\t\t\t// rectX: this.settings.width/2 + 10,\n\t\t\t}\n\t\t}\n\t}\n\n\tsetPointData(_plotDim: VolcanoPlotDimensions, controlColor: string, caseColor: string) {\n\t\t// Use the server-supplied radius so SVG overlay rings sit exactly on top\n\t\t// of the PNG rings. The view's renderDataPoints draws them at stroke-width\n\t\t// 1 to match the rust PNG's stroke geometry.\n\t\tconst radius = this.dotRadiusPx\n\t\tconst dataCopy: any = structuredClone(this.dataRows)\n\t\tfor (const d of dataCopy) {\n\t\t\tconst highlightKey = this.termType === DNA_METHYLATION ? d.promoter_id : d.gene_name\n\t\t\td.highlighted = this.config?.highlightedData?.includes(highlightKey)\n\t\t\t// Every row in response.data passed the server's thresholds by definition.\n\t\t\td.significant = true\n\t\t\tthis.getGenesColor(d, d.significant, controlColor, caseColor)\n\t\t\tif (d.significant) {\n\t\t\t\tthis.numSignificant++\n\t\t\t\tconst row = [\n\t\t\t\t\t{ value: roundValueAuto(d.fold_change) },\n\t\t\t\t\t{ value: roundValueAuto(d.original_p_value) },\n\t\t\t\t\t{ value: roundValueAuto(d.adjusted_p_value) }\n\t\t\t\t]\n\t\t\t\tif (this.termType == DNA_METHYLATION) {\n\t\t\t\t\trow.splice(0, 0, { value: d.promoter_id || '' }, { value: d.gene_name || '' })\n\t\t\t\t} else {\n\t\t\t\t\trow.splice(0, 0, { value: d.gene_name || '' })\n\t\t\t\t}\n\t\t\t\t//Do not create p-value table data unless user opts to show the table\n\t\t\t\tif (this.settings.showPValueTable) this.pValueTable.rows.push(row)\n\t\t\t} else {\n\t\t\t\tthis.numNonSignificant++\n\t\t\t}\n\t\t\t// Use the exact pixel coords plotters used to rasterize this dot in\n\t\t\t// the PNG (echoed back from rust per-point). Translating by plotX /\n\t\t\t// topPad shifts from inner-plot pixel space to SVG-absolute coords.\n\t\t\t// This is the manhattan trick \u2014 guarantees the SVG overlay ring lands\n\t\t\t// on the rasterized PNG dot regardless of float-vs-int conventions.\n\t\t\td.x = d.pixel_x + this.plotX\n\t\t\td.y = d.pixel_y + this.topPad\n\t\t\td.radius = radius\n\t\t}\n\t\t// Use the server's pre-truncation count so stats are correct even when\n\t\t// dots was capped by maxInteractiveDots.\n\t\tthis.numSignificant = this.response.data.totalSignificantRows\n\t\tthis.numNonSignificant = Math.max(0, this.response.data.totalRows - this.numSignificant)\n\t\t//Sort so the highlighted points appear on top\n\t\tdataCopy.sort((a: any, b: any) => a.highlighted - b.highlighted)\n\t\treturn dataCopy\n\t}\n\n\tgetGenesColor(d: DataPointEntry, significant: boolean, controlColor: string, caseColor: string) {\n\t\tif (!d.gene_name && this.termType != DNA_METHYLATION)\n\t\t\tthrow new Error(`Missing gene_name in data: ${JSON.stringify(d)}`)\n\t\tif (significant) {\n\t\t\tif (controlColor && caseColor) d.color = d.fold_change > 0 ? caseColor : controlColor\n\t\t\telse d.color = this.settings.defaultSignColor\n\t\t} else d.color = this.settings.defaultNonSignColor\n\t}\n\n\tsetStatsData() {\n\t\tconst tableRows = [\n\t\t\t{\n\t\t\t\tlabel: `Percentage of significant ${this.dataType}`,\n\t\t\t\tvalue: roundValueAuto((this.numSignificant * 100) / (this.numSignificant + this.numNonSignificant))\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Number of significant ${this.dataType}`,\n\t\t\t\tvalue: this.numSignificant\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Number of total ${this.dataType}`,\n\t\t\t\tvalue: this.numSignificant + this.numNonSignificant\n\t\t\t}\n\t\t]\n\t\tif (this.termType == GENE_EXPRESSION || this.termType == DNA_METHYLATION) {\n\t\t\ttableRows.push(\n\t\t\t\t{\n\t\t\t\t\tlabel: this.config.samplelst.groups[0].name + ' sample size (control group)',\n\t\t\t\t\tvalue: this.response.sample_size1\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: this.config.samplelst.groups[1].name + ' sample size (case group)',\n\t\t\t\t\tvalue: this.response.sample_size2\n\t\t\t\t}\n\t\t\t)\n\t\t}\n\n\t\tif (this.response.bcv !== undefined && this.response.bcv !== null) {\n\t\t\ttableRows.push({\n\t\t\t\tlabel: 'Biological coefficient of variation',\n\t\t\t\tvalue: roundValueAuto(this.response.bcv)\n\t\t\t})\n\t\t}\n\t\treturn tableRows\n\t}\n\n\tsetPTableColumns() {\n\t\tif (this.termType == DNA_METHYLATION) {\n\t\t\tthis.pValueTable.columns.splice(0, 0, { label: 'Promoter', sortable: true }, { label: 'Gene(s)', sortable: true })\n\t\t} else {\n\t\t\tthis.pValueTable.columns.splice(0, 0, { label: 'Gene Name', sortable: true })\n\t\t}\n\t}\n\n\tsetUserActions() {\n\t\tconst userActions = {\n\t\t\tnoShow: new Set<string>()\n\t\t}\n\t\tif (this.termType == GENE_EXPRESSION) {\n\t\t\tif (this.settings.method == 'edgeR' && getSampleNum(this.config) > 100) {\n\t\t\t\tuserActions.noShow.add('Confounding factors')\n\t\t\t}\n\t\t\tif (this.settings.method == 'wilcoxon') userActions.noShow.add('Confounding factors')\n\t\t}\n\t\treturn userActions\n\t}\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { downloadTable, GeneSetEditUI, MultiTermWrapperEditUI } from '#dom'\nimport { to_svg } from '#src/client'\nimport type { VolcanoDom, VolcanoPlotConfig } from '../VolcanoTypes'\nimport { DNA_METHYLATION, GENE_EXPRESSION } from '#shared/terms.js'\nimport { getGEunit } from '#tw/geneExpression'\n\nexport class VolcanoInteractions {\n\tapp: MassAppApi\n\tdom: VolcanoDom\n\tid: string\n\tpValueTableData: any\n\tdata: any\n\n\tconstructor(app: MassAppApi, id: string, dom: VolcanoDom) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.id = id\n\t\tthis.pValueTableData = []\n\t\tthis.data = []\n\t}\n\n\t/** Launches a multi-term select tree\n\t * On submit, dispatches a plot_edit action with the new confounders */\n\tasync confoundersMenu() {\n\t\tconst state = this.app.getState()\n\t\tconst config = state.plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\t\tif (config.termType !== GENE_EXPRESSION && config.termType !== DNA_METHYLATION) return\n\n\t\t/** Find terms used to create the groups and disable in the\n\t\t * termsetting UI. Prevents users from trying to control for\n\t\t * variables used to create the groups.*/\n\t\tconst allowedGroupNames = new Set([config.samplelst.groups[0].name, config.samplelst.groups[1].name])\n\t\tconst grpTerms: Set<string> = new Set(\n\t\t\t(this.app?.vocabApi?.state.groups || [])\n\t\t\t\t.filter(g => allowedGroupNames.has(g.name))\n\t\t\t\t.flatMap(g =>\n\t\t\t\t\tg.filter.lst.flatMap(f => {\n\t\t\t\t\t\tif (f.tvs?.term) return f.tvs.term\n\t\t\t\t\t\telse return f.lst.map(l => l.tvs.term)\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t)\n\t\tconst disable_terms: any[] = grpTerms.size ? Array.from(grpTerms) : []\n\t\tconst maxNum = config.settings.volcano.method == 'edgeR' ? 1 : 2\n\n\t\tconst ui = new MultiTermWrapperEditUI({\n\t\t\tapp: this.app,\n\t\t\tcallback: async (tws: any) => {\n\t\t\t\tthis.dom.actionsTip.hide()\n\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: { confounderTws: tws }\n\t\t\t\t})\n\t\t\t},\n\t\t\tholder: this.dom.actionsTip.d as any,\n\t\t\theaderText: 'Select confounders',\n\t\t\tmaxNum,\n\t\t\tstate,\n\t\t\ttwList: config.confounderTws,\n\t\t\tdisable_terms\n\t\t})\n\t\tawait ui.renderUI()\n\t}\n\n\tdownload(termType: string) {\n\t\tthis.dom.actionsTip.clear().showunder(this.dom.controls.select('div').node())\n\t\tconst opts = [\n\t\t\t{\n\t\t\t\ttext: 'Download plot',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tconst svg = this.dom.holder.select('svg').node() as Node\n\t\t\t\t\tto_svg(svg, `Differential ${termType} analysis volcano`, { apply_dom_styles: true })\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: 'Download p value table',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tdownloadTable(this.pValueTableData.rows, this.pValueTableData.columns)\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t\tfor (const opt of opts) {\n\t\t\tthis.dom.actionsTip.d.append('div').attr('class', 'sja_menuoption').text(opt.text).on('click', opt.callback)\n\t\t}\n\t}\n\n\tasync highlightDataPoint(value: string) {\n\t\tconst config = this.app.getState().plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\t\tconst highlightedData = config.highlightedData.includes(value)\n\t\t\t? config.highlightedData.filter(d => d !== value)\n\t\t\t: [...config.highlightedData, value]\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { highlightedData }\n\t\t})\n\t}\n\n\t/** When clicking on a data point, launches the box plot in a separate sandbox\n\t * For geneExpression, value == gene symbol */\n\tlaunchBoxPlot(value: string) {\n\t\tconst config = this.app.getState().plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\t\tconst values = {}\n\t\tfor (const group of config.samplelst.groups) {\n\t\t\tvalues[group.name] = {\n\t\t\t\tkey: group.name,\n\t\t\t\tlabel: group.name,\n\t\t\t\tlist: group.values\n\t\t\t}\n\t\t}\n\t\t/** Gene variant and expression terms do not have an id\n\t\t * need to be handled separately.\n\t\t * TODO: In the future with more use cases, simplify this logic. */\n\t\tconst setTerm = () => {\n\t\t\tif (config.termType == GENE_EXPRESSION) {\n\t\t\t\treturn {\n\t\t\t\t\tq: { mode: 'continuous' },\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tgene: value,\n\t\t\t\t\t\tname: value,\n\t\t\t\t\t\ttype: config.termType\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else return config.term\n\t\t}\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'summary',\n\t\t\t\tchildType: 'boxplot',\n\t\t\t\tterm: setTerm(),\n\t\t\t\tterm2: {\n\t\t\t\t\tq: { groups: config.tw.q.groups, type: 'custom-samplelst' },\n\t\t\t\t\tterm: config.tw.term\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\t/** Launch a violin plot for a gene expression data point. */\n\tlaunchViolinGeneExp(value: string) {\n\t\tconst config = this.app.getState().plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'summary',\n\t\t\t\tchildType: 'violin',\n\t\t\t\tterm: {\n\t\t\t\t\tq: { mode: 'continuous' },\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tgene: value,\n\t\t\t\t\t\tname: value,\n\t\t\t\t\t\ttype: config.termType\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tterm2: {\n\t\t\t\t\tq: { groups: config.tw.q.groups, type: 'custom-samplelst' },\n\t\t\t\t\tterm: config.tw.term\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tlaunchGeneSetEdit() {\n\t\tconst plotConfig = this.app.getState().plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\t\tconst holder = this.dom.actionsTip.d.append('div').style('padding', '5px') as any\n\t\tconst limitedGenesList =\n\t\t\tplotConfig.termType === DNA_METHYLATION ? this.data.map(d => d.promoter_id) : this.data.map(d => d.gene_name)\n\t\tnew GeneSetEditUI({\n\t\t\tholder,\n\t\t\tgenome: this.app.opts.genome,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tlimitedGenesList,\n\t\t\tgeneList: plotConfig.highlightedData.map(d => {\n\t\t\t\treturn { gene: d } //Formatted to Gene type in GeneSetEditUI\n\t\t\t}),\n\t\t\tcustomInputs: [\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Cancel highlight',\n\t\t\t\t\tgetDisplayStyle: () => (plotConfig.highlightedData.length > 0 ? '' : 'none'),\n\t\t\t\t\tshowInput: async () => {\n\t\t\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: { highlightedData: [] }\n\t\t\t\t\t\t})\n\t\t\t\t\t\tthis.dom.actionsTip.hide()\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t],\n\t\t\tcallback: async result => {\n\t\t\t\tconst highlightedData = result.geneList.map(d => d.gene)\n\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: { highlightedData }\n\t\t\t\t})\n\t\t\t\tthis.dom.actionsTip.hide()\n\t\t\t}\n\t\t})\n\t}\n\n\t/** When clicking on a DM data point, dispatches a DMR plot that runs DMRCate\n\t * analysis and renders a genome browser Block with DMR regions on their own\n\t * track. */\n\tasync launchDmr(d: { chr: string; start: number; stop: number; promoterId?: string }) {\n\t\tconst config = this.app.getState().plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\n\t\tconst controlColor = config?.tw?.term?.values?.[config?.samplelst?.groups[0].name]?.color || '#ff0000'\n\t\tconst caseColor = config?.tw?.term?.values?.[config?.samplelst?.groups[1].name]?.color || '#0000ff'\n\n\t\tconst label = d.promoterId || `${d.chr}:${d.start}-${d.stop}`\n\t\tconst dmrConfig: any = {\n\t\t\tchartType: 'dmr',\n\t\t\theaderText: `DMR: ${label}`,\n\t\t\tcoordinateOverride: { chr: d.chr, start: d.start, stop: d.stop },\n\t\t\tgroup1: config.samplelst.groups[0].values || [],\n\t\t\tgroup2: config.samplelst.groups[1].values || [],\n\t\t\tgroup1Name: config.samplelst.groups[0].name,\n\t\t\tgroup2Name: config.samplelst.groups[1].name,\n\t\t\tsettings: {\n\t\t\t\tcolors: { group1: controlColor, group2: caseColor }\n\t\t\t}\n\t\t}\n\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: dmrConfig\n\t\t})\n\t}\n\n\t/** Launch a violin/box plot for a DNA methylation promoter.\n\t * Creates a methylation term using the promoter's chr/start/stop coordinates.\n\t * The tw handler fills in id and unit from termdbConfig. */\n\tlaunchDNAMethViolin(d: { chr: string; start: number; stop: number; gene_name?: string; promoter_id?: string }) {\n\t\tconst config = this.app.getState().plots.find((p: VolcanoPlotConfig) => p.id === this.id)\n\t\tconst genomicFeatureType = d.promoter_id ? 'promoter' : 'gene'\n\t\tconst featureName = genomicFeatureType === 'gene' ? d.gene_name?.split(',')[0]?.trim() || '' : ''\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'summary',\n\t\t\t\tchildType: 'violin',\n\t\t\t\tterm: {\n\t\t\t\t\tq: { mode: 'continuous' },\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tgenomicFeatureType,\n\t\t\t\t\t\tfeatureName,\n\t\t\t\t\t\ttype: DNA_METHYLATION,\n\t\t\t\t\t\tchr: d.chr,\n\t\t\t\t\t\tstart: d.start,\n\t\t\t\t\t\tstop: d.stop\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tterm2: {\n\t\t\t\t\tq: { groups: config.tw.q.groups, type: 'custom-samplelst' },\n\t\t\t\t\tterm: config.tw.term\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tasync launchDEGClustering() {\n\t\t//Sort the DEG rows by q-value in ascending order\n\t\tconst geneIndex = this.pValueTableData.columns.findIndex(col => col.label === 'Gene Name')\n\t\tconst adjustedPValIndex = this.pValueTableData.columns.findIndex(col => col.label === 'Adjusted p-value')\n\t\tconst rowsSorted = [...this.pValueTableData.rows].sort((a, b) => {\n\t\t\tconst aQVal = Number(a[adjustedPValIndex].value)\n\t\t\tconst bQVal = Number(b[adjustedPValIndex].value)\n\t\t\treturn aQVal - bQVal\n\t\t})\n\n\t\t// Launch hierCluster for up to 100 DEGs with the smallest q-values\n\t\tconst geneList = rowsSorted.slice(0, 100).map(r => ({ gene: r[geneIndex].value }))\n\n\t\tconst tws = geneList.map(d => {\n\t\t\tconst gene = d.gene\n\t\t\tconst unit = getGEunit(this.app.vocabApi)\n\t\t\tconst name = `${gene} ${unit}`\n\t\t\tconst term = { gene, name, type: GENE_EXPRESSION }\n\t\t\treturn { term, q: {} }\n\t\t})\n\n\t\tconst group = { lst: tws, type: 'hierCluster' }\n\t\tconst customVariable = this.app.getState().plots.find((p: any) => p.id === this.id).tw\n\t\tconst annotationGroup = { lst: [customVariable] }\n\t\tconst config = {\n\t\t\tchartType: 'hierCluster',\n\t\t\ttermgroups: [group, annotationGroup],\n\t\t\tdataType: GENE_EXPRESSION,\n\t\t\tfilter: {\n\t\t\t\tin: true,\n\t\t\t\tjoin: '',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tlst: [{ type: 'tvs', tvs: { term: customVariable.term } }]\n\t\t\t}\n\t\t}\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: structuredClone(config)\n\t\t})\n\t}\n}\n", "import { roundValueAuto } from '#shared/roundValue.js'\nimport type { VolcanoInteractions } from '../interactions/VolcanoInteractions'\nimport type { DataPointEntry } from '../VolcanoTypes'\nimport { DNA_METHYLATION, GENE_EXPRESSION } from '#shared/terms.js'\n\nexport type ActionMenuOpt = {\n\tlabel: string\n\tonClick: () => Promise<void> | void\n}\n\n/** Returns the per-data-point action menu items (Violin / DMR / Box-plot). Used\n * by both the single-gene click flow and the multi-gene click-menu rows so the\n * launchers stay in lock-step. */\nexport function getActionMenuOpts(\n\td: DataPointEntry,\n\ttermType: string,\n\tinteractions: VolcanoInteractions\n): ActionMenuOpt[] {\n\tconst all = [\n\t\t{\n\t\t\tlabel: 'Violin plot',\n\t\t\tisVisible: () => termType === DNA_METHYLATION || termType === GENE_EXPRESSION,\n\t\t\tonClick: async () => {\n\t\t\t\tif (termType === DNA_METHYLATION) interactions.launchDNAMethViolin(d as any)\n\t\t\t\tif (termType === GENE_EXPRESSION) interactions.launchViolinGeneExp(d.gene_name)\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'DMR analysis',\n\t\t\tisVisible: () => termType === DNA_METHYLATION,\n\t\t\tonClick: async () => {\n\t\t\t\tconst dm = d as DataPointEntry & {\n\t\t\t\t\tchr: string\n\t\t\t\t\tstart: number\n\t\t\t\t\tstop: number\n\t\t\t\t\tpromoter_id?: string\n\t\t\t\t\tgene_name?: string\n\t\t\t\t}\n\t\t\t\tawait interactions.launchDmr({\n\t\t\t\t\tchr: dm.chr,\n\t\t\t\t\tstart: dm.start,\n\t\t\t\t\tstop: dm.stop,\n\t\t\t\t\tpromoterId: dm.promoter_id\n\t\t\t\t})\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Box plot',\n\t\t\tisVisible: () => termType === GENE_EXPRESSION,\n\t\t\tonClick: async () => {\n\t\t\t\tinteractions.launchBoxPlot(d.gene_name)\n\t\t\t}\n\t\t}\n\t]\n\treturn all.filter(o => o.isVisible()).map(({ label, onClick }) => ({ label, onClick }))\n}\n\n/** Populates a `table2col` instance with the standard volcano hover rows\n * (gene/promoter, fold-change, original + adjusted p-values). */\nexport function addTooltipRows(d: DataPointEntry, table: any, termType: string) {\n\tif (termType === DNA_METHYLATION) {\n\t\tif ('promoter_id' in d) addTooltipRow(table, 'Promoter', (d as any).promoter_id)\n\t\tif (d.gene_name) addTooltipRow(table, 'Gene(s)', d.gene_name)\n\t} else {\n\t\taddTooltipRow(table, 'Gene name', d.gene_name)\n\t}\n\taddTooltipRow(table, 'log<sub>2</sub>(fold-change)', roundValueAuto(d.fold_change))\n\taddTooltipRow(table, 'Original p-value', roundValueAuto(d.original_p_value))\n\taddTooltipRow(table, 'Adjusted p-value', roundValueAuto(d.adjusted_p_value))\n}\n\nfunction addTooltipRow(table: any, text: string, value: number | string) {\n\tconst [td1, td2] = table.addRow()\n\ttd1.html(text)\n\ttd2.text(value)\n}\n", "import { axisBottom, axisLeft } from 'd3-axis'\nimport { axisstyle, Menu, table2col, renderTable } from '#dom'\nimport { selectAll } from 'd3-selection'\nimport { rgb } from 'd3-color'\nimport { quadtree } from 'd3-quadtree'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport type { DataPointEntry, VolcanoDom, VolcanoPlotDimensions, VolcanoViewData } from '../VolcanoTypes'\nimport type { VolcanoPlotDom } from './VolcanoPlotDom'\nimport type { VolcanoInteractions } from '../interactions/VolcanoInteractions'\nimport { addTooltipRows, getActionMenuOpts } from './DataPointMouseEvents'\nimport { findPointsInRadius } from '../../shared/quadtreeHitTest'\nimport { showResultsTable } from '../../shared/resultsTable'\nimport { DNA_METHYLATION, GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#shared/terms.js'\nimport type { ValidatedVolcanoSettings } from '../settings/Settings'\n\nexport class VolcanoPlotView {\n\tdom: VolcanoDom\n\tinteractions: VolcanoInteractions\n\tsettings: any\n\ttermType: string\n\tvolcanoDom: VolcanoPlotDom\n\tviewData!: VolcanoViewData\n\n\tconstructor(dom: VolcanoDom, interactions: VolcanoInteractions, termType: string) {\n\t\tthis.dom = dom\n\t\tthis.interactions = interactions\n\t\tthis.termType = termType\n\t\tconst actions = this.dom.holder\n\t\t\t.append('div')\n\t\t\t.attr('id', 'sjpp-volcano-actions')\n\t\t\t.style('display', 'block')\n\t\t\t.style('z-index', 1)\n\t\t\t.style('position', 'relative')\n\t\tconst svg = this.dom.holder\n\t\t\t.append('svg')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.attr('id', 'sjpp-volcano-svg')\n\t\t\t.style('vertical-align', 'top')\n\t\tthis.volcanoDom = {\n\t\t\tactions,\n\t\t\tsvg,\n\t\t\tpValueTable: undefined,\n\t\t\ttop: undefined,\n\t\t\txAxis: undefined,\n\t\t\txAxisLabel: undefined,\n\t\t\tyAxis: undefined,\n\t\t\tyAxisLabel: undefined,\n\t\t\tplot: undefined\n\t\t} as Partial<VolcanoPlotDom> as VolcanoPlotDom\n\t}\n\n\trender(settings: ValidatedVolcanoSettings, viewData: VolcanoViewData) {\n\t\tthis.settings = settings\n\t\tthis.viewData = viewData\n\t\tconst plotDim = this.viewData.plotDim\n\n\t\tthis.initDom()\n\n\t\tthis.renderUserActions()\n\t\tthis.renderPlot(plotDim)\n\t\trenderDataPoints(this)\n\t\tthis.renderFoldChangeLine(plotDim)\n\t\tthis.setupOverlayInteractions(plotDim)\n\t\tif (this.settings.showPValueTable) this.renderPValueTable()\n\t}\n\n\tinitDom() {\n\t\tthis.volcanoDom.actions.selectAll('*').remove()\n\t\tthis.volcanoDom.svg.selectAll('*').remove()\n\n\t\tconst svg = this.volcanoDom.svg\n\t\tthis.volcanoDom.top = svg.append('g').attr('id', 'sjpp-volcano-top')\n\t\tthis.volcanoDom.xAxis = svg.append('g').attr('id', 'sjpp-volcano-xAxis')\n\t\tthis.volcanoDom.yAxis = svg.append('g').attr('id', 'sjpp-volcano-yAxis')\n\t\tthis.volcanoDom.xAxisLabel = svg.append('text').attr('id', 'sjpp-volcano-xAxisLabel').attr('text-anchor', 'middle')\n\t\tthis.volcanoDom.yAxisLabel = svg.append('text').attr('id', 'sjpp-volcano-yAxisLabel').attr('text-anchor', 'middle')\n\t\tthis.volcanoDom.plot = svg.append('g').attr('id', 'sjpp-volcano-plot')\n\n\t\tif (!this.settings.showPValueTable) return\n\t\tthis.volcanoDom.pValueTable = this.dom.holder\n\t\t\t.append('div')\n\t\t\t.attr('id', 'sjpp-volcano-pValueTable')\n\t\t\t.attr('data-testid', 'sjpp-volcano-pValueTable')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t}\n\n\trenderUserActions() {\n\t\t//Images may have a large margin. Hide the overflow.\n\t\tthis.dom.actionsTip.d.style('overflow', 'hidden')\n\t\tthis.volcanoDom.actions.style('margin-left', '20px').style('padding', '5px')\n\t\tthis.addActionButton('Confounding factors', [GENE_EXPRESSION, DNA_METHYLATION], () =>\n\t\t\tthis.interactions.confoundersMenu()\n\t\t)\n\t\tthis.addActionButton('Highlight genes', [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION], () =>\n\t\t\tthis.interactions.launchGeneSetEdit()\n\t\t)\n\t\tthis.addActionButton('Statistics', [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION], () => {\n\t\t\tthis.renderStatsMenu()\n\t\t})\n\t\tconst sigLabel =\n\t\t\tthis.termType == DNA_METHYLATION ? 'Number of significant promoters' : 'Number of significant genes'\n\t\tconst numSigGenes = this.viewData.statsData.find(d => d.label == sigLabel)?.value\n\t\tif (numSigGenes) {\n\t\t\tconst sigText = this.termType == DNA_METHYLATION ? `${numSigGenes} DM promoters:` : `${numSigGenes} DE genes:`\n\t\t\tthis.volcanoDom.actions.append('span').text(sigText).style('margin-left', '10px').style('font-weight', 'bold')\n\n\t\t\tthis.addActionButton('Show p-value table', [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION], async () => {\n\t\t\t\t/** TODO: This is very slow to render. Need to optimize rendering\n\t\t\t\t * and server response to increase performance.*/\n\t\t\t\tconst showTable = !this.settings.showPValueTable\n\t\t\t\tawait this.interactions.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.interactions.id,\n\t\t\t\t\tconfig: { settings: { volcano: { showPValueTable: showTable } } }\n\t\t\t\t})\n\t\t\t})\n\t\t}\n\t\tif (numSigGenes && numSigGenes >= 3) {\n\t\t\t// Launch hierCluster for DEGs between the two groups\n\t\t\tthis.addActionButton(\n\t\t\t\t`Hierarchical clustering of ${numSigGenes > 100 ? 'top 100' : numSigGenes} DE genes`,\n\t\t\t\t[GENE_EXPRESSION],\n\t\t\t\tasync () => {\n\t\t\t\t\tawait this.interactions.launchDEGClustering()\n\t\t\t\t}\n\t\t\t)\n\t\t}\n\t}\n\n\t/** Use the termTypes arr to render the buttons in a consistent order */\n\taddActionButton(text: string, termTypes: string[], callback: any) {\n\t\tif (this.viewData.userActions.noShow.has(text)) return\n\t\tif (!termTypes.includes(this.termType)) return\n\t\tconst button = this.volcanoDom.actions\n\t\t\t.append('button')\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.style('margin', '3px')\n\t\t\t.style('padding', '3px')\n\t\t\t.text(text)\n\t\t\t.on('click', async () => {\n\t\t\t\tthis.dom.actionsTip.clear().showunder(button.node())\n\t\t\t\tawait callback()\n\t\t\t})\n\t}\n\n\trenderPlot(plotDim: VolcanoPlotDimensions) {\n\t\tthis.volcanoDom.svg.attr('width', plotDim.svg.width).attr('height', plotDim.svg.height)\n\n\t\tthis.renderTermInfo(plotDim)\n\n\t\tthis.volcanoDom.yAxisLabel.attr(\n\t\t\t'transform',\n\t\t\t`translate(${plotDim.yAxisLabel.x}, ${plotDim.yAxisLabel.y}) rotate(-90)`\n\t\t)\n\t\tthis.setSvgSubscriptLabel(this.volcanoDom.yAxisLabel, '-log', '10', `(${this.settings.pValueType} p-value)`)\n\n\t\tthis.volcanoDom.xAxisLabel.attr('transform', `translate(${plotDim.xAxisLabel.x}, ${plotDim.xAxisLabel.y})`)\n\t\tthis.setSvgSubscriptLabel(this.volcanoDom.xAxisLabel, 'log', '2', '(fold-change)')\n\n\t\tthis.renderScale(plotDim.xScale)\n\t\tthis.renderScale(plotDim.yScale, true)\n\n\t\t// Server-rendered PNG of the full scatter (every dot, non-interactive).\n\t\t// Drawn first so overlay circles + the border rect sit on top. The volcano\n\t\t// binary emits a borderless image whose data extent matches the client's\n\t\t// scales, so placing it over the plot rect aligns dot-for-dot.\n\t\tif (this.viewData.volcanoPng) {\n\t\t\tthis.volcanoDom.plot\n\t\t\t\t.append('image')\n\t\t\t\t.attr('href', `data:image/png;base64,${this.viewData.volcanoPng}`)\n\t\t\t\t.attr('x', plotDim.plot.x)\n\t\t\t\t.attr('y', plotDim.plot.y)\n\t\t\t\t.attr('width', plotDim.plot.width)\n\t\t\t\t.attr('height', plotDim.plot.height)\n\t\t\t\t.attr('preserveAspectRatio', 'none')\n\t\t}\n\t}\n\n\trenderTermInfo(plotDim) {\n\t\tif (this.viewData.termInfo == undefined) return\n\t\tthis.volcanoDom.top.attr('transform', `translate(${plotDim.top.x}, ${plotDim.top.y})`)\n\n\t\tconst y = this.viewData.termInfo.y\n\t\tconst addLabel = term => {\n\t\t\treturn (\n\t\t\t\tthis.volcanoDom.top\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('font-size', '0.9em')\n\t\t\t\t\t.attr('transform', `translate(${term.x}, ${y + 10})`)\n\t\t\t\t\t// .attr('text-anchor', 'start')\n\t\t\t\t\t.text(term.label)\n\t\t\t)\n\t\t}\n\n\t\t// const addRect = (term) => {\n\t\t// \tthis.volcanoDom.top.append('rect')\n\t\t// \t\t.attr('width', 10)\n\t\t// \t\t.attr('height', 10)\n\t\t// \t\t.attr('transform', `translate(${term.rectX}, ${y})`)\n\t\t// \t\t.attr('fill', term.color)\n\t\t// }\n\n\t\tconst firstTerm = this.viewData.termInfo.first\n\t\taddLabel(firstTerm)\n\t\t// addRect(firstTerm)\n\n\t\tconst secondTerm = this.viewData.termInfo.second\n\t\t// addRect(secondTerm)\n\t\tconst secondLabel = addLabel(secondTerm)\n\t\tsecondLabel.attr('text-anchor', 'end')\n\t}\n\n\trenderScale(scale: any, isLeft = false) {\n\t\tconst scaleG = this.volcanoDom[isLeft ? 'yAxis' : 'xAxis']\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${scale.x}, ${scale.y})`)\n\t\t\t.call(isLeft ? axisLeft(scale.scale) : axisBottom(scale.scale))\n\n\t\taxisstyle({\n\t\t\taxis: scaleG,\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t}\n\n\trenderFoldChangeLine(plotDim: VolcanoPlotDimensions) {\n\t\t//logFoldChangeLine\n\t\tthis.volcanoDom.plot\n\t\t\t.append('line')\n\t\t\t.attr('stroke', '#ccc')\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t.attr('x1', plotDim.logFoldChangeLine.x)\n\t\t\t.attr('x2', plotDim.logFoldChangeLine.x)\n\t\t\t.attr('y1', plotDim.logFoldChangeLine.y1)\n\t\t\t.attr('y2', plotDim.logFoldChangeLine.y2)\n\t}\n\n\t/** Quadtree-driven hover & click overlay. Mirrors the manhattan plot:\n\t *   - a transparent SVG rect (cover) sits over the plot rect and absorbs\n\t *     mouse events so coincident dots are all reachable;\n\t *   - hover finds every point within (dotRadiusPx + 3) px and shows a\n\t *     single-gene table2col tooltip OR a multi-gene sortable table;\n\t *   - click launches the per-gene action menu directly for one hit, or\n\t *     opens a click-menu with a row-clickable table for many hits. */\n\tsetupOverlayInteractions(plotDim: VolcanoPlotDimensions) {\n\t\t// Skip for term types with no data point actions (e.g. SCCT) \u2014 preserves\n\t\t// existing behavior where SCCT volcanoes have no per-dot interactions.\n\t\tif (this.termType === SINGLECELL_CELLTYPE) return\n\n\t\tconst points = this.viewData.pointData as DataPointEntry[]\n\t\tif (!points || points.length === 0) return\n\n\t\t// PNG-aligned radius for hover fills + hit-radius. The SVG overlay rings\n\t\t// (points[0].radius) are deliberately drawn smaller to keep their outer\n\t\t// stroke from overhanging the PNG dot.\n\t\tconst dotRadiusPx = this.viewData.plotExtent.dotRadiusPx\n\t\tconst hitRadius = dotRadiusPx + 3\n\t\tconst maxTooltipGenes = this.settings.maxTooltipGenes\n\n\t\t// Hover-ring layer \u2014 visual only, never intercepts mouse events so the\n\t\t// cover keeps absorbing them.\n\t\tconst hoverLayer = this.volcanoDom.plot.append('g').attr('id', 'sjpp-volcano-hover').style('pointer-events', 'none')\n\n\t\t// Cover rect \u2014 last child of plot group so it sits on top of dots,\n\t\t// hover rings, and the fold-change line.\n\t\tconst cover = this.volcanoDom.plot\n\t\t\t.append('rect')\n\t\t\t.attr('id', 'sjpp-volcano-cover')\n\t\t\t.attr('x', plotDim.plot.x)\n\t\t\t.attr('y', plotDim.plot.y)\n\t\t\t.attr('width', plotDim.plot.width)\n\t\t\t.attr('height', plotDim.plot.height)\n\t\t\t.attr('fill', 'transparent')\n\t\t\t.style('pointer-events', 'all')\n\t\t\t.style('cursor', 'default')\n\n\t\t// Quadtree in cover-local space \u2014 d.x/d.y are SVG-absolute, so subtract\n\t\t// the plot rect's origin once when building the tree.\n\t\tconst qt = quadtree<DataPointEntry>()\n\t\t\t.x(d => d.x - plotDim.plot.x)\n\t\t\t.y(d => d.y - plotDim.plot.y)\n\t\t\t.addAll(points)\n\n\t\tconst hoverTip = this.dom.tip\n\t\tconst clickMenu = new Menu({\n\t\t\tpadding: '',\n\t\t\tonHide: () => {\n\t\t\t\tclickMenuIsShown = false\n\t\t\t\t// Drop the persisted highlight once the user dismisses the menu.\n\t\t\t\tdrawHoverRings([])\n\t\t\t}\n\t\t})\n\t\tlet clickMenuIsShown = false\n\n\t\tconst highlightColor = this.settings.defaultHighlightColor\n\t\t// Inset by stroke-width/2 (= 0.5 px for stroke=1) so the orange fill\n\t\t// stops at the ring's inner edge \u2014 the colored stroke stays fully\n\t\t// visible around the highlight instead of being painted over.\n\t\tconst highlightRadius = Math.max(0.5, dotRadiusPx - 0.5)\n\t\tconst drawHoverRings = (dots: DataPointEntry[]) => {\n\t\t\thoverLayer.selectAll('circle').remove()\n\t\t\tfor (const d of dots) {\n\t\t\t\thoverLayer\n\t\t\t\t\t.append('circle')\n\t\t\t\t\t.attr('cx', d.x)\n\t\t\t\t\t.attr('cy', d.y)\n\t\t\t\t\t.attr('r', highlightRadius)\n\t\t\t\t\t.attr('fill', highlightColor)\n\t\t\t\t\t.attr('fill-opacity', 0.9)\n\t\t\t}\n\t\t}\n\n\t\tconst findCandidates = (event: MouseEvent) => {\n\t\t\tconst rect = (cover.node() as SVGRectElement).getBoundingClientRect()\n\t\t\tconst mx = event.clientX - rect.left\n\t\t\tconst my = event.clientY - rect.top\n\t\t\tconst candidates = findPointsInRadius<DataPointEntry>(\n\t\t\t\tqt,\n\t\t\t\tmx,\n\t\t\t\tmy,\n\t\t\t\thitRadius,\n\t\t\t\td => d.x - plotDim.plot.x,\n\t\t\t\td => d.y - plotDim.plot.y\n\t\t\t)\n\t\t\tcandidates.sort((a, b) => a.distance - b.distance)\n\t\t\treturn candidates.map(c => c.point)\n\t\t}\n\n\t\tcover.on('mousemove', (event: MouseEvent) => {\n\t\t\tif (clickMenuIsShown) return\n\t\t\tconst all = findCandidates(event)\n\t\t\tconst shown = all.slice(0, maxTooltipGenes)\n\t\t\tconst additionalCount = all.length - maxTooltipGenes\n\n\t\t\tif (shown.length === 0) {\n\t\t\t\tdrawHoverRings([])\n\t\t\t\thoverTip.hide()\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tdrawHoverRings(shown)\n\t\t\thoverTip.clear().show(event.clientX, event.clientY)\n\n\t\t\tif (shown.length === 1) {\n\t\t\t\tconst table = table2col({ holder: hoverTip.d.append('table') })\n\t\t\t\taddTooltipRows(shown[0], table, this.termType)\n\t\t\t} else {\n\t\t\t\tconst holder = hoverTip.d.append('div').style('margin', '10px')\n\t\t\t\trenderVolcanoGeneTable(holder, shown, this.termType, this.settings.pValueType)\n\t\t\t\tif (additionalCount > 0) {\n\t\t\t\t\tholder\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t\t\t.style('color', '#666')\n\t\t\t\t\t\t.style('font-style', 'italic')\n\t\t\t\t\t\t.text(`and ${additionalCount} more gene${additionalCount > 1 ? 's' : ''}...`)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tcover.on('mouseleave', () => {\n\t\t\t// Don't clear rings while the click menu is showing \u2014 the highlight\n\t\t\t// must stay on the picked dots until the user dismisses the menu.\n\t\t\tif (!clickMenuIsShown) drawHoverRings([])\n\t\t\thoverTip.hide()\n\t\t})\n\n\t\tcover.on('click', (event: MouseEvent) => {\n\t\t\tconst candidates = findCandidates(event)\n\t\t\tif (candidates.length === 0) return\n\t\t\thoverTip.hide()\n\t\t\t// Persist highlight on the picked dots \u2014 clickMenu.onHide clears it.\n\t\t\tdrawHoverRings(candidates)\n\t\t\tclickMenuIsShown = true\n\n\t\t\tif (candidates.length === 1) {\n\t\t\t\t// Use clickMenu (not hoverTip) so the cover's mouseleave handler\n\t\t\t\t// doesn't dismiss this menu when the cursor moves up to a button.\n\t\t\t\topenActionMenu(candidates[0], event, clickMenu, this.termType, this.interactions)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tclickMenu.clear().show(event.clientX, event.clientY)\n\t\t\tconst holder = clickMenu.d.append('div').style('margin', '10px')\n\t\t\trenderVolcanoGeneTable(holder, candidates, this.termType, this.settings.pValueType, {\n\t\t\t\t// Radio buttons (not checkboxes) \u2014 volcano actions only target one gene.\n\t\t\t\tsingleMode: true,\n\t\t\t\tnoButtonCallback: (i: number) => {\n\t\t\t\t\tconst d = candidates[i]\n\t\t\t\t\topenActionMenu(d, event, clickMenu, this.termType, this.interactions)\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\t}\n\n\trenderStatsMenu() {\n\t\t//Render any images. viewModel returns the response array of images or []\n\t\tfor (const img of this.viewData.images || []) {\n\t\t\tthis.dom.actionsTip.d\n\t\t\t\t.append('img')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.style('margin-top', '-30px')\n\t\t\t\t.attr('width', 450)\n\t\t\t\t.attr('height', 450)\n\t\t\t\t.attr('src', img.src)\n\t\t}\n\t\tconst tableHolder = this.dom.actionsTip.d\n\t\t\t.append('div')\n\t\t\t//Show the stats table underneath the images if > 1 image or to the right if only 1 image\n\t\t\t.style('display', this.viewData.images.length == 1 ? 'inline-block' : 'block')\n\t\t\t//Top margin is roughly inline with image however the margins are set by server\n\t\t\t//Likewise the image margins are undetectable.\n\t\t\t//This is a roughly satistifes the different image margin scenarios.\n\t\t\t.style('margin', `${this.viewData.images.length == 1 ? `40px 10px` : `0px 0px`} 0px 5px`)\n\t\t\t.style('vertical-align', 'top')\n\t\tconst table = table2col({ holder: tableHolder })\n\t\tfor (const d of this.viewData.statsData) {\n\t\t\tconst [td1, td2] = table.addRow()\n\t\t\ttd1.text(d.label)\n\t\t\ttd2.style('text-align', 'end').text(d.value)\n\t\t}\n\t}\n\n\trenderPValueTable() {\n\t\tif (!this.settings.showPValueTable) return\n\t\t// Cap rendered rows to prevent browser OOM with large datasets (e.g. 30k+ significant promoters).\n\t\t// The full data is still available in pValueTableData.rows for export/search.\n\t\tconst maxTableRows = 5000\n\t\tconst allRows = this.viewData.pValueTableData.rows\n\t\tconst rows = allRows.length > maxTableRows ? allRows.slice(0, maxTableRows) : allRows\n\t\tif (allRows.length > maxTableRows) {\n\t\t\tthis.volcanoDom.pValueTable\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('color', '#666')\n\t\t\t\t.text(\n\t\t\t\t\t`Showing top ${maxTableRows.toLocaleString()} of ${allRows.length.toLocaleString()} significant results (sorted by fold-change)`\n\t\t\t\t)\n\t\t}\n\t\trenderTable({\n\t\t\tcolumns: this.viewData.pValueTableData.columns,\n\t\t\trows,\n\t\t\tdiv: this.volcanoDom.pValueTable,\n\t\t\tshowLines: true,\n\t\t\tmaxHeight: `${this.viewData.pValueTableData.height}px`,\n\t\t\tresize: true,\n\t\t\theader: { allowSort: true },\n\t\t\tnoRadioBtn: true,\n\t\t\tnoButtonCallback: (i: number) => {\n\t\t\t\t//On click, persistently highlight the data point\n\t\t\t\t// if (this.termType != GENE_EXPRESSION) return\n\t\t\t\tconst gene = this.viewData.pValueTableData.rows[i][0].value as string\n\t\t\t\tif (!gene) return\n\t\t\t\tthis.interactions.highlightDataPoint(gene)\n\t\t\t},\n\t\t\thoverEffects: (tr, row) => {\n\t\t\t\t//May restrict termTypes later\n\t\t\t\t// if (this.termType != GENE_EXPRESSION) return\n\t\t\t\t//Highlight the data point when hovering over the table row\n\t\t\t\t//Previously highlighted data points are not affected\n\t\t\t\tconst circles = this.volcanoDom.plot.selectAll('circle').nodes()\n\t\t\t\tconst dataKey = this.termType === DNA_METHYLATION ? 'promoter_id' : 'gene_name'\n\t\t\t\tconst circle = circles.find((d: any) => d.__data__[dataKey] == row[0].value) as any\n\t\t\t\tif (!circle || circle.__data__.highlighted) return\n\n\t\t\t\t/** Circles may render behind several other circles, making it hard\n\t\t\t\t * to see the highlight. Clone the circle to appear on top of the\n\t\t\t\t * elements, then destroy. */\n\t\t\t\tlet clone\n\t\t\t\ttr.on('mouseover', () => {\n\t\t\t\t\tif (circle.__data__.highlighted || clone) return\n\t\t\t\t\tclone = this.volcanoDom.plot.node()?.appendChild(circle.cloneNode(true))\n\t\t\t\t\tclone.setAttribute('fill-opacity', 0.9)\n\t\t\t\t})\n\t\t\t\ttr.on('mouseleave', () => {\n\t\t\t\t\tif (!clone) return\n\t\t\t\t\tclone.remove()\n\t\t\t\t\tclone = null\n\t\t\t\t})\n\t\t\t\t//All other circles appear dimmed on hover\n\t\t\t\tthis.volcanoDom.pValueTable.on('mouseover', () => {\n\t\t\t\t\tselectAll(circles).attr('stroke-opacity', 0.075)\n\t\t\t\t})\n\t\t\t\tthis.volcanoDom.pValueTable.on('mouseleave', () => {\n\t\t\t\t\tselectAll(circles).attr('stroke-opacity', (d: any) => (d.significant ? 0.35 : 0.2))\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tsetSvgSubscriptLabel(textElem: any, prefix: string, subscript: string, suffix: string) {\n\t\ttextElem.text(null)\n\t\ttextElem.append('tspan').text(prefix)\n\t\ttextElem.append('tspan').attr('baseline-shift', 'sub').attr('font-size', '0.7em').text(subscript)\n\t\ttextElem.append('tspan').text(suffix)\n\t}\n}\n\nfunction renderDataPoints(self: any) {\n\t// Visual-only circles. The cover rect added in setupOverlayInteractions\n\t// drives all hover/click \u2014 we strip pointer-events here so events fall\n\t// through to the cover. The p-value table hover-clone effect at\n\t// renderPValueTable() still finds these via selectAll('circle').\n\tself.volcanoDom.plot\n\t\t.selectAll('circle')\n\t\t.data(self.viewData.pointData)\n\t\t.enter()\n\t\t.append('circle')\n\t\t.attr('stroke', (d: DataPointEntry) => rgb(d.color).formatHex())\n\t\t.attr('stroke-opacity', (d: DataPointEntry) => (d.significant ? 0.35 : 0.2))\n\t\t// Match the rust PNG's stroke-width (1) so the overlay ring sits\n\t\t// exactly on top of the rasterized dot.\n\t\t.attr('stroke-width', 1)\n\t\t.attr('fill', self.settings.defaultHighlightColor)\n\t\t.attr('fill-opacity', (d: DataPointEntry) => (d.highlighted ? 0.9 : 0))\n\t\t.attr('cx', (d: DataPointEntry) => d.x)\n\t\t.attr('cy', (d: DataPointEntry) => d.y)\n\t\t.attr('r', (d: DataPointEntry) => d.radius)\n\t\t.style('pointer-events', 'none')\n}\n\n/** Renders the multi-gene table used by both the hover tooltip (when >1 dot\n * is in range) and the click menu. Reuses showResultsTable for sortable\n * columns; volcano omits the `app` arg so manhattan-only Lollipop/Matrix\n * buttons stay hidden. The p-value column matches `settings.pValueType` so\n * the table aligns with the y-axis basis (original vs adjusted). */\nfunction renderVolcanoGeneTable(\n\tholder: any,\n\tdots: DataPointEntry[],\n\ttermType: string,\n\tpValueType: 'original' | 'adjusted',\n\textra: Record<string, any> = {}\n) {\n\tconst isDM = termType === DNA_METHYLATION\n\tconst pLabel = `${pValueType.charAt(0).toUpperCase()}${pValueType.slice(1)} p-value`\n\tconst pField = `${pValueType}_p_value` as 'original_p_value' | 'adjusted_p_value'\n\tconst columns = isDM\n\t\t? [\n\t\t\t\t{ label: 'Promoter' },\n\t\t\t\t{ label: 'Gene(s)' },\n\t\t\t\t{ label: 'log\u2082(FC)', sortable: true },\n\t\t\t\t{ label: pLabel, sortable: true }\n\t\t  ]\n\t\t: [{ label: 'Gene' }, { label: 'log\u2082(FC)', sortable: true }, { label: pLabel, sortable: true }]\n\tconst rows = dots.map(d => {\n\t\tconst fc = { value: roundValueAuto(d.fold_change) }\n\t\tconst pval = { value: roundValueAuto(d[pField]) }\n\t\tif (isDM) {\n\t\t\treturn [{ value: (d as any).promoter_id || '' }, { value: d.gene_name || '' }, fc, pval]\n\t\t}\n\t\treturn [{ value: d.gene_name || '' }, fc, pval]\n\t})\n\tshowResultsTable({\n\t\ttableDiv: holder,\n\t\tdataItems: dots,\n\t\tgetGene: (d: any) => d.gene_name,\n\t\tcolumns,\n\t\trows,\n\t\t...extra\n\t} as any)\n}\n\n/** Opens the per-gene action menu at the click point. Action buttons sit at\n * the top of the menu; the same single-gene info shown on hover (gene name,\n * fold-change, p-values) is rendered below so the user can confirm what\n * they're acting on. Used for both the single-hit click flow and the\n * row-drill-down from the multi-hit click menu. */\nfunction openActionMenu(\n\td: DataPointEntry,\n\tevent: MouseEvent,\n\thostMenu: any,\n\ttermType: string,\n\tinteractions: VolcanoInteractions\n) {\n\tconst opts = getActionMenuOpts(d, termType, interactions)\n\thostMenu.clear().show(event.clientX, event.clientY)\n\tconst container = hostMenu.d.append('div').style('margin', '10px')\n\n\tif (opts.length > 0) {\n\t\tconst buttonRow = container.append('div').style('margin-bottom', '10px')\n\t\tfor (const opt of opts) {\n\t\t\tbuttonRow\n\t\t\t\t.append('button')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t.text(opt.label)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\thostMenu.hide()\n\t\t\t\t\tawait opt.onClick()\n\t\t\t\t})\n\t\t}\n\t}\n\n\tconst table = table2col({ holder: container.append('table') })\n\taddTooltipRows(d, table, termType)\n}\n", "import type { ControlInputEntry } from '#mass/types/mass'\nimport type { VolcanoPlotConfig } from './VolcanoTypes'\nimport { getSampleNum } from './settings/defaults'\nimport { DNA_METHYLATION, GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#shared/terms.js'\n\n/** Handles settings the controls in the menu based on the app\n * termType.\n *\n * Add additional term type specific controls similar to\n * addGeneExpressionControlInputs(), called in\n * getVolcanoControlInputs(). Add the type to settings/Settings.ts\n *\n * If control should show for multiple but not all term types,\n * then use the getDisplayStyle arg in the control object.\n * //getDisplayStyle: () => {}\n *\n * Preferably, keep all the display (e.g. colors, sizes, etc.) controls\n * at the bottom of the list or at least together\n */\n\nexport class VolcanoControlInputs {\n\tconfig: any\n\tsampleNum?: number\n\t/** term type used to determine which controls to show */\n\ttermType: string\n\t/** control inputs for controls init */\n\tinputs: ControlInputEntry[]\n\tconstructor(config: VolcanoPlotConfig, termType: string) {\n\t\tthis.config = config\n\t\tif (this.config.termType == GENE_EXPRESSION) this.sampleNum = getSampleNum(config)\n\t\tthis.termType = termType\n\t\t//Populated with the default controls for the volcano plot\n\t\tthis.inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'P value significance (-log\u2081\u2080)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'pValue',\n\t\t\t\ttitle: 'The p-value threshold to determine statistical significance',\n\t\t\t\tmin: 0,\n\t\t\t\t// 5e-324 is the smallest positive number greater than 0 representable\n\t\t\t\t// in IEEE 64-bit floating point (i.e. javascripts native Number.MIN_VALUE)\n\t\t\t\t// -Math.log10(5e-324) = 323.3\n\t\t\t\tmax: 323.3,\n\t\t\t\tstep: 1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P value',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'pValueType',\n\t\t\t\ttitle: 'Toggle between original and adjusted pvalues for volcano plot',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Adjusted', value: 'adjusted' },\n\t\t\t\t\t{ label: 'Original', value: 'original' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Fold change (log\u2082)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'foldChangeCutoff',\n\t\t\t\ttitle: 'The fold change threshold to determine biological significance',\n\t\t\t\tmin: -10,\n\t\t\t\tmax: 10\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Max interactive dots',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'maxInteractiveDots',\n\t\t\t\ttitle:\n\t\t\t\t\t'Cap on the number of top-significant points the server returns as interactive overlay circles. The PNG still shows every dot.',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 20000,\n\t\t\t\tstep: 100\n\t\t\t},\n\t\t\t//Preferably, keep all the display (e.g. colors, sizes, etc.) controls\n\t\t\t//at the bottom of the list or at least together\n\t\t\t{\n\t\t\t\tlabel: 'Plot height',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'height',\n\t\t\t\ttitle: 'Height of the plot in pixels',\n\t\t\t\tmin: 300,\n\t\t\t\tmax: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot width',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'width',\n\t\t\t\ttitle: 'Width of the plot in pixels',\n\t\t\t\tmin: 300,\n\t\t\t\tmax: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Significant value color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\ttitle: 'Default color for significant data points.',\n\t\t\t\tsettingsKey: 'defaultSignColor',\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\tif (this.config.termType == SINGLECELL_CELLTYPE) return 'none'\n\t\t\t\t\tconst controlColor = this.config.tw?.term?.values?.[this.config.samplelst.groups[0].name]?.color\n\t\t\t\t\tconst caseColor = this.config.tw?.term?.values?.[this.config.samplelst.groups[1].name].color\n\t\t\t\t\tif (controlColor && caseColor) return 'none'\n\t\t\t\t\telse return ''\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Non-significant value color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\ttitle: 'Default color for non-significant data points.',\n\t\t\t\tsettingsKey: 'defaultNonSignColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Highlight color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\ttitle: 'Default color for highlighted data points.',\n\t\t\t\tsettingsKey: 'defaultHighlightColor'\n\t\t\t}\n\t\t]\n\n\t\tthis.setVolcanoControlInputs()\n\t}\n\n\t/** Add more term type specific controls here. */\n\tsetVolcanoControlInputs() {\n\t\tthis.addGeneExpControlInputs()\n\t\tthis.addDNAMethControlInputs()\n\t\tthis.addSingleCellCTControlInputs()\n\t}\n\n\taddGeneExpControlInputs() {\n\t\tif (this.termType !== GENE_EXPRESSION) return\n\t\tconst geInputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Minimum read count',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'minCount',\n\t\t\t\ttitle: 'The smallest number of reads required for a gene to be considered in the analysis',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 10000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Minimum total read count',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'minTotalCount',\n\t\t\t\ttitle: 'The smallest total number of reads required for a gene to be considered in the analysis',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 10000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'CPM cutoff',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'cpmCutoff',\n\t\t\t\ttitle: 'The minimum normalized expression threshold to retain only genes with sufficient expression',\n\t\t\t\tmin: 0\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Method',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'method',\n\t\t\t\ttitle: 'Toggle between analysis methods',\n\t\t\t\toptions: this.getMethodOptions()\n\t\t\t}\n\t\t\t// {\n\t\t\t// \tlabel: 'Rank Genes by',\n\t\t\t// \ttype: 'radio',\n\t\t\t// \tchartType: 'volcano',\n\t\t\t// \tsettingsKey: 'rankBy',\n\t\t\t// \ttitle: 'Rank genes by either the absolute value of the fold change or the variance',\n\t\t\t// \toptions: [\n\t\t\t// \t\t{ label: 'abs(Fold Change)', value: 'abs(foldChange)' },\n\t\t\t// \t\t{ label: 'Variance', value: 'variance' }\n\t\t\t// \t],\n\t\t\t// \t//TODO: will enable this feature when there is backhand support\n\t\t\t// \tgetDisplayStyle: () => 'none'\n\t\t\t// }\n\t\t]\n\n\t\tthis.inputs.splice(0, 0, ...geInputs)\n\t}\n\n\taddDNAMethControlInputs() {\n\t\tif (this.termType !== DNA_METHYLATION) return\n\t\tconst dmInputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Min samples per group',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'minSamplesPerGroup',\n\t\t\t\ttitle: 'Minimum non-NA samples required per group for a promoter to be tested',\n\t\t\t\tmin: 1,\n\t\t\t\tmax: 100\n\t\t\t}\n\t\t]\n\t\tthis.inputs.splice(0, 0, ...dmInputs)\n\t}\n\n\taddSingleCellCTControlInputs() {\n\t\tif (this.termType !== SINGLECELL_CELLTYPE) return\n\n\t\tconst scctInputs = []\n\n\t\tthis.inputs.splice(0, 0, ...scctInputs)\n\t}\n\n\tgetMethodOptions() {\n\t\tif (this.termType !== GENE_EXPRESSION) return\n\t\tconst settings = this.config.settings.volcano\n\t\tconst features = JSON.parse(sessionStorage.getItem('optionalFeatures') as string)\n\t\tif (features?.runDE_methods?.length) {\n\t\t\tconst opts: { label: string; value: string }[] = []\n\t\t\tfor (const m of features.runDE_methods) {\n\t\t\t\topts.push({ label: m, value: m.toLowerCase() })\n\t\t\t}\n\t\t\treturn opts\n\t\t}\n\t\tif (this.sampleNum! < settings!.sampleNumCutoff) {\n\t\t\treturn [\n\t\t\t\t{ label: 'edgeR', value: 'edgeR' },\n\t\t\t\t{ label: 'Wilcoxon', value: 'wilcoxon' },\n\t\t\t\t{ label: 'Limma', value: 'limma' }\n\t\t\t]\n\t\t} else return [{ label: 'Wilcoxon', value: 'wilcoxon' }]\n\t}\n}\n", "import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent, type AppApi } from '#rx'\nimport { PlotBase } from '../PlotBase'\nimport { fillTermWrapper } from '#termsetting'\nimport { Menu, sayerror } from '#dom'\nimport { controlsInit } from '../controls'\nimport { getDefaultVolcanoSettings, validateVolcanoSettings } from './settings/defaults'\nimport type { VolcanoOpts, VolcanoDom } from './VolcanoTypes'\nimport { VolcanoModel } from './model/VolcanoModel'\nimport { VolcanoViewModel } from './viewModel/VolcanoViewModel'\nimport { VolcanoInteractions } from './interactions/VolcanoInteractions'\nimport { VolcanoPlotView } from './view/VolcanoPlotView'\nimport { VolcanoControlInputs } from './VolcanoControlInputs'\nimport { getCombinedTermFilter } from '#filter'\nimport { GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#shared/terms.js'\n\nclass Volcano extends PlotBase implements RxComponent {\n\tstatic type = 'volcano'\n\ttype: string\n\tcomponents: { controls: any }\n\tdom: VolcanoDom\n\tinteractions?: VolcanoInteractions\n\tmodel!: VolcanoModel\n\tview!: VolcanoPlotView\n\ttermType: string\n\n\tconstructor(opts: VolcanoOpts, api) {\n\t\tsuper(opts, api)\n\t\tif (this.opts.parentId) this.parentId = this.opts.parentId\n\t\tthis.type = Volcano.type\n\t\tthis.components = {\n\t\t\tcontrols: {}\n\t\t}\n\n\t\tthis.termType = opts.termType\n\t\tconst holder = opts.holder\n\t\t\t.classed('sjpp-volcano-main', true)\n\t\t\t.attr('data-testid', `sjpp-volcano-main-${opts.termType}`)\n\t\t//Either allow a node to be passed or create a new div\n\t\tconst controls = typeof opts.controls == 'object' ? opts.controls : holder || (holder as any).append('div')\n\t\tconst error = opts.holder\n\t\t\t.append('div')\n\t\t\t.attr('id', 'sjpp-volcano-error')\n\t\t\t.attr('data-testid', `sjpp-volcano-error-${opts.termType}`)\n\t\t\t.style('opacity', 0.75) as any\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tcontrols,\n\t\t\terror,\n\t\t\twait: holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('id', 'sjpp-volcano-wait')\n\t\t\t\t.attr('data-testid', `sjpp-volcano-wait-${opts.termType}`)\n\t\t\t\t.style('opacity', 0.75)\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.text('Loading...') as any,\n\t\t\ttip: new Menu({ padding: '' }),\n\t\t\tactionsTip: new Menu({ padding: '' })\n\t\t}\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config: any = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\tconst parentConfig: any = this.parentId && 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: Object.assign({}, config, {\n\t\t\t\tsettings: {\n\t\t\t\t\tvolcano: config.settings.volcano\n\t\t\t\t}\n\t\t\t}),\n\t\t\ttermfilter\n\t\t}\n\t}\n\n\tasync setControls() {\n\t\tconst plotConfig = this.app.getState().plots.find((p: any) => p.id === this.id)\n\t\tconst controls = new VolcanoControlInputs(plotConfig, this.termType)\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.controls.style('display', 'inline-block'),\n\t\t\tinputs: controls.inputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.volcano', () => this.interactions!.download(this.termType))\n\t\tif (plotConfig.chartType == 'differentialAnalysis')\n\t\t\tthis.components.controls.on('helpClick.differentialAnalysis', () =>\n\t\t\t\t//Opens the page for the differential analysis wiki\n\t\t\t\t//Can't put in parent as DA does not have a controls component\n\t\t\t\twindow.open('https://github.com/stjude/proteinpaint/wiki/Differential-analysis')\n\t\t\t)\n\t}\n\n\tasync init() {\n\t\tthis.interactions = new VolcanoInteractions(this.app, this.id, this.dom)\n\t\tthis.model = new VolcanoModel(this.app, this.termType)\n\t\tthis.view = new VolcanoPlotView(this.dom, this.interactions, this.termType)\n\t\tawait this.setControls()\n\t}\n\n\tasync main() {\n\t\tif (!this.interactions) throw new Error('Volcano Interactions not initialized')\n\t\tif (!this.model) throw new Error('Volcano Model not initialized')\n\t\tif (!this.view) throw new Error('Volcano View not initialized')\n\n\t\tconst config = structuredClone(this.state.config)\n\t\t//TODO: Fix this to use parentId instead\n\t\tif (config.chartType != this.type && config.childType != this.type) return\n\n\t\tconst settings = config.settings.volcano\n\t\ttry {\n\t\t\t//Only show Loading for data requests that take longer than 500ms\n\t\t\tconst showWait = setTimeout(() => {\n\t\t\t\tthis.dom.wait.style('display', 'block')\n\t\t\t}, 500)\n\n\t\t\t/** Fetch data */\n\t\t\tconst response = await this.model.getData(config, settings)\n\t\t\tthis.dom.error.text('')\n\t\t\tif (!response || response.error || !response.data || !response.data.volcanoPng || !response.data.totalRows) {\n\t\t\t\tsayerror(this.dom.error, response?.error || 'No data returned from server')\n\t\t\t\tclearTimeout(showWait)\n\t\t\t\tthis.dom.wait.style('display', 'none')\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t/** Format response into an object for rendering */\n\t\t\tconst viewModel = new VolcanoViewModel(config, response, settings)\n\t\t\t//Pass table data for downloading\n\t\t\tthis.interactions.pValueTableData = viewModel.viewData.pValueTableData\n\t\t\tthis.interactions.data = response.data.dots\n\n\t\t\t/** Render formatted data */\n\t\t\tthis.view.render(settings, viewModel.viewData)\n\n\t\t\tif (!response.data.dots.length) {\n\t\t\t\tthis.dom.error.text('No points passed the significance thresholds').style('color', '#555')\n\t\t\t}\n\n\t\t\tclearTimeout(showWait)\n\t\t\tthis.dom.wait.style('display', 'none')\n\t\t} catch (e: any) {\n\t\t\tif (e instanceof Error) console.error(e.message || e)\n\t\t\telse if (e.stack) console.log(e.stack)\n\t\t\tthrow e\n\t\t}\n\t}\n}\n\nexport const volcanoInit = getCompInit(Volcano)\nexport const componentInit = volcanoInit\n\nexport async function getPlotConfig(opts: any, app: AppApi) {\n\tif (!opts.termType) throw new Error('.termType is required')\n\n\tconst config = {\n\t\tsettings: {\n\t\t\tvolcano: getDefaultVolcanoSettings(opts.overrides, opts)\n\t\t},\n\t\thighlightedData: opts.highlightedData || [],\n\t\ttermType: opts.termType\n\t}\n\n\t//Define Gene Expression config\n\tif (opts.termType == GENE_EXPRESSION) {\n\t\tif (opts.confounderTws) {\n\t\t\ttry {\n\t\t\t\tfor (const tw of opts.confounderTws) {\n\t\t\t\t\tawait fillTermWrapper(tw, app.vocabApi)\n\t\t\t\t}\n\t\t\t} catch (e: any) {\n\t\t\t\tconsole.error(e.message || e)\n\t\t\t\tthrow new Error(`Volcano getPlotConfig() failed to fill confounder term wrappers: ${e}`)\n\t\t\t}\n\t\t}\n\t\tObject.assign(config, {\n\t\t\tconfounderTws: opts.confounderTws || [],\n\t\t\tsamplelst: opts.samplelst\n\t\t})\n\t}\n\n\t//Define Single Cell Cell Type config\n\tif (opts.termType == SINGLECELL_CELLTYPE) {\n\t\tObject.assign(config, {\n\t\t\t//TODO: Fix this logic\n\t\t\tsample: opts.experimentID || opts.sample || opts.samples?.[0]?.experiments[0]?.experimentID,\n\t\t\ttermId: app.vocabApi.termdbConfig.queries.singleCell.DEgenes.termId,\n\t\t\t//TODO: 'Cluster' is a fallback for development\n\t\t\t//Should require opts.categoryName in the future\n\t\t\tcategoryName: opts.categoryName || 'Cluster'\n\t\t})\n\t}\n\n\t//Validate user submitted unavailable/inappropriate settings\n\tvalidateVolcanoSettings(config, opts)\n\n\treturn copyMerge(config, opts)\n}\n"],
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