@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/Volcano-FCCWUMX7.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/volcano/promoterLabel.ts", "../plots/volcano/viewModel/VolcanoViewModel.ts", "../plots/volcano/interactions/VolcanoInteractions.ts", "../plots/volcano/view/VolcanoPlotView.ts", "../plots/volcano/VolcanoControlInputs.ts", "../plots/volcano/Volcano.ts"],
-  "sourcesContent": ["import type { DiffMethEntry } from '#types'\n\n/** Display label for a differential methylation promoter.\n *\n * promoter_id is built at ingest as `<gene>.p<n>_<chr>:<start>-<stop>` (or\n * `<gene>_<chr>:<start>-<stop>` when the gene has a single promoter) \u2014 see\n * utils/dnaMeth/build_element_matrix.py. It is an identifier, not a label: it\n * is the highlight key and the handle for the DMR drill-down, so it is never\n * rewritten, only formatted for display.\n *\n * Every place this is shown already has a separate Gene(s) column, making the\n * gene prefix pure duplication. What is left that a reader actually needs is\n * which TSS of the gene it is, plus a copy-pasteable region:\n *\n *   NKAP.p4_chrX:119943104-119945251  ->  p4 \u00B7 chrX:119943104-119945251\n *\n * Coordinates are printed unformatted so the region can be copied straight into\n * a genome browser or a tabix query.\n *\n * Coordinates come from the entry's own chr/start/stop fields rather than by\n * re-parsing the id, so a gene symbol containing '_' or ':' cannot corrupt them.\n * Only the `p<n>` segment is recovered from the id, and only when the id really\n * has that shape \u2014 anything unexpected falls back to the raw id unchanged.\n */\n/** Noun for the rows of a differential methylation result, for counts and column\n * headers: \"35,584 DM promoters\" is wrong when the run tested eQTM blocks.\n *\n * Derived from the selected element class rather than from the server response, so\n * it needs no extra plumbing: the picker already knows which class was requested,\n * and an absent or 'promoter' value is the legacy single-matrix case.\n *\n * Deliberately not a lookup keyed by every possible class name. Dataset configs can\n * declare arbitrary keys, so an unrecognised one falls back to the neutral\n * \"elements\" instead of mislabelling rows as promoters. Add a case here only for a\n * class whose singular/plural reads badly as the generic term.\n */\nexport function elementNoun(elementType?: string): { one: string; many: string } {\n\tswitch (elementType) {\n\t\tcase undefined:\n\t\tcase '':\n\t\tcase 'promoter':\n\t\t\treturn { one: 'Promoter', many: 'promoters' }\n\t\t/* Two different promoter DEFINITIONS, deliberately given distinct nouns. 'promoter' is\n\t\tthe TSS -1500/+500 window (Bibikova 2011 / Sandoval 2011 -- the 450K array's\n\t\tTSS1500+TSS200 categories); 'promoter_pls' is the ENCODE cCRE promoter-like element,\n\t\t~349 bp, i.e. the CpG-island core with the shores removed. They cover different numbers\n\t\tof genes and their hit counts are NOT comparable, so the UI must never call both\n\t\t\"promoters\". */\n\t\tcase 'promoter_pls':\n\t\t\treturn { one: 'cCRE promoter', many: 'cCRE promoters' }\n\t\tcase 'eqtm_block':\n\t\t\treturn { one: 'eQTM block', many: 'eQTM blocks' }\n\t\tcase 'enhancer':\n\t\t\treturn { one: 'Enhancer', many: 'enhancers' }\n\t\t/* Distal and proximal are separate ENCODE classes and separate hypotheses -- dELS are\n\t\tthe intronic/intergenic enhancers where myeloma hypermethylation concentrates, pELS sit\n\t\twithin 2 kb of a TSS and behave more promoter-like. There are 4.5x as many dELS, so their\n\t\thit counts are not comparable to each other either. Naming them apart keeps a reader from\n\t\treading two runs as the same analysis. */\n\t\tcase 'enhancer_distal':\n\t\t\treturn { one: 'Distal enhancer', many: 'distal enhancers' }\n\t\tcase 'enhancer_proximal':\n\t\t\treturn { one: 'Proximal enhancer', many: 'proximal enhancers' }\n\t\tdefault:\n\t\t\treturn { one: 'Element', many: 'elements' }\n\t}\n}\n\nexport function formatPromoterLabel(d: Partial<DiffMethEntry> | undefined): string {\n\tif (!d) return ''\n\tconst id = d.promoter_id || ''\n\tconst { chr, start, stop } = d as DiffMethEntry\n\t// without coordinates there is nothing better to show than the id itself\n\tif (!chr || !Number.isFinite(start) || !Number.isFinite(stop)) return id\n\n\tconst region = `${chr}:${start}-${stop}`\n\n\t/* Match the promoter index only when it sits immediately before the trailing\n\t   `_<chr>:<start>-<stop>`, so a gene literally named e.g. \"ABC.p2\" cannot be\n\t   mistaken for an index. Genes with one promoter carry no index at all. */\n\tconst idx = id.match(/\\.(p\\d+)_[^_]*:\\d+-\\d+$/)\n\treturn idx ? `${idx[1]} \u00B7 ${region}` : region\n}\n", "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 { formatPromoterLabel, elementNoun } from '../promoterLabel'\nimport { getGroupColors } from '../colors'\nimport { DATermTypes as tt, enabledTermTypes } from '../../diffAnalysis/enabledTermTypes'\n\n/* Group names are user-supplied and can be arbitrarily long, so they are shortened before going\ninto any label. Shared by the two group labels above the plot and by the delta-beta axis label,\nso the two shorten identically rather than drifting apart. */\nfunction shortenGroupName(name: string) {\n\tif (name.length >= 25) return name.substring(0, 20) + '...'\n\treturn name\n}\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// DAP files carry a single FDR (adjusted p-value); other term types report\n\t\t\t\t// both a raw and an adjusted p-value.\n\t\t\t\t...(config.termType == tt.PROTEOME_DAP\n\t\t\t\t\t? [{ label: 'FDR', sortable: true }]\n\t\t\t\t\t: [\n\t\t\t\t\t\t\t{ label: 'Original p-value', sortable: true },\n\t\t\t\t\t\t\t{ label: 'Adjusted p-value', sortable: true }\n\t\t\t\t\t  ])\n\t\t\t],\n\t\t\t/** Filled in setPointData(), one row per threshold-passing dot. Populated even when the\n\t\t\t * table is hidden \u2014 the download reads it. */\n\t\t\trows: [],\n\t\t\trowKeys: new Map(),\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\t// sort by fold change, for the rendered table and the downloaded one alike\n\t\tconst foldChangeIdx = this.pValueTable.columns.findIndex(c => c.label.includes('log\u2082(fold-change)'))\n\t\tthis.pValueTable.rows.sort((a: any, b: any) => b[foldChangeIdx].value - a[foldChangeIdx].value)\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\tprovenance: this.setProvenance(),\n\t\t\tuserActions: this.setUserActions(),\n\t\t\tdeltaBetaAxisLabel: this.setDeltaBetaAxisLabel(),\n\t\t\tvolcanoPng: response.data.volcanoPng,\n\t\t\tplotExtent: response.data.plotExtent\n\t\t}\n\t}\n\n\t/* The delta-beta axis used to read \"\u0394\u03B2 (case \u2212 control)\". Those are positional roles, not\n\tnames, so the plot showed the size of an effect but not its direction -- you had to already\n\tknow which group landed in which slot, or open a downloaded file and read the provenance line.\n\tName the groups instead, in subtraction order (case first), so the axis states what it plots.\n\n\tReturns undefined when the group names are not available; the view falls back to the old\n\twording rather than rendering a broken label. */\n\tsetDeltaBetaAxisLabel(): string | undefined {\n\t\tconst groups = this.config?.samplelst?.groups\n\t\tconst control = groups?.[0]?.name\n\t\tconst cases = groups?.[1]?.name\n\t\tif (!control || !cases) return undefined\n\t\treturn `\u0394\u03B2 (${shortenGroupName(cases)} \u2212 ${shortenGroupName(control)})`\n\t}\n\n\tsetDataType() {\n\t\tif (this.termType == tt.GENE_EXPRESSION) return 'genes'\n\t\t/* Methylation rows are only promoters when the promoter class was tested. With an\n\t\telement class selected they are eQTM blocks or cCREs, and calling them promoters\n\t\tmisreports what was analysed in the stats panel, the row count, and the p-value\n\t\ttable header. Taken from the selected class rather than the server response so no\n\t\textra field has to be plumbed through. */\n\t\tif (this.termType == tt.DNA_METHYLATION) return elementNoun(this.settings?.elementType).many\n\t\tif (this.termType == tt.SINGLECELL_CELLTYPE) return 'genes'\n\t\tif (this.termType == tt.PROTEOME_DAP) return 'proteins'\n\t\tif (this.termType == tt.SINGLECELL_GENE_EXPRESSION) return 'cells'\n\t\tthrow 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: this.termType == tt.PROTEOME_DAP ? '-log10(FDR)' : `-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 (!enabledTermTypes.has(this.termType as any)) return\n\n\t\tif (this.termType == tt.PROTEOME_DAP) {\n\t\t\t// FIXME this shouldn't be needed. there should be a way for caller to supply names for each group, and avoid this special logic and SINGLECELL_CELLTYPE\n\t\t\treturn {\n\t\t\t\ty: plotDim.top.y + 10,\n\t\t\t\tfirst: {\n\t\t\t\t\tlabel: shortenGroupName(`Control (${this.response.sample_size1})`),\n\t\t\t\t\tx: 0\n\t\t\t\t},\n\t\t\t\tsecond: {\n\t\t\t\t\tlabel: shortenGroupName(`Case (${this.response.sample_size2})`),\n\t\t\t\t\tx: this.settings.width\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (this.termType == tt.SINGLECELL_CELLTYPE) {\n\t\t\t/* quick fix - this only works for gdc's precomputed DE genes (selected cluster vs rest of cells)\n\t\t\tthis won't work for dynamic DE (user-selected cluster A vs cluster B)\n\t\t\tthus not okay to hardcode `Not in` here\n\t\t\t!! FIXME !!\n\t\t\tsc should come up with actual names, and cell counts, for precompute/dynamic groups\n\t\t\t*/\n\t\t\tconst groupLabel = `${this.config.termId} ${this.config.categoryName}`\n\t\t\treturn {\n\t\t\t\ty: plotDim.top.y + 10,\n\t\t\t\tfirst: {\n\t\t\t\t\tlabel: shortenGroupName(`Not in ${groupLabel}`),\n\t\t\t\t\tx: 0\n\t\t\t\t},\n\t\t\t\tsecond: {\n\t\t\t\t\tlabel: shortenGroupName(groupLabel),\n\t\t\t\t\tx: this.settings.width\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn {\n\t\t\t//Set slightly above the plot\n\t\t\ty: plotDim.top.y + 10,\n\t\t\tfirst: {\n\t\t\t\t// color: controlColor || this.settings.defaultSignColor,\n\t\t\t\tlabel: shortenGroupName(`${this.config.samplelst.groups[0].name} (${this.response.sample_size1})`),\n\t\t\t\tx: 0\n\t\t\t\t// rectX: this.settings.width/2 - 10,\n\t\t\t},\n\t\t\tsecond: {\n\t\t\t\t// color: caseColor || this.settings.defaultSignColor,\n\t\t\t\tlabel: shortenGroupName(`${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\t// rebuilt from scratch on every call, like pointData below -- appending would double the rows\n\t\t// if this ever ran twice on one view model\n\t\tthis.pValueTable.rows = []\n\t\tthis.pValueTable.rowKeys.clear()\n\t\tconst dataCopy: any = structuredClone(this.dataRows)\n\t\tfor (const d of dataCopy) {\n\t\t\tconst highlightKey = this.termType === tt.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\t// DAP carries a single FDR (in original_p_value); keep the row cells in\n\t\t\t\t// lock-step with the column set built in the constructor.\n\t\t\t\tconst row =\n\t\t\t\t\tthis.termType == tt.PROTEOME_DAP\n\t\t\t\t\t\t? [{ value: roundValueAuto(d.fold_change) }, { value: roundValueAuto(d.original_p_value) }]\n\t\t\t\t\t\t: [\n\t\t\t\t\t\t\t\t{ value: roundValueAuto(d.fold_change) },\n\t\t\t\t\t\t\t\t{ value: roundValueAuto(d.original_p_value) },\n\t\t\t\t\t\t\t\t{ value: d.adjusted_p_value != undefined ? roundValueAuto(d.adjusted_p_value) : '' }\n\t\t\t\t\t\t  ]\n\t\t\t\tif (this.termType == tt.DNA_METHYLATION) {\n\t\t\t\t\t/* Two splices, in this order, mirroring setPTableColumns exactly: the beta cells\n\t\t\t\t\tgo in after fold-change (index 1) while it is still at index 0, then the\n\t\t\t\t\tPromoter/Gene prefix shifts everything right. Swapping the order puts \u0394\u03B2 under the\n\t\t\t\t\twrong header. */\n\t\t\t\t\trow.splice(\n\t\t\t\t\t\t1,\n\t\t\t\t\t\t0,\n\t\t\t\t\t\t{ value: roundValueAuto((d as any).delta_beta) },\n\t\t\t\t\t\t{ value: roundValueAuto((d as any).mean_beta_control) },\n\t\t\t\t\t\t{ value: roundValueAuto((d as any).mean_beta_case) }\n\t\t\t\t\t)\n\t\t\t\t\trow.splice(0, 0, { value: formatPromoterLabel(d as any) }, { value: d.gene_name || '' })\n\t\t\t\t} else if (this.termType == tt.PROTEOME_DAP) {\n\t\t\t\t\trow.splice(0, 0, { value: d.gene_name || '' }, { value: d.gene || '' })\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/* Always collected, whether or not the table is displayed: \"Download p-value table\"\n\t\t\t\treads these rows, and gating them on showPValueTable made that download emit a\n\t\t\t\theader with no rows. `row` above is built either way, so this only adds the push. */\n\t\t\t\tthis.pValueTable.rows.push(row)\n\t\t\t\t/* Record the dot identity for this row. The methylation Promoter cell shows a\n\t\t\t\tformatted label (formatPromoterLabel), so row[0].value can no longer be used to\n\t\t\t\tfind the dot -- hover/click highlighting must go through this map instead. Reuses\n\t\t\t\tthe same highlightKey compared against config.highlightedData above, so the three\n\t\t\t\tstay in lock-step by construction. */\n\t\t\t\tthis.pValueTable.rowKeys.set(row, highlightKey)\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 != tt.DNA_METHYLATION)\n\t\t\tthrow new Error(`Missing gene_name in data: ${JSON.stringify(d)}`)\n\t\tif (significant) {\n\t\t\tif (controlColor && caseColor) d.color = d.fold_change > 0 ? caseColor : controlColor\n\t\t\telse d.color = this.settings.defaultSignColor\n\t\t} else d.color = this.settings.defaultNonSignColor\n\t}\n\n\t/** One line describing what produced this result: which groups, how many samples actually\n\t * entered the model, and every setting that changes the numbers.\n\t *\n\t * This exists because an exported table is the artifact that outlives the session. Re-running\n\t * a contrast months later and getting different counts is impossible to diagnose when the\n\t * original run's group sizes and options were never written down anywhere -- the file, the\n\t * screenshot and the memory of it all look identical regardless of how it was configured.\n\t * Only settings that can change the result are listed; cosmetic ones are deliberately left\n\t * out so the line stays readable and a difference in it always means a real difference. */\n\tsetProvenance(): string {\n\t\tconst s = this.settings\n\t\tconst parts: string[] = []\n\n\t\tif (this.config.samplelst?.groups?.length == 2) {\n\t\t\tconst [g1, g2] = this.config.samplelst.groups\n\t\t\t// The sizes reported by the server are post-filtering -- what the model actually used,\n\t\t\t// not what the group nominally contained.\n\t\t\tparts.push(`group1 (control) \"${g1.name}\" n=${this.response.sample_size1}`)\n\t\t\tparts.push(`group2 (case) \"${g2.name}\" n=${this.response.sample_size2}`)\n\t\t}\n\n\t\tconst conf = this.config.confounderTws?.map((t: any) => t?.term?.name || t?.term?.id).filter(Boolean)\n\t\tparts.push(`confounders: ${conf?.length ? conf.join(' + ') : 'none'}`)\n\n\t\tif (this.termType == tt.DNA_METHYLATION) {\n\t\t\t/* Recorded FIRST because it is the only setting that changes what was tested rather\n\t\t\tthan how: promoters, cCRE promoters, eQTM blocks and the full cCRE set are different\n\t\t\tfeatures with different coordinates and wildly different test counts, so two exports\n\t\t\tare not comparable without it. Everything else here was already recorded; this was\n\t\t\tthe one missing field, which made a saved p-value table impossible to attribute to a\n\t\t\tmatrix after the fact. */\n\t\t\tparts.push(`element class: ${s.elementType || 'promoter'}`)\n\t\t\t// Which effect size the run was thresholded on. Two exports with the same p cutoff but\n\t\t\t// different axes are not comparable, and nothing else in the line would reveal it.\n\t\t\tparts.push(`x axis: ${s.xAxis === 'delta_beta' ? 'delta-beta' : 'log2(fold-change)'}`)\n\t\t\tparts.push(`min samples per group: ${s.minSamplesPerGroup}`)\n\t\t\tparts.push(`exclude sex chromosomes: ${s.excludeSexChr ? 'yes' : 'no'}`)\n\t\t} else if (this.termType == tt.GENE_EXPRESSION) {\n\t\t\tparts.push(`method: ${s.method}`)\n\t\t}\n\n\t\t// Name the effect-size measure the cutoff was applied to, not just its number \u2014 the\n\t\t// threshold moves to deltaBetaCutoff when the axis does, and \"0.1\" alone is ambiguous.\n\t\tconst onDeltaBeta = this.termType == tt.DNA_METHYLATION && s.xAxis === 'delta_beta'\n\t\tconst effect = onDeltaBeta ? `|delta-beta| > ${s.deltaBetaCutoff}` : `|log2(fold-change)| > ${s.foldChangeCutoff}`\n\t\tparts.push(`significance: ${s.pValueType} p < ${roundValueAuto(Math.pow(10, -s.pValue))}, ${effect}`)\n\n\t\treturn parts.join('; ')\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 == tt.GENE_EXPRESSION || this.termType == tt.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} else if (this.termType == tt.PROTEOME_DAP) {\n\t\t\ttableRows.push(\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Control sample size',\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: 'Case sample size',\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 == tt.DNA_METHYLATION) {\n\t\t\t/* \u0394\u03B2 sits next to log\u2082(fold-change) so the two effect sizes read as a pair: the\n\t\t\tfold-change is a logit difference and does not say how much methylation moved, \u0394\u03B2 does.\n\t\t\tThe group means follow because a \u0394\u03B2 of 0.2 means something different at 0.1\u21920.3 than at\n\t\t\t0.7\u21920.9. Insert at 1 (after fold-change) BEFORE the Promoter/Gene prefix shifts indices \u2014\n\t\t\tsetPointData splices its cells in the same order for the same reason. */\n\t\t\tthis.pValueTable.columns.splice(\n\t\t\t\t1,\n\t\t\t\t0,\n\t\t\t\t{ label: '\u0394\u03B2', sortable: true },\n\t\t\t\t{ label: 'Mean \u03B2 (group 1)', sortable: true },\n\t\t\t\t{ label: 'Mean \u03B2 (group 2)', sortable: true }\n\t\t\t)\n\t\t\t/* This column header is what lands in the downloaded p-value table, so a block\n\t\t\trun exported a column titled \"Promoter\" holding block coordinates. */\n\t\t\tthis.pValueTable.columns.splice(\n\t\t\t\t0,\n\t\t\t\t0,\n\t\t\t\t{ label: elementNoun(this.settings?.elementType).one, sortable: true },\n\t\t\t\t{ label: 'Gene(s)', sortable: true }\n\t\t\t)\n\t\t} else if (this.termType == tt.PROTEOME_DAP) {\n\t\t\tthis.pValueTable.columns.splice(0, 0, { label: 'Identifier', sortable: true }, { label: 'Gene', 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 == tt.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, fileDateStamp, GeneSetEditUI, MultiTermWrapperEditUI } from '#dom'\nimport { to_svg } from '#src/client'\nimport type { VolcanoDom, VolcanoPlotConfig } from '../VolcanoTypes'\nimport { PROTEOME_DAP, DNA_METHYLATION, GENE_EXPRESSION } from '#types'\nimport { getGEunit } from '#tw/geneExpression'\nimport { getDNAMethUnit, getDNAMethTermName } from '#tw/dnaMethylation'\nimport { elementNoun } from '../promoterLabel'\n\nexport class VolcanoInteractions {\n\tapp: MassAppApi\n\tdom: VolcanoDom\n\tid: string\n\tpValueTableData: any\n\tdata: any\n\t/** Significant rows before maxInteractiveDots capped them. When this exceeds the rows on\n\t * screen, the download re-fetches the uncapped set via fetchAllRows(). */\n\ttotalSignificantRows: number\n\t/** Groups, sample sizes and result-affecting settings, written into downloads. */\n\tprovenance: string\n\t/** Re-requests the current contrast with the maxInteractiveDots cap lifted and returns the\n\t * full significance table, formatted by the same view model the on-screen table uses.\n\t * Set by Volcano.main() after each fetch; absent until the first response arrives. */\n\tfetchAllRows?: () => Promise<{ rows: any[]; columns: 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\tthis.totalSignificantRows = 0\n\t\tthis.provenance = ''\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\t// DAP volcanoes report a single FDR rather than a p-value.\n\t\t\t\ttext: termType === PROTEOME_DAP ? 'Download FDR table' : 'Download p-value table',\n\t\t\t\tcallback: (itemDiv: any) => this.downloadPvalueTable(termType, itemDiv)\n\t\t\t}\n\t\t]\n\t\tfor (const opt of opts) {\n\t\t\tconst itemDiv = this.dom.actionsTip.d.append('div').attr('class', 'sja_menuoption').text(opt.text)\n\t\t\titemDiv.on('click', () => opt.callback(itemDiv))\n\t\t}\n\t}\n\n\t/* The interactive table only holds the most-significant maxInteractiveDots rows, because the\n\tdot overlay has to stay responsive. The download has no such constraint, so it should be the\n\tCOMPLETE set of significant rows: when the two differ, re-request with the cap lifted and write\n\tthose rows instead.\n\n\tThat second request is cheap. volcanoRender is deliberately not part of the DA cache key (see\n\tdmKeyInputs in server/routes/termdb.diffMeth.ts), so lifting the cap re-uses the cached R result\n\tand pays only for a re-render.\n\n\tIf the re-request fails the download still happens, with the capped rows and a note saying so --\n\tlosing the file entirely would be a worse outcome than a disclosed subset. */\n\tasync downloadPvalueTable(termType: string, itemDiv?: any) {\n\t\t// name the file after what is in it and when it was run -- these downloads pile up in\n\t\t// one folder across cohorts and reruns\n\t\tconst date = fileDateStamp()\n\t\tconst label = termType === PROTEOME_DAP ? 'fdr' : 'p-value'\n\t\tlet { rows, columns } = this.pValueTableData\n\t\tlet subsetNote: string | undefined\n\n\t\t/* Without a note, nothing in a capped file reveals that \"how many were significant\" is\n\t\tunanswerable from it. Only reachable now when the full fetch is unavailable or fails. */\n\t\tconst cappedNote = (reason: string) =>\n\t\t\t`Top ${rows.length.toLocaleString()} of ${this.totalSignificantRows.toLocaleString()} significant results, ` +\n\t\t\t`selected by adjusted p-value and sorted by fold-change. This file is not the complete result set (${reason}).`\n\n\t\tif (this.totalSignificantRows > rows.length) {\n\t\t\tif (!this.fetchAllRows) subsetNote = cappedNote('complete set unavailable')\n\t\t\telse {\n\t\t\t\t// a full table can be tens of thousands of rows; say something before the wait\n\t\t\t\tconst restore = itemDiv?.text()\n\t\t\t\titemDiv?.text(`Preparing ${this.totalSignificantRows.toLocaleString()} rows...`)\n\t\t\t\ttry {\n\t\t\t\t\tconst full = await this.fetchAllRows()\n\t\t\t\t\trows = full.rows\n\t\t\t\t\tcolumns = full.columns\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tsubsetNote = cappedNote(`could not retrieve the complete set: ${e?.message || e}`)\n\t\t\t\t} finally {\n\t\t\t\t\tif (restore) itemDiv?.text(restore)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t/* Provenance rides along with the rows. Comparing two exports months apart is\n\t\totherwise guesswork: differing counts could be a code change, a settings change or a\n\t\tdifferent group definition, and nothing in the file distinguishes them.\n\t\tJoined with ' | ' rather than a newline because downloadTable collapses newlines to\n\t\tkeep the note on one '#' line -- writing '\\n' here would look intentional and quietly\n\t\tbecome a space. */\n\t\tconst note = [subsetNote, this.provenance && `Run: ${this.provenance}`].filter(Boolean).join(' | ')\n\t\tdownloadTable(rows, columns, `${label}-table-${date}.tsv`, note || undefined)\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\tconst term: any = {\n\t\t\tgenomicFeatureType,\n\t\t\tfeatureName,\n\t\t\ttype: DNA_METHYLATION,\n\t\t\tchr: d.chr,\n\t\t\tstart: d.start,\n\t\t\tstop: d.stop\n\t\t}\n\t\t/* Name the term after the element class actually tested. Every class carries its id in\n\t\tpromoter_id, so genomicFeatureType is 'promoter' for a distal enhancer too and the sandbox\n\t\theader read \"Promoter Average M-value (chr9:...)\" for something that is not a promoter.\n\t\tBuilt here, where the selected class is known, rather than left to the tw fill step, which\n\t\tonly sees the term. */\n\t\tif (genomicFeatureType === 'promoter') {\n\t\t\tconst noun = elementNoun(config?.settings?.volcano?.elementType).one\n\t\t\tconst unit = getDNAMethUnit(genomicFeatureType, this.app.vocabApi)\n\t\t\tterm.unit = unit\n\t\t\tterm.name = getDNAMethTermName(term, unit, noun)\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: '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},\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 { axisstyle, table2col, renderTable, DataPointInteractions, type ActionMenuItem } from '#dom'\nimport { axisBottom, axisLeft, rgb, select, selectAll } from 'd3'\nimport type { DataPointEntry, VolcanoDom, VolcanoPlotDimensions, VolcanoViewData } from '../VolcanoTypes'\nimport type { VolcanoPlotDom } from './VolcanoPlotDom'\nimport type { VolcanoInteractions } from '../interactions/VolcanoInteractions'\nimport { DATermTypes as tt } from '../../diffAnalysis/enabledTermTypes'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport type { ValidatedVolcanoSettings } from '../settings/Settings'\nimport { formatPromoterLabel, elementNoun } from '../promoterLabel'\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.attachInteractions(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\t// Always clear the previous p-value table div before deciding whether\n\t\t// to recreate it. Without this, toggling showPValueTable off leaves\n\t\t// the old div in dom.holder (the table never closes), and toggling\n\t\t// it on repeatedly appends additional divs.\n\t\tthis.dom.holder.select('#sjpp-volcano-pValueTable').remove()\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', [tt.GENE_EXPRESSION, tt.DNA_METHYLATION], () =>\n\t\t\tthis.interactions.confoundersMenu()\n\t\t)\n\t\tthis.addActionButton('Highlight genes', [tt.GENE_EXPRESSION, tt.SINGLECELL_CELLTYPE, tt.DNA_METHYLATION], () =>\n\t\t\tthis.interactions.launchGeneSetEdit()\n\t\t)\n\t\tthis.addActionButton(\n\t\t\t'Statistics',\n\t\t\t[tt.GENE_EXPRESSION, tt.SINGLECELL_CELLTYPE, tt.DNA_METHYLATION],\n\t\t\t() => {\n\t\t\t\tthis.renderStatsMenu()\n\t\t\t},\n\t\t\t{ whenOpen: 'Hide statistics' }\n\t\t)\n\t\t/* Must match the label the view model built from the same helper, otherwise the\n\t\tfind() below silently misses and the count disappears from the action bar. */\n\t\tconst dmNoun = elementNoun(this.settings?.elementType)\n\t\tconst sigLabel =\n\t\t\tthis.termType == tt.DNA_METHYLATION ? `Number of significant ${dmNoun.many}` : 'Number of significant genes'\n\t\tconst numSigGenes = this.viewData.statsData.find(d => d.label == sigLabel)?.value\n\t\tif (numSigGenes) {\n\t\t\t// grouped: these run to five and six figures, and \"84302\" vs \"8430\" is hard to tell apart at a glance\n\t\t\tconst n = numSigGenes.toLocaleString()\n\t\t\tconst sigText = this.termType == tt.DNA_METHYLATION ? `${n} DM ${dmNoun.many}:` : `${n} DE genes:`\n\t\t\tthis.volcanoDom.actions.append('span').text(sigText).style('margin-left', '10px').style('font-weight', 'bold')\n\n\t\t\tconst pValueTableButtonText = this.settings.showPValueTable ? 'Hide p-value table' : 'Show p-value table'\n\t\t\tthis.addActionButton(\n\t\t\t\tpValueTableButtonText,\n\t\t\t\t[tt.GENE_EXPRESSION, tt.SINGLECELL_CELLTYPE, tt.DNA_METHYLATION],\n\t\t\t\tasync () => {\n\t\t\t\t\t/** TODO: This is very slow to render. Need to optimize rendering\n\t\t\t\t\t * and server response to increase performance.*/\n\t\t\t\t\tconst showTable = !this.settings.showPValueTable\n\t\t\t\t\tawait this.interactions.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.interactions.id,\n\t\t\t\t\t\tconfig: { settings: { volcano: { showPValueTable: showTable } } }\n\t\t\t\t\t})\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[tt.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\t *\n\t * Pass `opts.whenOpen` to make the button a toggle: clicking once opens\n\t * the actionsTip with the callback's content and swaps the button text\n\t * to `whenOpen` (\"Hide statistics\", etc.); clicking again hides the tip\n\t * and restores the original text. The text also restores when the tip\n\t * closes via Esc or outside-click (Menu.onHide hook), and when another\n\t * action button hijacks the tip (the loop below resets all toggles\n\t * before showing the new content). */\n\taddActionButton(text: string, termTypes: string[], callback: any, opts?: { whenOpen?: string }) {\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\tconst whenOpen = opts?.whenOpen\n\t\t\t\tif (whenOpen && button.text() === whenOpen) {\n\t\t\t\t\t// Toggle close: tip is currently showing this button's\n\t\t\t\t\t// content. Hide it; onHide resets the label and untags\n\t\t\t\t\t// the button so the body's mousedown handler will treat\n\t\t\t\t\t// it as outside the tip again.\n\t\t\t\t\tthis.dom.actionsTip.hide()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// Reset any other toggle buttons whose tip content we're\n\t\t\t\t// about to overwrite. Tagging via data-attr keeps the state\n\t\t\t\t// on the DOM node so we don't need a class field.\n\t\t\t\tthis.volcanoDom.actions.selectAll('button[data-volcano-toggle-open=\"1\"]').each(function () {\n\t\t\t\t\tconst b = select(this as HTMLButtonElement)\n\t\t\t\t\tconst closed = b.attr('data-volcano-toggle-closed')\n\t\t\t\t\tif (closed) b.text(closed).attr('data-volcano-toggle-open', null)\n\t\t\t\t\t;(this as any).parent_menu = undefined\n\t\t\t\t\tconst eh = (this as any).__volcanoEscHandler\n\t\t\t\t\tif (eh) {\n\t\t\t\t\t\tdocument.removeEventListener('keydown', eh)\n\t\t\t\t\t\t;(this as any).__volcanoEscHandler = undefined\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tthis.dom.actionsTip.clear().showunder(button.node())\n\t\t\t\tif (whenOpen) {\n\t\t\t\t\tbutton.text(whenOpen).attr('data-volcano-toggle-open', '1').attr('data-volcano-toggle-closed', text)\n\t\t\t\t\t// Tag the button as a \"parent_menu\" of the tip so Menu's\n\t\t\t\t\t// body-mousedown outside-click handler skips it (see\n\t\t\t\t\t// menu.js, body.on('mousedown.menu') \u2014 checks\n\t\t\t\t\t// event.target.parent_menu === this.dnode). Without this,\n\t\t\t\t\t// clicking the toggle button to close would fire the\n\t\t\t\t\t// body handler first \u2192 tip hides + onHide resets label \u2192\n\t\t\t\t\t// the click handler then sees the closed label and\n\t\t\t\t\t// reopens, repainting instead of closing.\n\t\t\t\t\t;(button.node() as any).parent_menu = this.dom.actionsTip.dnode\n\t\t\t\t\t// Menu has a built-in keyup Escape handler on its own div,\n\t\t\t\t\t// but it only fires when the tip itself has keyboard\n\t\t\t\t\t// focus \u2014 typically lost the moment the user moves their\n\t\t\t\t\t// mouse over plot content. Attach a document-level\n\t\t\t\t\t// listener for the lifetime of the open toggle so Esc\n\t\t\t\t\t// closes from anywhere. Removed in both cleanup paths\n\t\t\t\t\t// (onHide below + the toggle-reset loop above).\n\t\t\t\t\tconst escHandler = (e: KeyboardEvent) => {\n\t\t\t\t\t\tif (e.key === 'Escape') this.dom.actionsTip.hide()\n\t\t\t\t\t}\n\t\t\t\t\tdocument.addEventListener('keydown', escHandler)\n\t\t\t\t\t;(button.node() as any).__volcanoEscHandler = escHandler\n\t\t\t\t\tthis.dom.actionsTip.onHide = () => {\n\t\t\t\t\t\tbutton.text(text).attr('data-volcano-toggle-open', null)\n\t\t\t\t\t\t;(button.node() as any).parent_menu = undefined\n\t\t\t\t\t\tdocument.removeEventListener('keydown', escHandler)\n\t\t\t\t\t\t;(button.node() as any).__volcanoEscHandler = undefined\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\t// Clear any stale onHide left by a previous toggle button\n\t\t\t\t\t// so an outside-click after this non-toggle open doesn't\n\t\t\t\t\t// reset the wrong button.\n\t\t\t\t\tthis.dom.actionsTip.onHide = undefined\n\t\t\t\t}\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}, ${plotDim.yAxisLabel.y}) rotate(-90)`\n\t\t)\n\t\tthis.setSvgSubscriptLabel(\n\t\t\tthis.volcanoDom.yAxisLabel,\n\t\t\t'-log',\n\t\t\t'10',\n\t\t\tthis.termType === tt.PROTEOME_DAP ? '(FDR)' : `(${this.settings.pValueType} p-value)`\n\t\t)\n\n\t\tthis.volcanoDom.xAxisLabel.attr('transform', `translate(${plotDim.xAxisLabel.x}, ${plotDim.xAxisLabel.y})`)\n\t\t/* The axis must name what it is actually plotting. Delta-beta has no subscript, so it is\n\t\twritten as plain text rather than forced through the log-subscript helper. */\n\t\tif (this.termType === tt.DNA_METHYLATION && this.settings.xAxis === 'delta_beta') {\n\t\t\tthis.volcanoDom.xAxisLabel.selectAll('*').remove()\n\t\t\t/* Prefer the group-named form built by the view model (\"\u0394\u03B2 (NSD2 Higher \u2212 NSD2 Lower)\"):\n\t\t\tcase/control are slot names, so the role-based wording does not say which direction a\n\t\t\tpositive value points. Fall back to it only when the names are unavailable. */\n\t\t\tthis.volcanoDom.xAxisLabel.text(this.viewData.deltaBetaAxisLabel || '\u0394\u03B2 (case \u2212 control)')\n\t\t} else {\n\t\t\tthis.volcanoDom.xAxisLabel.text(null)\n\t\t\tthis.setSvgSubscriptLabel(this.volcanoDom.xAxisLabel, 'log', '2', '(fold-change)')\n\t\t}\n\n\t\tthis.renderScale(plotDim.xScale)\n\t\tthis.renderScale(plotDim.yScale, true)\n\n\t\t// Server-rendered PNG of the full scatter (every dot, non-interactive).\n\t\t// Drawn first so overlay circles + the border rect sit on top. The volcano\n\t\t// binary emits a borderless image whose data extent matches the client's\n\t\t// scales, so placing it over the plot rect aligns dot-for-dot.\n\t\tif (this.viewData.volcanoPng) {\n\t\t\tthis.volcanoDom.plot\n\t\t\t\t.append('image')\n\t\t\t\t.attr('href', `data:image/png;base64,${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}, ${scale.y})`)\n\t\t\t.call(isLeft ? axisLeft(scale.scale) : axisBottom(scale.scale))\n\n\t\taxisstyle({\n\t\t\taxis: scaleG,\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t}\n\n\trenderFoldChangeLine(plotDim: VolcanoPlotDimensions) {\n\t\t//logFoldChangeLine\n\t\tthis.volcanoDom.plot\n\t\t\t.append('line')\n\t\t\t.attr('stroke', '#ccc')\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t.attr('x1', plotDim.logFoldChangeLine.x)\n\t\t\t.attr('x2', plotDim.logFoldChangeLine.x)\n\t\t\t.attr('y1', plotDim.logFoldChangeLine.y1)\n\t\t\t.attr('y2', plotDim.logFoldChangeLine.y2)\n\t}\n\n\trenderStatsMenu() {\n\t\t//Render any images. viewModel returns the response array of images or []\n\t\tfor (const img of this.viewData.images || []) {\n\t\t\tthis.dom.actionsTip.d\n\t\t\t\t.append('img')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.style('margin-top', '-30px')\n\t\t\t\t.attr('width', 450)\n\t\t\t\t.attr('height', 450)\n\t\t\t\t.attr('src', img.src)\n\t\t}\n\t\tconst tableHolder = this.dom.actionsTip.d\n\t\t\t.append('div')\n\t\t\t//Show the stats table underneath the images if > 1 image or to the right if only 1 image\n\t\t\t.style('display', this.viewData.images.length == 1 ? 'inline-block' : 'block')\n\t\t\t//Top margin is roughly inline with image however the margins are set by server\n\t\t\t//Likewise the image margins are undetectable.\n\t\t\t//This is a roughly satistifes the different image margin scenarios.\n\t\t\t.style('margin', `${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\t/* Group the counts, but only the counts: statsData also carries a percentage that the\n\t\t\tview model already put through roundValueAuto(), and toLocaleString() would re-round it\n\t\t\tto three decimals. Integer test rather than a per-label check so a row added later is\n\t\t\tformatted correctly without touching this. */\n\t\t\ttd2.style('text-align', 'end').text(Number.isInteger(d.value) ? d.value.toLocaleString() : 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\t// Index into the same array handed to renderTable: it sorts rows in place, so\n\t\t\t\t// the unsliced pValueTableData.rows would be misindexed once a header is sorted.\n\t\t\t\tconst key = this.viewData.pValueTableData.rowKeys.get(rows[i])\n\t\t\t\tif (!key) return\n\t\t\t\tthis.interactions.highlightDataPoint(key)\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 key = this.viewData.pValueTableData.rowKeys.get(row)\n\t\t\t\tconst dataKey = this.termType === tt.DNA_METHYLATION ? 'promoter_id' : 'gene_name'\n\t\t\t\tconst circle = circles.find((d: any) => d.__data__[dataKey] == key) 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\tprivate attachInteractions(plotDim: VolcanoPlotDimensions) {\n\t\tconst points = this.viewData.pointData as DataPointEntry[]\n\t\tif (!points || points.length === 0) return\n\n\t\tconst dotRadiusPx = this.viewData.plotExtent.dotRadiusPx\n\t\tconst hitRadius = dotRadiusPx + 3\n\t\t// Inset by stroke-width/2 so the orange fill stops at the dot's stroke inner edge.\n\t\tconst highlightRadius = Math.max(0.5, dotRadiusPx - 0.5)\n\t\tconst highlightColor = this.settings.defaultHighlightColor\n\n\t\t// Hover-ring layer \u2014 visual only, never intercepts mouse events.\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// Circle as an SVG path so it can flow through the generic\n\t\t// `drawHoverShapes` helper (which renders `<path>` elements).\n\t\tconst circlePath = (r: number) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`\n\n\t\tnew DataPointInteractions<DataPointEntry>({\n\t\t\tcover,\n\t\t\thoverLayer,\n\t\t\thoverTip: this.dom.tip,\n\t\t\tpoints,\n\t\t\t// Quadtree in cover-local space \u2014 d.x/d.y are SVG-absolute, so subtract\n\t\t\t// the plot rect's origin once when building the tree.\n\t\t\tgetX: d => d.x - plotDim.plot.x,\n\t\t\tgetY: d => d.y - plotDim.plot.y,\n\t\t\thitRadius,\n\t\t\ttoHoverSpec: d => ({\n\t\t\t\tpath: circlePath(highlightRadius),\n\t\t\t\t// Hover layer lives in the same coord space as the dots (SVG-absolute),\n\t\t\t\t// so translate by d.x/d.y \u2014 NOT the cover-local pair.\n\t\t\t\ttransform: `translate(${d.x},${d.y})`,\n\t\t\t\tfill: highlightColor,\n\t\t\t\tfillOpacity: 0.9,\n\t\t\t\tstroke: 'none'\n\t\t\t}),\n\t\t\tmaxTooltipRows: this.settings.maxTooltipGenes,\n\t\t\titemNoun: 'gene',\n\t\t\trenderSingleHoverTooltip: (d, container) => {\n\t\t\t\tconst table = table2col({ holder: container.append('table') })\n\t\t\t\tthis.addTooltipRows(d, table)\n\t\t\t},\n\t\t\tbuildMultiHitTableData: dots => this.buildMultiHitTable(dots),\n\t\t\tgetActions: d => this.getActionMenuOpts(d),\n\t\t\trenderSingleHitInfo: (d, container) => {\n\t\t\t\tconst tbl = table2col({ holder: container.append('table') })\n\t\t\t\tthis.addTooltipRows(d, tbl)\n\t\t\t},\n\t\t\tgetRowKey: d => d.gene_name\n\t\t}).attach()\n\t}\n\n\t/** Whether the effect size on show is delta-beta rather than log2 fold-change. Methylation\n\t * fold-change is a difference of logits: it ranks elements correctly but says nothing about\n\t * how much methylation moved, so it must not be what a reader is handed next to a delta-beta\n\t * axis. Read by both hover paths -- the single-point tooltip and the multi-point table -- so\n\t * the two cannot disagree about which number they show. */\n\tprivate get onDeltaBeta() {\n\t\treturn this.termType === tt.DNA_METHYLATION && this.settings.xAxis === 'delta_beta'\n\t}\n\n\tprivate buildMultiHitTable(dots: DataPointEntry[]): { columns: any[]; rows: any[] } {\n\t\tconst isDM = this.termType === tt.DNA_METHYLATION\n\t\tconst isDAP = this.termType === tt.PROTEOME_DAP\n\t\tconst effectLabel = this.onDeltaBeta ? '\u0394\u03B2' : 'log\u2082(FC)'\n\t\tconst pValueType = this.settings.pValueType\n\t\t// DAP files carry a single FDR (stored in original_p_value); label it as such\n\t\t// rather than \"Original/Adjusted p-value\".\n\t\tconst pLabel = isDAP ? 'FDR' : `${pValueType.charAt(0).toUpperCase()}${pValueType.slice(1)} p-value`\n\t\tconst pField = (isDAP ? 'original_p_value' : `${pValueType}_p_value`) as 'original_p_value' | 'adjusted_p_value'\n\t\tconst columns = isDM\n\t\t\t? [\n\t\t\t\t\t{ label: elementNoun(this.settings?.elementType).one },\n\t\t\t\t\t{ label: 'Gene(s)' },\n\t\t\t\t\t{ label: effectLabel, sortable: true },\n\t\t\t\t\t{ label: pLabel, sortable: true }\n\t\t\t  ]\n\t\t\t: isDAP\n\t\t\t? [\n\t\t\t\t\t{ label: 'Identifier' },\n\t\t\t\t\t{ label: 'Gene' },\n\t\t\t\t\t{ label: effectLabel, sortable: true },\n\t\t\t\t\t{ label: pLabel, sortable: true }\n\t\t\t  ]\n\t\t\t: [{ label: 'Gene' }, { label: effectLabel, sortable: true }, { label: pLabel, sortable: true }]\n\t\tconst rows = dots.map(d => {\n\t\t\t// must match effectLabel above, or the column header names one number and the cell holds another\n\t\t\tconst fc = { value: roundValueAuto(this.onDeltaBeta ? (d as any).delta_beta : d.fold_change) }\n\t\t\tconst pval = { value: roundValueAuto(d[pField]) }\n\t\t\tif (isDM) {\n\t\t\t\treturn [{ value: formatPromoterLabel(d as any) }, { value: d.gene_name || '' }, fc, pval]\n\t\t\t}\n\t\t\tif (isDAP) {\n\t\t\t\treturn [{ value: d.gene_name || '' }, { value: (d as any).gene || '' }, fc, pval]\n\t\t\t}\n\t\t\treturn [{ value: d.gene_name || '' }, fc, pval]\n\t\t})\n\t\treturn { columns, rows }\n\t}\n\n\t/** Per-data-point action menu items (Violin / DMR / Box-plot). Used by\n\t * both the single-gene click flow and the multi-gene click-menu rows so\n\t * the launchers stay in lock-step. */\n\tprivate getActionMenuOpts(d: DataPointEntry): ActionMenuItem[] {\n\t\tconst termType = this.termType\n\t\tconst interactions = this.interactions\n\t\tconst all = [\n\t\t\t{\n\t\t\t\tlabel: 'Violin plot',\n\t\t\t\tisVisible: () => termType === tt.DNA_METHYLATION || termType === tt.GENE_EXPRESSION,\n\t\t\t\tonClick: async () => {\n\t\t\t\t\tif (termType === tt.DNA_METHYLATION) interactions.launchDNAMethViolin(d as any)\n\t\t\t\t\tif (termType === tt.GENE_EXPRESSION) interactions.launchViolinGeneExp(d.gene_name)\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'DMR analysis',\n\t\t\t\tisVisible: () => termType === tt.DNA_METHYLATION,\n\t\t\t\tonClick: async () => {\n\t\t\t\t\tconst dm = d as DataPointEntry & {\n\t\t\t\t\t\tchr: string\n\t\t\t\t\t\tstart: number\n\t\t\t\t\t\tstop: number\n\t\t\t\t\t\tpromoter_id?: string\n\t\t\t\t\t\tgene_name?: string\n\t\t\t\t\t}\n\t\t\t\t\tawait interactions.launchDmr({\n\t\t\t\t\t\tchr: dm.chr,\n\t\t\t\t\t\tstart: dm.start,\n\t\t\t\t\t\tstop: dm.stop,\n\t\t\t\t\t\tpromoterId: dm.promoter_id\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Box plot',\n\t\t\t\tisVisible: () => termType === tt.GENE_EXPRESSION,\n\t\t\t\tonClick: async () => {\n\t\t\t\t\tinteractions.launchBoxPlot(d.gene_name)\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t\treturn all.filter(o => o.isVisible()).map(({ label, onClick }) => ({ label, onClick }))\n\t}\n\n\t/** Populates a `table2col` instance with the standard volcano hover rows\n\t * (gene/promoter, fold-change, original + adjusted p-values). */\n\tprivate addTooltipRows(d: DataPointEntry, table: any) {\n\t\tif (this.termType === tt.DNA_METHYLATION) {\n\t\t\tif ('promoter_id' in d)\n\t\t\t\taddTooltipRow(table, elementNoun(this.settings?.elementType).one, formatPromoterLabel(d as any))\n\t\t\tif (d.gene_name) addTooltipRow(table, 'Gene(s)', d.gene_name)\n\t\t} else if (this.termType === tt.PROTEOME_DAP) {\n\t\t\taddTooltipRow(table, 'Identifier', d.gene_name)\n\t\t\tif ('gene' in d) addTooltipRow(table, 'Gene', (d as any).gene)\n\t\t} else {\n\t\t\taddTooltipRow(table, 'Gene name', d.gene_name)\n\t\t}\n\t\t// report the effect size the plot is actually drawing -- see the onDeltaBeta getter\n\t\tif (this.onDeltaBeta) {\n\t\t\taddTooltipRow(table, '\u0394\u03B2', roundValueAuto((d as any).delta_beta))\n\t\t} else {\n\t\t\taddTooltipRow(table, 'log<sub>2</sub>(fold-change)', roundValueAuto(d.fold_change))\n\t\t}\n\t\tif (this.termType === tt.PROTEOME_DAP) {\n\t\t\t// DAP carries a single FDR (adjusted p-value), stored in original_p_value.\n\t\t\taddTooltipRow(table, 'FDR', roundValueAuto(d.original_p_value))\n\t\t} else {\n\t\t\taddTooltipRow(table, 'Original p-value', roundValueAuto(d.original_p_value))\n\t\t\tif (d.adjusted_p_value != undefined) addTooltipRow(table, 'Adjusted p-value', roundValueAuto(d.adjusted_p_value))\n\t\t}\n\t}\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\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", "import type { ControlInputEntry } from '#mass/types/mass'\nimport type { VolcanoPlotConfig } from './VolcanoTypes'\nimport { getSampleNum } from './settings/defaults'\nimport { PROTEOME_DAP, DNA_METHYLATION, GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#types'\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\t/** Regulatory-element classes this dataset can test, from\n\t * termdbConfig.queries.dnaMethylation.elementTypes. Empty or single-entry means\n\t * there is nothing to choose between, and the element picker stays hidden. */\n\telementTypes: { key: string; label: string }[]\n\tconstructor(config: VolcanoPlotConfig, termType: string, elementTypes?: { key: string; label: 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\tthis.elementTypes = elementTypes || []\n\t\t//Populated with the default controls for the volcano plot\n\t\tthis.inputs = [\n\t\t\t{\n\t\t\t\t// DAP volcanoes threshold a single FDR (adjusted p-value); other term types\n\t\t\t\t// threshold a p-value.\n\t\t\t\tlabel: this.config.termType == PROTEOME_DAP ? 'FDR significance (-log\u2081\u2080)' : '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:\n\t\t\t\t\tthis.config.termType == PROTEOME_DAP\n\t\t\t\t\t\t? 'The FDR threshold to determine statistical significance'\n\t\t\t\t\t\t: '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\t// DAP files carry only a single FDR, so there is nothing to toggle between.\n\t\t\t\tgetDisplayStyle: () => (this.config.termType == PROTEOME_DAP ? 'none' : ''),\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/* Hidden for differential methylation: a DM run plots and thresholds on delta-beta,\n\t\t\tso a log2 cutoff would set a limit in units the plot never shows. Every other term\n\t\t\ttype still gets it. */\n\t\t\t...(this.termType === DNA_METHYLATION\n\t\t\t\t? []\n\t\t\t\t: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Fold change (log\u2082)',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'volcano',\n\t\t\t\t\t\t\tsettingsKey: 'foldChangeCutoff',\n\t\t\t\t\t\t\ttitle: 'The fold change threshold to determine biological significance',\n\t\t\t\t\t\t\tmin: -10,\n\t\t\t\t\t\t\tmax: 10\n\t\t\t\t\t\t}\n\t\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: any[] = [\n\t\t\t/* Element class comes FIRST because it is categorically different from the\n\t\t\tcontrols below it: those tune how the test is run, this one changes what is\n\t\t\tbeing tested. Promoters, eQTM blocks, and cCRE classes are different genomic\n\t\t\tfeatures with different coordinates and different test counts, so switching\n\t\t\tproduces a different analysis rather than a refined one.\n\n\t\t\tHidden unless the dataset offers a genuine choice -- a single class means\n\t\t\tthere is nothing to pick, and a dataset using the legacy promoter-only config\n\t\t\tgets no new UI at all. */\n\t\t\t...(this.elementTypes.length > 1\n\t\t\t\t? [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Element class',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType: 'volcano',\n\t\t\t\t\t\t\tsettingsKey: 'elementType',\n\t\t\t\t\t\t\toptions: this.elementTypes.map(e => ({ value: e.key, label: e.label })),\n\t\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t\t'Which regulatory elements to test. This changes the features being analysed, not just the thresholds: promoters are TSS windows (-1500/+500 bp, the 450K array definition), cCRE promoters are the ~349 bp ENCODE promoter-like elements (the CpG-island core, no shores), eQTM blocks are runs of CpGs whose methylation correlates with a gene, and the other cCRE classes are ENCODE enhancer and CTCF annotations. Hit counts are not comparable across classes because the number of tests and the genes covered both differ. Narrow elements recover focal signal that a wide window averages away; wide windows do better on broad marks.'\n\t\t\t\t\t\t}\n\t\t\t\t  ]\n\t\t\t\t: []),\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\t{\n\t\t\t\tlabel: 'Exclude sex chromosomes',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'excludeSexChr',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttitle:\n\t\t\t\t\t'Drop chrX/chrY promoters. Recommended for mixed-sex cohorts \u2014 X-inactivation makes chrX methylation strongly sex-dependent, so a sex-imbalanced comparison reports sex rather than the grouping variable.'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Min \u0394\u03B2',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'volcano',\n\t\t\t\tsettingsKey: 'deltaBetaCutoff',\n\t\t\t\ttitle:\n\t\t\t\t\t'Effect-size cutoff for differential methylation, applied to \u0394\u03B2. 0.1 is a 10-percentage-point change in methylation, the conventional floor for calling a region differentially methylated. Kept separate from the log\u2082 cutoff because the two are not interchangeable.',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 1,\n\t\t\t\tstep: 0.01\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, type ComponentApi } 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, DNA_METHYLATION } from '#types'\nimport { uiLabel } from '#shared'\n\n/* Below this many samples in the smaller group, the wilcoxon p-values are worth a caveat.\nrust/src/stats_functions.rs only runs the exact test when both groups are under 50 AND no value is\ntied; rna-seq counts always tie on zero, so every run takes the normal approximation. Its tie\ncorrection shrinks sigma as the tied block grows, and for a gene that is zero in nearly every sample\n-- a Y gene in a 99% female cohort, say -- that inflates z far past what the group sizes can\nactually support (observed: p = 1e-81 from 14 vs 1356, where the exact test floor is 1e-33).\n20 is the conventional floor for the normal approximation; the tie inflation is worse.\nponytail: gated on group size alone, which catches the case that motivated it. Catching a\ntie-dominated gene in an otherwise well-sized cohort needs per-gene tie counts back from rust. */\nconst MIN_WILCOXON_GROUP_SIZE = 20\n\nexport class 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: ComponentApi) {\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(\n\t\t\tplotConfig,\n\t\t\tthis.termType,\n\t\t\tthis.app.vocabApi.termdbConfig?.queries?.dnaMethylation?.elementTypes\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.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, 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\tconst msg = response?.error || 'No data returned from server'\n\t\t\t\tif (response?.code === 'CACHE_BUSY') {\n\t\t\t\t\tif (window.confirm(msg)) this.main()\n\t\t\t\t} else sayerror(this.dom.error, msg)\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\t\t\t//pre-cap count, so the download knows whether the on-screen rows are a subset\n\t\t\tthis.interactions.totalSignificantRows = response.data.totalSignificantRows\n\t\t\t//groups, sample sizes and settings, so a downloaded table records how it was produced\n\t\t\tthis.interactions.provenance = viewModel.viewData.provenance\n\t\t\t/* Lets the download write every significant row while the interactive table keeps only\n\t\t\tthe most-significant maxInteractiveDots (the dot overlay does not scale past that).\n\t\t\tmaxInteractiveDots null tells renderVolcano to keep them all; it is not part of the DA\n\t\t\tcache key, so this re-uses the cached analysis and only re-renders. Rebuilt on each\n\t\t\tresponse so it closes over the current config/settings rather than a stale pair. */\n\t\t\tthis.interactions.fetchAllRows = async () => {\n\t\t\t\tconst full = await new VolcanoModel(this, this.termType).getData(config, {\n\t\t\t\t\t...settings,\n\t\t\t\t\tmaxInteractiveDots: null\n\t\t\t\t})\n\t\t\t\tif (!full || full.error || !full.data?.dots) throw new Error(full?.error || 'no rows returned')\n\t\t\t\treturn new VolcanoViewModel(config, full, settings).viewData.pValueTableData\n\t\t\t}\n\n\t\t\t/** Render formatted data */\n\t\t\tthis.view.render(settings, viewModel.viewData)\n\n\t\t\t/* Non-fatal notes on how to read the result. Both can apply at once, so they are collected\n\t\t\tand shown together rather than one overwriting the other. */\n\t\t\tconst notes: string[] = []\n\t\t\tif (!response.data.dots.length) notes.push('No points passed the significance thresholds.')\n\t\t\tconst smallestGroup = Math.min(response.sample_size1, response.sample_size2)\n\t\t\tif (settings.method == 'wilcoxon' && smallestGroup < MIN_WILCOXON_GROUP_SIZE) {\n\t\t\t\t// gdc users are the most likely readers of this sentence, and gdc calls them cases\n\t\t\t\tconst samplesLabel = uiLabel(this.app.vocabApi.termdbConfig?.uiLabels, 'samples', 'samples')\n\t\t\t\tnotes.push(\n\t\t\t\t\t`The smaller group has ${smallestGroup.toLocaleString()} ${samplesLabel}. Wilcoxon p-values are ` +\n\t\t\t\t\t\t`approximated here, and a gene that is zero in most ${samplesLabel} can be assigned a p-value far ` +\n\t\t\t\t\t\t`smaller than its group sizes can support. Rank these results by fold change rather than by ` +\n\t\t\t\t\t\t`p-value magnitude, and do not compare the p-values against another analysis.`\n\t\t\t\t)\n\t\t\t}\n\t\t\tif (notes.length) this.dom.error.text(notes.join(' ')).style('color', '#555')\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\t// app is passed through so the defaults can read the dataset's preferred starting\n\t\t\t// element class from termdbConfig; opts alone does not carry it\n\t\t\tvolcano: getDefaultVolcanoSettings(opts.overrides, { ...opts, app })\n\t\t},\n\t\thighlightedData: opts.highlightedData || [],\n\t\ttermType: opts.termType\n\t}\n\n\t//Define Gene Expression and DNA Methylation config. Both run confounder-adjusted\n\t//two-group analyses off a samplelst, so both need their confounder tws filled here\n\t//-- otherwise a session rehydrated with confounders already set carries unfilled tws.\n\tif (opts.termType == GENE_EXPRESSION || opts.termType == DNA_METHYLATION) {\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"],
-  "mappings": 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