@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/DmrPlot-QKUX5XUW.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/dmr/settings/defaults.ts", "../plots/dmr/model/DmrModel.ts", "../plots/dmr/viewModel/DmrViewModel.ts", "../plots/dmr/view/DmrView.ts", "../plots/dmr/DmrPlot.ts"],
-  "sourcesContent": ["import type { DMRSettings } from './Settings.ts'\n\nexport function getDefaultDMRSettings(opts: any): DMRSettings {\n\tconst overrides = opts.settings || {}\n\tconst defaults = {\n\t\tblockWidth: 800,\n\t\tpad: 2000,\n\t\tlambda: 1000,\n\t\tC: 2,\n\t\tfdr_cutoff: 0.05,\n\t\tcolors: {\n\t\t\tgroup1: '#3b5ee6',\n\t\t\tgroup2: '#c04e00',\n\t\t\thyper: '#e66101',\n\t\t\thypo: '#5e81f4'\n\t\t},\n\t\tmaxLoessRegion: 250_000,\n\t\tminProbesForCi: 10,\n\t\tbackend: 'rust' as const,\n\t\tmaxRegionSize: 5_000_000\n\t}\n\n\t// Deep-merge colors so hyper/hypo defaults are preserved\n\t// when only group colors are overridden\n\tif (overrides.colors) {\n\t\tObject.assign(defaults.colors, overrides.colors)\n\t\tdelete overrides.colors\n\t}\n\n\treturn Object.assign(defaults, overrides)\n}\n", "import { dofetch3 } from '#common/dofetch'\nimport type { TermdbDmrResponse } from '#types'\nimport type { DmrConfig } from '../DmrTypes.ts'\n\nexport class DmrModel {\n\tprivate config: DmrConfig\n\tprivate vocab: { genome: string; dslabel: string }\n\n\tconstructor(config: DmrConfig, vocab: { genome: string; dslabel: string }) {\n\t\tthis.config = config\n\t\tthis.vocab = vocab\n\t}\n\n\tasync fetchDmr(chr: string, start: number, stop: number, signal?: AbortSignal): Promise<TermdbDmrResponse> {\n\t\tconst { group1, group2, settings } = this.config\n\t\tconst { genome, dslabel } = this.vocab\n\t\treturn dofetch3('termdb/dmr', {\n\t\t\tsignal,\n\t\t\tbody: {\n\t\t\t\tgenome,\n\t\t\t\tdslabel,\n\t\t\t\tchr,\n\t\t\t\tstart,\n\t\t\t\tstop,\n\t\t\t\tgroup1,\n\t\t\t\tgroup2,\n\t\t\t\tlambda: settings.dmr.lambda,\n\t\t\t\tC: settings.dmr.C,\n\t\t\t\tfdr_cutoff: settings.dmr.fdr_cutoff,\n\t\t\t\tgroup1Name: this.config.group1Name,\n\t\t\t\tgroup2Name: this.config.group2Name,\n\t\t\t\tblockWidth: settings.dmr.blockWidth,\n\t\t\t\tdevicePixelRatio: typeof window !== 'undefined' ? window.devicePixelRatio : 1,\n\t\t\t\tmaxLoessRegion: settings.dmr.maxLoessRegion,\n\t\t\t\tcolors: settings.dmr.colors,\n\t\t\t\tbackend: settings.dmr.backend\n\t\t\t}\n\t\t}) as Promise<TermdbDmrResponse>\n\t}\n}\n", "import { first_genetrack_tolist } from '#common/1stGenetk'\nimport type { TermdbDmrSuccessResponse, DmrDiagnostic } from '#types'\nimport type { DmrConfig, BedItem, LegendRow, DmrViewData } from '../DmrTypes.ts'\n\nexport class DmrViewModel {\n\tviewData: DmrViewData\n\n\tconstructor(\n\t\tdmrResult: TermdbDmrSuccessResponse,\n\t\tconfig: DmrConfig,\n\t\tgenomeObj: any,\n\t\tqueryChr: string,\n\t\tqueryStart?: number,\n\t\tqueryStop?: number\n\t) {\n\t\tconst { settings } = config\n\t\tconst dmrBedItems = this.makeDmrBedItems(dmrResult, settings)\n\t\tconst sigCpgBedItems = this.makeSigCpgBedItems(dmrResult, settings, queryChr, queryStart, queryStop)\n\n\t\tconst xRange = (queryStop ?? 0) - (queryStart ?? 0)\n\t\tconst loess = dmrResult.diagnostic?.loess\n\t\tconst showLoess = !!(loess && loess.group1_fitted.length > 0 && loess.group2_fitted.length > 0)\n\t\tconst showDots = xRange <= settings.dmr.maxLoessRegion\n\n\t\tconst betaTrackResult = dmrResult.diagnostic\n\t\t\t? this.renderBetaTrack(\n\t\t\t\t\tdmrResult.diagnostic,\n\t\t\t\t\tconfig,\n\t\t\t\t\tsettings.dmr.blockWidth,\n\t\t\t\t\tshowLoess,\n\t\t\t\t\tshowDots,\n\t\t\t\t\tqueryStart,\n\t\t\t\t\tqueryStop\n\t\t\t  )\n\t\t\t: undefined\n\n\t\tthis.viewData = {\n\t\t\ttklst: this.buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackResult?.img),\n\t\t\tlegendRows: this.buildLegendData(\n\t\t\t\tconfig,\n\t\t\t\tdmrResult.dmrs,\n\t\t\t\tsigCpgBedItems,\n\t\t\t\tshowLoess,\n\t\t\t\tshowDots,\n\t\t\t\tbetaTrackResult?.showCi ?? false\n\t\t\t),\n\t\t\tdiagnostic: dmrResult.diagnostic,\n\t\t\tdmrs: dmrResult.dmrs,\n\t\t\tdmrBedItems,\n\t\t\tshowLoess,\n\t\t\tshowDots\n\t\t}\n\t}\n\n\tprivate buildTrackList(\n\t\tdmrBedItems: BedItem[],\n\t\tsigCpgBedItems: BedItem[],\n\t\tgenomeObj: any,\n\t\tbetaTrackImg?: { minv: number; maxv: number; src: string }\n\t): any[] {\n\t\tconst tklst: any[] = []\n\t\tfirst_genetrack_tolist(genomeObj, tklst)\n\t\ttklst.push({ type: 'bedj', name: 'DMRs', bedItems: dmrBedItems })\n\t\ttklst.push({ type: 'bedj', name: 'Sig. CpGs', bedItems: sigCpgBedItems })\n\t\tif (betaTrackImg) {\n\t\t\ttklst.push({\n\t\t\t\ttype: 'bigwig',\n\t\t\t\tname: 'Per-CpG Means',\n\t\t\t\theight: 150,\n\t\t\t\timgData: betaTrackImg\n\t\t\t})\n\t\t}\n\t\treturn tklst\n\t}\n\n\tprivate buildLegendData(\n\t\tconfig: DmrConfig,\n\t\tdmrs: TermdbDmrSuccessResponse['dmrs'],\n\t\tsigCpgBedItems: BedItem[],\n\t\tshowLoess: boolean,\n\t\tshowDots: boolean,\n\t\tshowCi: boolean\n\t): LegendRow[] {\n\t\tconst { colors } = config.settings.dmr\n\t\tconst g1 = config.group1Name || 'Group 1'\n\t\tconst g2 = config.group2Name || 'Group 2'\n\t\tconst meansItems: LegendRow['items'] = []\n\t\tif (showDots) {\n\t\t\tmeansItems.push({ text: `${g1} (control)`, color: colors.group1 }, { text: `${g2} (case)`, color: colors.group2 })\n\t\t}\n\t\tif (showLoess) {\n\t\t\tconst ciLabel = showCi ? ' + 95% CI' : ''\n\t\t\tmeansItems.push(\n\t\t\t\t{ text: `${g1} LOESS trend${ciLabel}`, color: colors.group1, style: showCi ? 'shaded' : 'dashed' },\n\t\t\t\t{ text: `${g2} LOESS trend${ciLabel}`, color: colors.group2, style: showCi ? 'shaded' : 'dashed' }\n\t\t\t)\n\t\t}\n\t\tconst rows: LegendRow[] = [{ label: 'Per-CpG Means', items: meansItems }]\n\t\t// Only show DMR legend entries for directions present in the results\n\t\tconst hasHyper = dmrs.some(d => d.direction === 'hyper')\n\t\tconst hasHypo = dmrs.some(d => d.direction === 'hypo')\n\t\tif (hasHyper || hasHypo) {\n\t\t\tconst items: LegendRow['items'] = []\n\t\t\tif (hasHyper) items.push({ text: 'Hypermethylated', color: colors.hyper })\n\t\t\tif (hasHypo) items.push({ text: 'Hypomethylated', color: colors.hypo })\n\t\t\trows.push({ label: 'DMR', items })\n\t\t}\n\t\tif (sigCpgBedItems.length) {\n\t\t\tconst items: LegendRow['items'] = []\n\t\t\tconst hasHyperCpg = sigCpgBedItems.some(b => b.color === colors.hyper)\n\t\t\tconst hasHypoCpg = sigCpgBedItems.some(b => b.color === colors.hypo)\n\t\t\tif (hasHyperCpg) items.push({ text: 'Hyper (FDR sig.)', color: colors.hyper })\n\t\t\tif (hasHypoCpg) items.push({ text: 'Hypo (FDR sig.)', color: colors.hypo })\n\t\t\trows.push({ label: 'Sig. CpGs', items })\n\t\t}\n\t\treturn rows\n\t}\n\n\t/**\n\t * Render the per-CpG means scatter plot to an offscreen canvas and return\n\t * a data URI suitable for the bigwig imgData track.\n\t */\n\tprivate renderBetaTrack(\n\t\tdiagnostic: DmrDiagnostic,\n\t\tconfig: DmrConfig,\n\t\tblockWidth: number,\n\t\tshowLoess: boolean,\n\t\tshowDots: boolean,\n\t\tqueryStart?: number,\n\t\tqueryStop?: number\n\t): { img: { minv: number; maxv: number; src: string }; showCi: boolean } | undefined {\n\t\tconst { probes } = diagnostic\n\t\tif (!probes.positions.length) return undefined\n\n\t\tconst { colors, fdr_cutoff, minProbesForCi } = config.settings.dmr\n\t\tconst dpr = typeof window !== 'undefined' && window.devicePixelRatio > 1 ? window.devicePixelRatio : 1\n\t\tconst width = blockWidth\n\t\tconst height = 150\n\n\t\tconst canvas = document.createElement('canvas')\n\t\tcanvas.width = width * dpr\n\t\tcanvas.height = height * dpr\n\t\tconst ctx = canvas.getContext('2d')\n\t\tif (!ctx) return undefined\n\t\tctx.scale(dpr, dpr)\n\n\t\t// Use the full block view range so dots align with bedj tracks above.\n\t\t// The block stretches the image to fill the view from queryStart to queryStop.\n\t\tconst xMin = queryStart ?? probes.positions[0]\n\t\tconst xMax = queryStop ?? probes.positions[probes.positions.length - 1]\n\t\tconst xRange = xMax - xMin || 1\n\t\tconst scaleX = (val: number) => ((val - xMin) / xRange) * width\n\t\tconst scaleY = (val: number) => height - val * height // beta 0-1\n\n\t\t// Transparent background so block mouse events (yellow line) show through\n\t\tctx.clearRect(0, 0, width, height)\n\n\t\t// DMR region shading omitted \u2014 already shown as a bedj track above\n\n\t\t// Draw LOESS curves with shaded CI regions, clipped to probe data range.\n\t\t// Only show CIs when there are enough probes for a reliable estimate.\n\t\tlet showCi = false\n\t\tif (showLoess && diagnostic.loess) {\n\t\t\tconst { loess } = diagnostic\n\t\t\tconst firstProbePos = probes.positions[0]\n\t\t\tconst lastProbePos = probes.positions[probes.positions.length - 1]\n\t\t\tshowCi = probes.positions.length >= minProbesForCi\n\n\t\t\tfor (const [fitted, ciLower, ciUpper, color] of [\n\t\t\t\t[loess.group1_fitted, loess.group1_ci_lower, loess.group1_ci_upper, colors.group1],\n\t\t\t\t[loess.group2_fitted, loess.group2_ci_lower, loess.group2_ci_upper, colors.group2]\n\t\t\t] as [number[], number[], number[], string][]) {\n\t\t\t\tif (!fitted.length) continue\n\t\t\t\tconst lPos = loess.positions\n\n\t\t\t\t// Find LOESS indices within the range of actual probe positions\n\t\t\t\tlet iStart = 0\n\t\t\t\tlet iEnd = lPos.length - 1\n\t\t\t\twhile (iStart < lPos.length && lPos[iStart] < firstProbePos) iStart++\n\t\t\t\twhile (iEnd >= 0 && lPos[iEnd] > lastProbePos) iEnd--\n\t\t\t\tif (iStart > iEnd) continue\n\n\t\t\t\tif (showCi) {\n\t\t\t\t\t// Draw CI as shaded region\n\t\t\t\t\tctx.globalAlpha = 0.12\n\t\t\t\t\tctx.fillStyle = color\n\t\t\t\t\tctx.beginPath()\n\t\t\t\t\tfor (let i = iStart; i <= iEnd; i++) {\n\t\t\t\t\t\tctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciUpper[i]))))\n\t\t\t\t\t}\n\t\t\t\t\tfor (let i = iEnd; i >= iStart; i--) {\n\t\t\t\t\t\tctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciLower[i]))))\n\t\t\t\t\t}\n\t\t\t\t\tctx.closePath()\n\t\t\t\t\tctx.fill()\n\t\t\t\t}\n\n\t\t\t\t// Draw LOESS fitted curve (dashed when no CI, solid otherwise)\n\t\t\t\tctx.globalAlpha = 0.8\n\t\t\t\tctx.strokeStyle = color\n\t\t\t\tctx.lineWidth = 2\n\t\t\t\tctx.setLineDash(showCi ? [] : [6, 4])\n\t\t\t\tctx.beginPath()\n\t\t\t\tfor (let i = iStart; i <= iEnd; i++) {\n\t\t\t\t\tctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, fitted[i]))))\n\t\t\t\t}\n\t\t\t\tctx.stroke()\n\t\t\t\tctx.setLineDash([])\n\t\t\t}\n\t\t}\n\n\t\t// Draw dots (hidden for large regions where only LOESS is shown)\n\t\tif (!showDots) {\n\t\t\tctx.globalAlpha = 1\n\t\t\treturn { img: { minv: 0, maxv: 1, src: canvas.toDataURL('image/png') }, showCi }\n\t\t}\n\t\tfor (let i = 0; i < probes.positions.length; i++) {\n\t\t\tconst x = scaleX(probes.positions[i])\n\t\t\tconst isSig = probes.fdr[i] < fdr_cutoff\n\t\t\tconst alpha = isSig ? 0.85 : 0.3\n\n\t\t\t// Group 1 (control)\n\t\t\tctx.globalAlpha = alpha\n\t\t\tctx.fillStyle = colors.group1\n\t\t\tconst m1 = probes.mean_group1[i]\n\t\t\tif (m1 != null) {\n\t\t\t\tctx.beginPath()\n\t\t\t\tctx.arc(x, scaleY(m1), 4, 0, Math.PI * 2)\n\t\t\t\tctx.fill()\n\t\t\t}\n\n\t\t\t// Group 2 (case)\n\t\t\tctx.fillStyle = colors.group2\n\t\t\tconst m2 = probes.mean_group2[i]\n\t\t\tif (m2 != null) {\n\t\t\t\tctx.beginPath()\n\t\t\t\tctx.arc(x, scaleY(m2), 4, 0, Math.PI * 2)\n\t\t\t\tctx.fill()\n\t\t\t}\n\t\t}\n\t\tctx.globalAlpha = 1\n\n\t\treturn { img: { minv: 0, maxv: 1, src: canvas.toDataURL('image/png') }, showCi }\n\t}\n\n\tprivate makeDmrBedItems(dmrResult: TermdbDmrSuccessResponse, settings: DmrConfig['settings']): BedItem[] {\n\t\treturn dmrResult.dmrs.map(dmr => {\n\t\t\t// Map -log10(min_smoothed_fdr) to alpha: more significant = more opaque\n\t\t\tconst negLog = -Math.log10(Math.max(dmr.min_smoothed_fdr, 1e-300))\n\t\t\tconst alpha = Math.round(Math.min(255, Math.max(50, (negLog / 10) * 255)))\n\t\t\tconst hex = alpha.toString(16).padStart(2, '0')\n\t\t\tconst base = dmr.direction === 'hyper' ? settings.dmr.colors.hyper : settings.dmr.colors.hypo\n\t\t\treturn { chr: dmr.chr, start: dmr.start, stop: dmr.stop, color: base + hex }\n\t\t})\n\t}\n\n\tprivate makeSigCpgBedItems(\n\t\tdmrResult: TermdbDmrSuccessResponse,\n\t\tsettings: DmrConfig['settings'],\n\t\tchr: string,\n\t\tqueryStart?: number,\n\t\tqueryStop?: number\n\t): BedItem[] {\n\t\tconst diag = dmrResult.diagnostic\n\t\tif (!diag) return []\n\t\tconst { probes } = diag\n\t\tconst items: BedItem[] = []\n\t\tconst minDeltaBeta = 0.05\n\t\tfor (let i = 0; i < probes.positions.length; i++) {\n\t\t\tif (probes.fdr[i] >= settings.dmr.fdr_cutoff) continue\n\t\t\tconst pos = probes.positions[i]\n\t\t\tif (queryStart != null && queryStop != null && (pos < queryStart || pos > queryStop)) continue\n\t\t\tconst mg1 = probes.mean_group1[i]\n\t\t\tconst mg2 = probes.mean_group2[i]\n\t\t\tif (mg1 == null || mg2 == null) continue\n\t\t\tconst deltaBeta = mg2 - mg1\n\t\t\tif (Math.abs(deltaBeta) < minDeltaBeta) continue\n\t\t\tconst color = deltaBeta >= 0 ? settings.dmr.colors.hyper : settings.dmr.colors.hypo\n\t\t\titems.push({ chr, start: pos, stop: pos + 1, color })\n\t\t}\n\t\treturn items\n\t}\n}\n", "import { table2col } from '#dom'\nimport { formatElapsedTime } from '#shared'\nimport type { DmrDiagnostic } from '#types'\nimport type { DmrDom, LegendRow, DmrViewData } from '../DmrTypes.ts'\n\nexport class DmrView {\n\tprivate dom: DmrDom\n\n\tconstructor(dom: DmrDom) {\n\t\tthis.dom = dom\n\t}\n\n\tasync renderBlock(\n\t\tviewData: DmrViewData,\n\t\tgenomeObj: any,\n\t\tsettings: { blockWidth: number },\n\t\tchr: string,\n\t\tstart: number,\n\t\tstop: number,\n\t\tonCoordinateChange: (rglst: { chr: string; start: number; stop: number }[]) => void\n\t) {\n\t\tconst { Block } = await import('#src/block')\n\t\treturn new Block({\n\t\t\tholder: this.dom.holder,\n\t\t\tgenome: genomeObj,\n\t\t\tchr,\n\t\t\tstart,\n\t\t\tstop,\n\t\t\ttklst: viewData.tklst,\n\t\t\tnobox: true,\n\t\t\twidth: settings.blockWidth,\n\t\t\tonCoordinateChange\n\t\t})\n\t}\n\n\tupdateTracks(viewData: DmrViewData, blockInstance: any) {\n\t\tfor (const tk of blockInstance.tklst) {\n\t\t\tconst updated = viewData.tklst.find((t: any) => t.name === tk.name)\n\t\t\tif (!updated) continue\n\t\t\tif (tk.type === 'bedj' && updated.bedItems) {\n\t\t\t\ttk.bedItems = updated.bedItems\n\t\t\t\tblockInstance.tk_load(tk)\n\t\t\t} else if (tk.type === 'bigwig' && updated.imgData) {\n\t\t\t\ttk.imgData = updated.imgData\n\t\t\t\tblockInstance.tk_load(tk)\n\t\t\t}\n\t\t}\n\t}\n\n\tupdateLegend(blockInstance: any, legendRows: LegendRow[]) {\n\t\tif (!blockInstance?.legend?.holder) return\n\t\tconst labels = ['Per-CpG Means', 'DMR', 'Sig. CpGs']\n\t\tblockInstance.legend.holder\n\t\t\t.selectAll('tr')\n\t\t\t.filter((_d: any, i: number, nodes: any) => {\n\t\t\t\tconst td = nodes[i].querySelector('td')\n\t\t\t\treturn td && labels.includes(td.textContent)\n\t\t\t})\n\t\t\t.remove()\n\t\tthis.renderLegend(blockInstance, legendRows)\n\t}\n\n\trenderLegend(blockInstance: any, legendRows: LegendRow[]) {\n\t\tif (!blockInstance?.legend?.holder) return\n\t\tconst { legendcolor, vpad } = blockInstance.legend\n\n\t\tfor (const row of legendRows) {\n\t\t\tconst tr = blockInstance.legend.holder.append('tr')\n\t\t\ttr.append('td')\n\t\t\t\t.text(row.label)\n\t\t\t\t.attr('style', `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (const entry of row.items) {\n\t\t\t\tconst item = td\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('style', `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`)\n\t\t\t\tif (entry.style === 'shaded') {\n\t\t\t\t\t// Shaded region with line marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`\n\t\t\t\t\t\t)\n\t\t\t\t} else if (entry.style === 'dashed') {\n\t\t\t\t\t// Dashed line marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`\n\t\t\t\t\t\t)\n\t\t\t\t} else {\n\t\t\t\t\t// Default square marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\titem.append('div').attr('style', 'display:inline-block;color:#555;font-size:.8em').text(entry.text)\n\t\t\t}\n\t\t}\n\t}\n\n\trenderDiagnostics(\n\t\tdiagnostic: DmrDiagnostic,\n\t\tdmrs: { start: number; stop: number; direction: string }[],\n\t\tfdr_cutoff: number\n\t) {\n\t\tconst panel = this.dom.diagnosticPanel\n\t\tpanel.selectAll('*').remove()\n\t\tpanel.style('display', 'block')\n\n\t\tconst { probes } = diagnostic\n\n\t\tconst toggle = panel.append('div').attr('style', 'cursor:default;font-size:12px;color:#888;padding:2px 0')\n\t\tconst statsContent = panel.append('div').style('display', 'none')\n\t\tlet expanded = false\n\t\ttoggle.text('+ Diagnostic details').on('click', () => {\n\t\t\texpanded = !expanded\n\t\t\ttoggle.text((expanded ? '\\u2212 ' : '+ ') + 'Diagnostic details')\n\t\t\tstatsContent.style('display', expanded ? 'block' : 'none')\n\t\t})\n\n\t\tconst spacings = diagnostic.probe_spacings\n\t\tconst medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0\n\t\tconst maxGap = spacings.length ? Math.max(...spacings) : 0\n\t\tconst gapsOver1kb = spacings.filter(s => s > 1000).length\n\t\tconst density =\n\t\t\tprobes.positions.length > 1\n\t\t\t\t? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1000)\n\t\t\t\t: 0\n\t\tconst sigFdrCount = probes.fdr.filter(f => f < fdr_cutoff).length\n\t\tconst minDeltaBeta = 0.05\n\t\tconst sigDualCount = probes.fdr.filter((f, i) => {\n\t\t\tif (f >= fdr_cutoff) return false\n\t\t\tconst m1 = probes.mean_group1[i]\n\t\t\tconst m2 = probes.mean_group2[i]\n\t\t\tif (m1 == null || m2 == null) return false\n\t\t\treturn Math.abs(m2 - m1) >= minDeltaBeta\n\t\t}).length\n\n\t\tconst t = table2col({ holder: statsContent, disableScroll: true })\n\t\tfor (const [k, v] of [\n\t\t\t['Probes in region', String(probes.positions.length)],\n\t\t\t['FDR significant', `${sigFdrCount} (FDR < ${fdr_cutoff})`],\n\t\t\t['FDR + effect size', `${sigDualCount} (FDR < ${fdr_cutoff} & |\\u0394\\u03B2| \\u2265 ${minDeltaBeta})`],\n\t\t\t['Probe density', `${density.toFixed(1)} probes/kb`],\n\t\t\t['Median spacing', `${medianSpacing.toFixed(0)} bp`],\n\t\t\t['Max gap', `${maxGap.toFixed(0)} bp`],\n\t\t\t['Gaps > 1kb', String(gapsOver1kb)],\n\t\t\t['DMRs called', String(dmrs.length)],\n\t\t\t...(diagnostic.total_probes_analyzed\n\t\t\t\t? [['Probes analyzed (genome-wide)', diagnostic.total_probes_analyzed.toLocaleString()]]\n\t\t\t\t: []),\n\t\t\t...(diagnostic.elapsed_ms != null ? [['Analysis time', formatElapsedTime(diagnostic.elapsed_ms)]] : []),\n\t\t\t...(diagnostic.peak_memory_mb != null ? [['Peak memory', `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : [])\n\t\t] as [string, string][]) {\n\t\t\tt.addRow(k, v)\n\t\t}\n\t}\n\n\tshowOverlay() {\n\t\tthis.dom.loadingOverlay.style('display', '')\n\t}\n\n\thideOverlay() {\n\t\tthis.dom.loadingOverlay.style('display', 'none')\n\t}\n\n\tclearDiagnostics() {\n\t\tthis.dom.diagnosticPanel.selectAll('*').remove()\n\t\tthis.dom.diagnosticPanel.style('display', 'none')\n\t}\n\n\tclearErrors() {\n\t\tthis.dom.error.selectAll('*').remove()\n\t}\n\n\tshowLoessNote(show: boolean) {\n\t\tthis.dom.error.selectAll('.sjpp-loess-note').remove()\n\t\tif (show) {\n\t\t\tthis.dom.error\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-loess-note')\n\t\t\t\t.style('color', '#888')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('padding', '4px 0')\n\t\t\t\t.text('Zoom in to see per-CpG dots.')\n\t\t}\n\t}\n}\n", "import { PlotBase } from '../PlotBase.ts'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { sayerror } from '#dom'\nimport type { DmrConfig, DmrDom } from './DmrTypes.ts'\nimport { getDefaultDMRSettings } from './settings/defaults.ts'\nimport { DmrModel } from './model/DmrModel.ts'\nimport { DmrViewModel } from './viewModel/DmrViewModel.ts'\nimport { DmrView } from './view/DmrView.ts'\n\nclass DmrPlot extends PlotBase implements RxComponent {\n\tstatic type = 'dmr'\n\n\ttype = DmrPlot.type\n\tdeclare dom: DmrDom\n\tblockInstance: InstanceType<any> | null = null\n\tanalyzedRegion: { chr: string; start: number; stop: number } | null = null\n\tview!: DmrView\n\tprivate model!: DmrModel\n\tprivate genomeObj: any\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tconst wrapper = opts.holder.append('div').style('position', 'relative')\n\t\tconst loadingOverlay = wrapper\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-spinner')\n\t\t\t.style('display', 'none')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('z-index', '10')\n\t\t\t.style('background-color', 'rgba(255,255,255,0.65)')\n\t\t// Backend toggle button (temporary \u2014 for R vs Rust validation)\n\t\tconst toggleDiv = opts.holder.append('div').style('padding', '2px 0')\n\t\tconst initBackend = opts.state?.config?.settings?.dmr?.backend || 'rust'\n\t\tconst toggleBtn = toggleDiv\n\t\t\t.append('button')\n\t\t\t.style('font-size', '11px')\n\t\t\t.text(`Backend: ${initBackend === 'rust' ? 'Rust' : 'R (DMRCate)'}`)\n\t\t\t.on('click', () => {\n\t\t\t\tconst config = this.state.config as DmrConfig\n\t\t\t\tconst curr = config.settings.dmr.backend || 'rust'\n\t\t\t\tconst next = curr === 'rust' ? 'r' : 'rust'\n\t\t\t\ttoggleBtn.text(`Backend: ${next === 'rust' ? 'Rust' : 'R (DMRCate)'}`)\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: { settings: { dmr: { ...config.settings.dmr, backend: next } } }\n\t\t\t\t})\n\t\t\t})\n\n\t\tthis.dom = {\n\t\t\theader: opts?.header,\n\t\t\tholder: wrapper.append('div'),\n\t\t\tloadingOverlay,\n\t\t\terror: opts.holder.append('div'),\n\t\t\tloading: opts.holder.append('div').text('Running DMR analysis\\u2026'),\n\t\t\tdiagnosticPanel: opts.holder.append('div').style('display', 'none')\n\t\t}\n\t\tthis.view = new DmrView(this.dom)\n\t}\n\n\tgetState(appState: { plots: DmrConfig[] }): { config: DmrConfig } {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw new Error(`No plot with id='${this.id}' found`)\n\t\treturn { config }\n\t}\n\n\tasync init(appState: any) {\n\t\tconst { config } = this.getState(appState)\n\t\tvalidateConfig(config)\n\t\tif (this.dom.header) this.dom.header.text(config.headerText || 'DMR Analysis')\n\t\tthis.genomeObj = this.app.opts.genome\n\t\tthis.model = new DmrModel(config, this.app.vocabApi.vocab)\n\n\t\t// First render: fetch data and build the block\n\t\tthis.dom.loading.style('display', 'block')\n\t\ttry {\n\t\t\tconst pad = config.settings.dmr.pad\n\t\t\tconst chr = config.coordinateOverride!.chr\n\t\t\tconst start = Math.max(0, Number(config.coordinateOverride!.start) - pad)\n\t\t\tconst stop = Number(config.coordinateOverride!.stop) + pad\n\n\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\tif ('error' in dmrResult) {\n\t\t\t\tsayerror(this.dom.error, dmrResult.error)\n\t\t\t\tthrow new Error(dmrResult.error)\n\t\t\t}\n\n\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop)\n\n\t\t\tthis.blockInstance = await this.view.renderBlock(\n\t\t\t\tvm.viewData,\n\t\t\t\tthis.genomeObj,\n\t\t\t\tconfig.settings.dmr,\n\t\t\t\tchr,\n\t\t\t\tstart,\n\t\t\t\tstop,\n\t\t\t\trglst => this.onBlockCoordinateChange(rglst)\n\t\t\t)\n\t\t\tthis.view.renderLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\tthis.view.showLoessNote(!vm.viewData.showDots)\n\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t} catch (e: unknown) {\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tconst msg = e instanceof Error ? e.message : String(e)\n\t\t\tsayerror(this.dom.error, msg)\n\t\t}\n\t\tthis.dom.loading.style('display', 'none')\n\t}\n\n\tasync main() {\n\t\t// Skip the first main() call \u2014 init() already rendered\n\t\tif (!this.analyzedRegion) return\n\n\t\tconst config = this.state.config as DmrConfig\n\t\tthis.model = new DmrModel(config, this.app.vocabApi.vocab)\n\n\t\tconst c = config.coordinateOverride\n\t\tif (!c) return\n\t\tconst pad = config.settings.dmr.pad\n\t\tconst chr = c.chr\n\t\tconst start = Math.max(0, Number(c.start) - pad)\n\t\tconst stop = Number(c.stop) + pad\n\n\t\tconst a = this.analyzedRegion\n\t\tconst coordsChanged = chr !== a.chr || start !== a.start || stop !== a.stop\n\n\t\tif (coordsChanged) {\n\t\t\t// New coordinates \u2014 re-fetch and update tracks in place\n\t\t\tthis.view.showOverlay()\n\t\t\tthis.view.clearErrors()\n\n\t\t\ttry {\n\t\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\t\tif ('error' in dmrResult) {\n\t\t\t\t\tsayerror(this.dom.error, dmrResult.error)\n\t\t\t\t\tthrow new Error(dmrResult.error)\n\t\t\t\t}\n\n\t\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\t\tconst blkRegion = this.blockInstance?.rglst?.[0]\n\t\t\t\tconst viewStart = blkRegion?.start ?? start\n\t\t\t\tconst viewStop = blkRegion?.stop ?? stop\n\t\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop)\n\n\t\t\t\tthis.view.updateTracks(vm.viewData, this.blockInstance)\n\t\t\t\tthis.view.updateLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\t\tthis.view.showLoessNote(!vm.viewData.showDots)\n\t\t\t\tthis.view.clearDiagnostics()\n\t\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t\t} catch (e: unknown) {\n\t\t\t\tif (this.app.isAbortError(e)) return\n\t\t\t\tconst msg = e instanceof Error ? e.message : String(e)\n\t\t\t\tsayerror(this.dom.error, msg)\n\t\t\t}\n\t\t\tthis.view.hideOverlay()\n\t\t} else {\n\t\t\t// Same coordinates but settings changed (e.g. backend toggle) \u2014 full rebuild\n\t\t\tthis.dom.holder.selectAll('*').remove()\n\t\t\tthis.view.clearErrors()\n\t\t\tthis.dom.loading.style('display', 'block')\n\t\t\tthis.blockInstance = null\n\n\t\t\ttry {\n\t\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\t\tif ('error' in dmrResult) {\n\t\t\t\t\tsayerror(this.dom.error, dmrResult.error)\n\t\t\t\t\tthrow new Error(dmrResult.error)\n\t\t\t\t}\n\n\t\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop)\n\n\t\t\t\tthis.blockInstance = await this.view.renderBlock(\n\t\t\t\t\tvm.viewData,\n\t\t\t\t\tthis.genomeObj,\n\t\t\t\t\tconfig.settings.dmr,\n\t\t\t\t\tchr,\n\t\t\t\t\tstart,\n\t\t\t\t\tstop,\n\t\t\t\t\trglst => this.onBlockCoordinateChange(rglst)\n\t\t\t\t)\n\t\t\t\tthis.view.renderLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\t\tthis.view.showLoessNote(!vm.viewData.showDots)\n\t\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t\t} catch (e: unknown) {\n\t\t\t\tif (this.app.isAbortError(e)) return\n\t\t\t\tconst msg = e instanceof Error ? e.message : String(e)\n\t\t\t\tsayerror(this.dom.error, msg)\n\t\t\t}\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t}\n\t}\n\n\tonBlockCoordinateChange(rglst: { chr: string; start: number; stop: number }[]) {\n\t\tif (!this.analyzedRegion || !rglst.length) return\n\t\tconst r = rglst[0]\n\t\tif (r.start >= r.stop || r.start < 0) return\n\t\tthis.view.clearErrors()\n\t\tconst a = this.analyzedRegion\n\t\tif (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }\n\t\t})\n\t}\n}\n\nexport const componentInit = getCompInit(DmrPlot)\n\nexport function getPlotConfig(opts: Partial<DmrConfig>): DmrConfig {\n\tvalidateConfig(opts)\n\n\tconst config = {\n\t\tsettings: {\n\t\t\tdmr: getDefaultDMRSettings(opts)\n\t\t}\n\t}\n\treturn copyMerge(config, opts)\n}\n\n/** Runs in both getPlotConfig and main() because will only run in main()\n * when plot is loaded from a saved state (e.g. mass session file).*/\nfunction validateConfig(opts) {\n\tif (!opts.coordinateOverride) throw new Error('coordinateOverride (chr/start/stop) is required for DMR plot')\n\tif (!opts.group1) throw new Error('group1 is required for DMR plot')\n\tif (!opts.group2) throw new Error('group2 is required for DMR plot')\n}\n\n/** Client-side region size guard (configurable via settings.dmr.maxRegionSize, default 5 Mb).\n *  The server also enforces a hard safety cap (10 Mb) to catch direct API calls or buggy clients. */\nfunction checkRegionSize(span: number, maxRegionSize: number) {\n\tif (span > maxRegionSize) {\n\t\tconst mbLimit = (maxRegionSize / 1_000_000).toFixed(0)\n\t\tconst mbSpan = (span / 1_000_000).toFixed(1)\n\t\tthrow new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`)\n\t}\n}\n"],
-  "mappings": 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