@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/proteinView-NRKT3C7H.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/proteinView.ts"],
-  "sourcesContent": ["import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { axisstyle } from '#src/client'\nimport { Menu, table2col, LegendCircleReference, addGeneSearchbox } from '#dom'\nimport { PlotBase } from './PlotBase'\nimport { dofetch3 } from '#common/dofetch'\nimport { axisBottom, axisLeft } from 'd3-axis'\nimport { scaleLinear } from 'd3-scale'\nimport { rgb } from 'd3-color'\nimport { shapeSelector, shapesArray } from '../dom/shapes.js'\nimport { NumericModes, TermTypes } from '#shared/terms.js'\nimport { aa2gmcoord } from '#src/coord'\nimport { mclass, getColors } from '#shared/common.js'\nimport { roundValue } from '#shared/roundValue.js'\n\nconst defaultConfig = {\n\tchartType: 'proteinView'\n}\n\nclass ProteinView extends PlotBase implements RxComponent {\n\tstatic type = 'proteinView'\n\ttype: string\n\tdom!: {\n\t\tholder: any\n\t\tbody: any\n\t\ttip: Menu\n\t}\n\tcomponents: any\n\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = ProteinView.type\n\t\tthis.components = {}\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div').style('padding', '10px')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tbody: holder.append('div'),\n\t\t\ttip: 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) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\tasync main() {\n\t\tconst term = this.state.config?.tw?.term\n\t\tif (!term?.name) throw new Error('proteinView: selected protein term is missing')\n\n\t\tconst body = {\n\t\t\tgenome: this.app.opts.state.vocab.genome,\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tterm: this.state.config.tw,\n\t\t\tfilter: this.state.config.filter,\n\t\t\tfilter0: this.state.config.filter0\n\t\t}\n\n\t\tconst data = await dofetch3('termdb/proteome', { body })\n\t\tif (data.error) throw data.error\n\t\tthis.dom.body.selectAll('*').remove()\n\t\trenderCohortVolcano(this.dom.body, data, this)\n\t\tconst ptmDataByIsoform = new Map<string, any[]>()\n\t\tfor (const cohortData of data.cohorts || []) {\n\t\t\tif (!cohortData.PTMType) continue // filter out non-PTM cohorts\n\t\t\tconst isoform = cohortData.isoform\n\t\t\tconst existingCohorts = ptmDataByIsoform.get(isoform)\n\t\t\tif (!existingCohorts) {\n\t\t\t\tptmDataByIsoform.set(isoform, [cohortData])\n\t\t\t} else {\n\t\t\t\texistingCohorts.push(cohortData)\n\t\t\t}\n\t\t}\n\n\t\tfor (const [isoform, ptmCohorts] of ptmDataByIsoform) {\n\t\t\tawait renderPTMLollipop(this.dom.body, ptmCohorts, this, isoform)\n\t\t}\n\t}\n}\n\nfunction renderCohortVolcano(holder: any, data: any, self: ProteinView) {\n\tconst dots: any[] = []\n\n\tfor (const cohortData of data?.cohorts || []) {\n\t\tconst log2fc = getLog2Ratio(cohortData.foldChange)\n\t\tconst pValue = Number(cohortData.pValue)\n\t\tconst testedN = Number(cohortData.testedN)\n\t\tconst controlN = Number(cohortData.controlN)\n\t\tif (log2fc === null || !Number.isFinite(pValue) || pValue <= 0) continue\n\t\tdots.push({\n\t\t\tassayName: cohortData.assayName,\n\t\t\tcohortName: cohortData.cohortName,\n\t\t\tPTMType: cohortData.PTMType,\n\t\t\tmodSites: cohortData.modSites,\n\t\t\tproteinAccession: cohortData.proteinAccession,\n\t\t\tuniqueIdentifier: cohortData.uniqueIdentifier,\n\t\t\tlog2fc,\n\t\t\tpValue,\n\t\t\tscore: -Math.log10(Math.max(pValue, 1e-300)),\n\t\t\ttestedN: Number.isFinite(testedN) ? testedN : 0,\n\t\t\tcontrolN: Number.isFinite(controlN) ? controlN : 0\n\t\t})\n\t}\n\n\tconst panel = holder.append('div').style('margin-bottom', '14px')\n\tpanel.append('div').style('font-weight', 600).style('margin-bottom', '6px').text('Cohort Volcano')\n\n\tif (!dots.length) {\n\t\tpanel\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.85em')\n\t\t\t.style('color', '#666')\n\t\t\t.text('No cohorts with valid fold-change and p-value to plot.')\n\t\treturn\n\t}\n\n\tconst width = 640\n\tconst height = 660\n\tconst margin = { top: 40, right: 70, bottom: 120, left: 70 }\n\tconst innerW = width - margin.left - margin.right\n\tconst innerH = height - margin.top - margin.bottom\n\n\tlet minX = Number.POSITIVE_INFINITY\n\tlet maxX = Number.NEGATIVE_INFINITY\n\tlet maxY = 0\n\tlet maxTestedN = 0\n\tlet minTestedN = Number.POSITIVE_INFINITY\n\tfor (const p of dots) {\n\t\tminX = Math.min(minX, p.log2fc)\n\t\tmaxX = Math.max(maxX, p.log2fc)\n\t\tmaxY = Math.max(maxY, p.score)\n\t\tmaxTestedN = Math.max(maxTestedN, p.testedN)\n\t\tif (p.testedN > 0) minTestedN = Math.min(minTestedN, p.testedN)\n\t}\n\n\tif (maxY < 1) maxY = 1\n\tif (!Number.isFinite(minTestedN)) minTestedN = 1\n\n\tconst xSpan = Math.max(0.05, maxX - minX)\n\tconst xPad = Math.max(0.01, xSpan * 0.1)\n\tconst xMin = Math.min(0, minX - xPad)\n\tconst xMax = Math.max(0, maxX + xPad)\n\tconst yMax = maxY * 1.15\n\n\tconst xScale = scaleLinear().domain([xMin, xMax]).range([0, innerW])\n\tconst yScale = scaleLinear().domain([0, yMax]).range([innerH, 0])\n\tconst radiusScale = scaleLinear()\n\t\t.domain([minTestedN, Math.max(minTestedN + 1, maxTestedN)])\n\t\t.range([4, 12])\n\n\tconst assayNames = [...new Set(dots.map((d: any) => d.assayName))].sort() as string[]\n\tconst cohortNames = [...new Set(dots.map((d: any) => d.cohortName))].sort() as string[]\n\tconst proteinAccessions = [...new Set(dots.map((d: any) => d.proteinAccession))].sort() as string[]\n\n\t// Create color scales for each grouping category\n\tconst assayColorScale = getColors(assayNames.length).domain(assayNames)\n\tconst cohortColorScale = getColors(cohortNames.length).domain(cohortNames)\n\tconst proteinColorScale = getColors(proteinAccessions.length).domain(proteinAccessions)\n\n\t// Store colors in maps\n\tconst assayColors = new Map<string, string>(assayNames.map(name => [name, rgb(assayColorScale(name)).formatHex()]))\n\tconst cohortColors = new Map<string, string>(cohortNames.map(name => [name, rgb(cohortColorScale(name)).formatHex()]))\n\tconst proteinColors = new Map<string, string>(\n\t\tproteinAccessions.map(acc => [acc, rgb(proteinColorScale(acc)).formatHex()])\n\t)\n\tconst makeShapeMap = (items: string[]) =>\n\t\tnew Map<string, number>(items.map((item, i) => [item, i % shapesArray.length]))\n\tconst assayShapes = makeShapeMap(assayNames)\n\tconst cohortShapes = makeShapeMap(cohortNames)\n\tconst proteinShapes = makeShapeMap(proteinAccessions)\n\n\tlet colorMode: 'none' | 'assayType' | 'cohort' | 'proteinAccession' = 'assayType'\n\tlet shapeMode: 'none' | 'assayType' | 'cohort' | 'proteinAccession' = 'none'\n\tconst defaultDotColor = '#9ca3af'\n\tconst getColor = (d: any) => {\n\t\tswitch (colorMode) {\n\t\t\tcase 'none':\n\t\t\t\treturn defaultDotColor\n\t\t\tcase 'assayType':\n\t\t\t\treturn assayColors.get(d.assayName) ?? '#888'\n\t\t\tcase 'cohort':\n\t\t\t\treturn cohortColors.get(d.cohortName) ?? '#888'\n\t\t\tcase 'proteinAccession':\n\t\t\t\treturn proteinColors.get(d.proteinAccession) ?? '#888'\n\t\t\tdefault:\n\t\t\t\treturn '#888'\n\t\t}\n\t}\n\tconst getShapeIndex = (d: any) => {\n\t\tswitch (shapeMode) {\n\t\t\tcase 'none':\n\t\t\t\treturn 0\n\t\t\tcase 'assayType':\n\t\t\t\treturn assayShapes.get(d.assayName) ?? 0\n\t\t\tcase 'cohort':\n\t\t\t\treturn cohortShapes.get(d.cohortName) ?? 0\n\t\t\tcase 'proteinAccession':\n\t\t\t\treturn proteinShapes.get(d.proteinAccession) ?? 0\n\t\t\tdefault:\n\t\t\t\treturn 0\n\t\t}\n\t}\n\tconst getShapePath = (d: any) => {\n\t\tconst index = getShapeIndex(d) % shapesArray.length\n\t\treturn shapesArray[index]\n\t}\n\tconst getShapeTransform = (d: any, sizeScale = 1) => {\n\t\tconst r = radiusScale(Math.max(minTestedN, d.testedN || minTestedN)) * sizeScale\n\t\tconst scale = r / 8\n\t\tconst x = xScale(d.log2fc) - 8 * scale\n\t\tconst y = yScale(d.score) - 8 * scale\n\t\treturn `translate(${x},${y}) scale(${scale})`\n\t}\n\tconst groupingModes: Array<{ key: 'none' | 'assayType' | 'cohort' | 'proteinAccession'; label: string }> = [\n\t\t{ key: 'none', label: 'Default' },\n\t\t{ key: 'assayType', label: 'Assay' },\n\t\t{ key: 'cohort', label: 'Cohort' },\n\t\t{ key: 'proteinAccession', label: 'Isoform' }\n\t]\n\tconst makeHiddenState = () => ({\n\t\tnone: new Set<string>(),\n\t\tassayType: new Set<string>(),\n\t\tcohort: new Set<string>(),\n\t\tproteinAccession: new Set<string>()\n\t})\n\tconst hiddenColor = makeHiddenState()\n\tconst hiddenShape = makeHiddenState()\n\tconst getValueByMode = (d: any, mode: 'none' | 'assayType' | 'cohort' | 'proteinAccession') => {\n\t\tswitch (mode) {\n\t\t\tcase 'none':\n\t\t\t\treturn ''\n\t\t\tcase 'assayType':\n\t\t\t\treturn d.assayName\n\t\t\tcase 'cohort':\n\t\t\t\treturn d.cohortName\n\t\t\tcase 'proteinAccession':\n\t\t\t\treturn d.proteinAccession\n\t\t\tdefault:\n\t\t\t\treturn ''\n\t\t}\n\t}\n\tconst isDotHidden = (d: any) => {\n\t\tconst colorValue = getValueByMode(d, colorMode)\n\t\tconst shapeValue = getValueByMode(d, shapeMode)\n\t\treturn hiddenColor[colorMode].has(colorValue) || hiddenShape[shapeMode].has(shapeValue)\n\t}\n\tconst getDotDistancePx = (d1: any, d2: any) => {\n\t\tconst x = xScale(d1.log2fc) - xScale(d2.log2fc)\n\t\tconst y = yScale(d1.score) - yScale(d2.score)\n\t\treturn Math.sqrt(x * x + y * y)\n\t}\n\tconst getClusterDots = (seed: any) => {\n\t\tconst thresholdPx = 5\n\t\treturn dots\n\t\t\t.filter(d => !isDotHidden(d) && getDotDistancePx(d, seed) < thresholdPx)\n\t\t\t.sort((a, b) => getDotDistancePx(a, seed) - getDotDistancePx(b, seed))\n\t}\n\tconst renderClusterTooltip = (clusterDots: any[]) => {\n\t\tconst tip = self.dom.tip.clear().d\n\n\t\tif (clusterDots.length > 1) {\n\t\t\ttip\n\t\t\t\t.append('div')\n\t\t\t\t.style('color', '#888')\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t.style('margin', '0 0 6px 0')\n\t\t\t\t.text(`${clusterDots.length} Cohorts`)\n\t\t}\n\n\t\tconst list = tip.append('div')\n\n\t\tif (clusterDots.length > 1) {\n\t\t\tconst grouped = new Map<string, any>()\n\t\t\tfor (const d of clusterDots) {\n\t\t\t\tconst key = [d.assayName, d.cohortName, d.modSites || ''].join('\\t')\n\t\t\t\tif (!grouped.has(key)) grouped.set(key, d)\n\t\t\t}\n\t\t\tfor (const d of grouped.values()) {\n\t\t\t\tconst block = list.append('div').style('padding', '3px 0').style('border-bottom', '1px solid #f1f1f1')\n\t\t\t\tconst table = table2col({ holder: block.append('table') })\n\t\t\t\ttable.addRow('Assay', d.assayName)\n\t\t\t\ttable.addRow('Cohort', d.cohortName)\n\t\t\t\tif (d.modSites) table.addRow('Modified Site', d.modSites)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\tfor (const d of clusterDots) {\n\t\t\tconst block = list.append('div').style('padding', '3px 0').style('border-bottom', '1px solid #f1f1f1')\n\t\t\tconst table = table2col({ holder: block.append('table') })\n\t\t\ttable.addRow('Assay', d.assayName)\n\t\t\ttable.addRow('Cohort', d.cohortName)\n\t\t\ttable.addRow('Protein Accession', d.proteinAccession)\n\t\t\tif (d.PTMType) {\n\t\t\t\ttable.addRow('PTM Type', d.PTMType)\n\t\t\t\ttable.addRow('Modified Site', d.modSites)\n\t\t\t\ttable.addRow('PTM', d.uniqueIdentifier)\n\t\t\t} else {\n\t\t\t\ttable.addRow('Isoform', d.uniqueIdentifier)\n\t\t\t}\n\t\t\ttable.addRow('log2 fold change', roundValue(d.log2fc, 3))\n\t\t\ttable.addRow('p value', d.pValue.toExponential(2))\n\t\t\ttable.addRow('-log10(p)', roundValue(d.score, 3))\n\t\t\ttable.addRow('Tested samples', d.testedN)\n\t\t\ttable.addRow('Control samples', d.controlN)\n\t\t}\n\t}\n\tconst updateDots = () => {\n\t\tcohortDots\n\t\t\t.attr('fill', (d: any) => getColor(d))\n\t\t\t.attr('stroke', (d: any) => getColor(d))\n\t\t\t.attr('d', (d: any) => getShapePath(d))\n\t\t\t.attr('transform', (d: any) => getShapeTransform(d))\n\t\t\t.style('opacity', (d: any) => (isDotHidden(d) ? 0 : 1))\n\t\t\t.style('pointer-events', (d: any) => (isDotHidden(d) ? 'none' : 'auto'))\n\t}\n\tconst getShapeMapInUse = () => {\n\t\tswitch (shapeMode) {\n\t\t\tcase 'none':\n\t\t\t\treturn assayShapes\n\t\t\tcase 'assayType':\n\t\t\t\treturn assayShapes\n\t\t\tcase 'cohort':\n\t\t\t\treturn cohortShapes\n\t\t\tcase 'proteinAccession':\n\t\t\t\treturn proteinShapes\n\t\t\tdefault:\n\t\t\t\treturn assayShapes\n\t\t}\n\t}\n\n\tconst plotAndLegend = panel\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'flex-start')\n\t\t.style('gap', '14px')\n\t\t.style('flex-wrap', 'wrap')\n\n\tconst svg = plotAndLegend\n\t\t.append('svg')\n\t\t.attr('width', width)\n\t\t.attr('height', height)\n\t\t.style('display', 'block')\n\t\t.style('max-width', '100%')\n\t\t.style('height', 'auto')\n\tconst g = svg.append('g').attr('transform', `translate(${margin.left},${margin.top})`)\n\n\tconst xAxis = g.append('g').attr('transform', `translate(0,${innerH})`).call(axisBottom(xScale))\n\taxisstyle({ axis: xAxis, color: 'black', showline: true })\n\n\tconst yAxis = g.append('g').call(axisLeft(yScale))\n\taxisstyle({ axis: yAxis, color: 'black', showline: true })\n\n\tconst x0 = xScale(0)\n\tconst pThreshold = -Math.log10(0.05)\n\tconst thresholdY = yScale(Math.min(yMax, pThreshold))\n\n\t// Guide lines\n\tg.append('line')\n\t\t.attr('x1', x0)\n\t\t.attr('x2', x0)\n\t\t.attr('y1', 0)\n\t\t.attr('y2', innerH)\n\t\t.attr('stroke', 'black')\n\t\t.attr('stroke-dasharray', '5 4')\n\t\t.attr('stroke-opacity', 0.4)\n\n\tg.append('line')\n\t\t.attr('x1', 0)\n\t\t.attr('x2', innerW)\n\t\t.attr('y1', thresholdY)\n\t\t.attr('y2', thresholdY)\n\t\t.attr('stroke', 'black')\n\t\t.attr('stroke-dasharray', '5 4')\n\t\t.attr('stroke-opacity', 0.4)\n\n\t// Axis labels\n\tg.append('text')\n\t\t.attr('x', innerW / 2)\n\t\t.attr('y', innerH + 44)\n\t\t.attr('text-anchor', 'middle')\n\t\t.style('font-weight', 600)\n\t\t.text('log2 fold change (disease / control)')\n\n\tg.append('text')\n\t\t.attr('transform', `translate(${-50},${innerH / 2}) rotate(-90)`)\n\t\t.attr('text-anchor', 'middle')\n\t\t.style('font-weight', 600)\n\t\t.text('-log10(p-value)')\n\n\t// Points\n\tconst cohortDots = g\n\t\t.selectAll('path.cohort-dot')\n\t\t.data(dots)\n\t\t.enter()\n\t\t.append('path')\n\t\t.attr('class', 'cohort-dot')\n\t\t.attr('transform', (d: any) => getShapeTransform(d, 0.9))\n\t\t.attr('d', (d: any) => getShapePath(d))\n\t\t.attr('fill', (d: any) => getColor(d))\n\t\t.attr('fill-opacity', 0.5)\n\t\t.attr('stroke', (d: any) => getColor(d))\n\t\t.attr('stroke-width', 1)\n\t\t.style('cursor', 'pointer')\n\n\tcohortDots\n\t\t.transition()\n\t\t.duration(350)\n\t\t.attr('d', (d: any) => getShapePath(d))\n\t\t.attr('transform', (d: any) => getShapeTransform(d, 1))\n\n\tupdateDots()\n\n\tcohortDots\n\t\t.on('mouseover', function (this: any, _event: any, d: any) {\n\t\t\tconst clusterDots = getClusterDots(d)\n\t\t\trenderClusterTooltip(clusterDots)\n\t\t\tself.dom.tip.showunder(this)\n\t\t})\n\t\t.on('mouseout', () => {\n\t\t\tself.dom.tip.hide()\n\t\t})\n\t\t.on('click', (_event: any, d: any) => launchViolinPlot(self, d.assayName, d.cohortName, d.uniqueIdentifier))\n\n\tconst legend = plotAndLegend\n\t\t.append('div')\n\t\t.style('margin', '0')\n\t\t.style('min-width', '220px')\n\t\t.style('font-size', '.75em')\n\t\t.style('color', '#374151')\n\n\tconst colorLegendDiv = legend.append('div').style('margin-bottom', '12px')\n\tconst shapeLegendDiv = legend.append('div').style('margin-bottom', '12px')\n\n\tfunction renderColorLegend() {\n\t\tcolorLegendDiv.selectAll('*').remove()\n\t\tshapeLegendDiv.selectAll('*').remove()\n\n\t\tconst modeRow = colorLegendDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', '10px')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('flex-wrap', 'wrap')\n\n\t\tmodeRow.append('span').text('Color by')\n\n\t\tfor (const { key, label } of groupingModes) {\n\t\t\tmodeRow\n\t\t\t\t.append('span')\n\t\t\t\t.text(label)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('font-weight', key === colorMode ? '600' : '400')\n\t\t\t\t.style('text-decoration', key === colorMode ? 'underline' : 'none')\n\t\t\t\t.style('color', key === colorMode ? '#111' : '#6b7280')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tcolorMode = key\n\t\t\t\t\tupdateDots()\n\t\t\t\t\trenderColorLegend()\n\t\t\t\t})\n\t\t}\n\n\t\tconst makeLegendItems = (items: string[], colorMap: Map<string, string>) => {\n\t\t\tconst openColorMenu = (event: any, name: string, swatch: any) => {\n\t\t\t\tconst menu = new Menu({ padding: '0px' })\n\t\t\t\tconst div = menu.d.append('div')\n\t\t\t\tconst hidden = hiddenColor[colorMode].has(name)\n\t\t\t\tconst hiddenCount = hiddenColor[colorMode].size\n\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text(hidden ? 'Show' : 'Hide')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (hidden) hiddenColor[colorMode].delete(name)\n\t\t\t\t\t\telse hiddenColor[colorMode].add(name)\n\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t})\n\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text('Show only')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\thiddenColor[colorMode].clear()\n\t\t\t\t\t\tfor (const item of items) {\n\t\t\t\t\t\t\tif (item != name) hiddenColor[colorMode].add(item)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t})\n\n\t\t\t\tif (hiddenCount > 1)\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text('Show all')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\thiddenColor[colorMode].clear()\n\t\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t})\n\n\t\t\t\tconst input: any = div\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t\t.text('Color:')\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.attr('value', colorMap.get(name) ?? '#888')\n\t\t\t\t\t.on('change', () => {\n\t\t\t\t\t\tconst newColor = input.node().value\n\t\t\t\t\t\tcolorMap.set(name, newColor)\n\t\t\t\t\t\tswatch.style('background', newColor)\n\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t})\n\t\t\t\tmenu.showunder(event.target)\n\t\t\t}\n\n\t\t\tfor (const name of items) {\n\t\t\t\tconst hidden = hiddenColor[colorMode].has(name)\n\t\t\t\tconst row = colorLegendDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'flex')\n\t\t\t\t\t.style('align-items', 'center')\n\t\t\t\t\t.style('gap', '6px')\n\t\t\t\t\t.style('margin-bottom', '3px')\n\t\t\t\tconst swatch = row\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('width', '10px')\n\t\t\t\t\t.style('height', '10px')\n\t\t\t\t\t.style('border-radius', '50%')\n\t\t\t\t\t.style('background', colorMap.get(name) ?? '#888')\n\t\t\t\t\t.style('opacity', hidden ? 0.35 : 0.8)\n\t\t\t\t\t.style('flex-shrink', '0')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\tswatch.on('click', (event: any) => openColorMenu(event, name, swatch))\n\t\t\t\trow\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.text(name)\n\t\t\t\t\t.style('text-decoration', hidden ? 'line-through' : 'none')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.on('click', (event: any) => openColorMenu(event, name, swatch))\n\t\t\t}\n\t\t}\n\n\t\tif (colorMode === 'assayType') {\n\t\t\tmakeLegendItems(assayNames, assayColors)\n\t\t} else if (colorMode === 'cohort') {\n\t\t\tmakeLegendItems(cohortNames, cohortColors)\n\t\t} else if (colorMode === 'proteinAccession') {\n\t\t\tmakeLegendItems(proteinAccessions, proteinColors)\n\t\t}\n\n\t\tconst shapeModeRow = shapeLegendDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('gap', '10px')\n\t\t\t.style('margin-bottom', '6px')\n\t\t\t.style('flex-wrap', 'wrap')\n\n\t\tshapeModeRow.append('span').text('Shape by')\n\n\t\tfor (const { key, label } of groupingModes) {\n\t\t\tshapeModeRow\n\t\t\t\t.append('span')\n\t\t\t\t.text(label)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('font-weight', key === shapeMode ? '600' : '400')\n\t\t\t\t.style('text-decoration', key === shapeMode ? 'underline' : 'none')\n\t\t\t\t.style('color', key === shapeMode ? '#111' : '#6b7280')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tshapeMode = key\n\t\t\t\t\tupdateDots()\n\t\t\t\t\trenderColorLegend()\n\t\t\t\t})\n\t\t}\n\n\t\tconst drawShapeLegend = (items: string[], shapeMap: Map<string, number>) => {\n\t\t\tconst openShapeMenu = (event: any, name: string) => {\n\t\t\t\tconst menu = new Menu({ padding: '0px' })\n\t\t\t\tconst activeShapeMap = getShapeMapInUse()\n\t\t\t\tconst div = menu.d.append('div')\n\t\t\t\tconst hidden = hiddenShape[shapeMode].has(name)\n\t\t\t\tconst hiddenCount = hiddenShape[shapeMode].size\n\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text(hidden ? 'Show' : 'Hide')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (hidden) hiddenShape[shapeMode].delete(name)\n\t\t\t\t\t\telse hiddenShape[shapeMode].add(name)\n\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t})\n\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text('Show only')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\thiddenShape[shapeMode].clear()\n\t\t\t\t\t\tfor (const item of items) {\n\t\t\t\t\t\t\tif (item != name) hiddenShape[shapeMode].add(item)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t})\n\n\t\t\t\tif (hiddenCount > 1)\n\t\t\t\t\tdiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t\t.text('Show all')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\thiddenShape[shapeMode].clear()\n\t\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t})\n\n\t\t\t\tdiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.text('Change shape')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tdiv.selectAll('*').remove()\n\t\t\t\t\t\tshapeSelector(div, (index: number) => {\n\t\t\t\t\t\t\tactiveShapeMap.set(name, index)\n\t\t\t\t\t\t\tupdateDots()\n\t\t\t\t\t\t\trenderColorLegend()\n\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\n\t\t\t\tmenu.showunder(event.target)\n\t\t\t}\n\n\t\t\tfor (const name of items) {\n\t\t\t\tconst hidden = hiddenShape[shapeMode].has(name)\n\t\t\t\tconst row = shapeLegendDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'flex')\n\t\t\t\t\t.style('align-items', 'center')\n\t\t\t\t\t.style('gap', '6px')\n\t\t\t\t\t.style('margin-bottom', '3px')\n\t\t\t\tconst icon = row\n\t\t\t\t\t.append('svg')\n\t\t\t\t\t.attr('width', 16)\n\t\t\t\t\t.attr('height', 16)\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\ticon\n\t\t\t\t\t.append('path')\n\t\t\t\t\t.attr('transform', 'scale(0.8)')\n\t\t\t\t\t.attr('d', shapesArray[(shapeMap.get(name) || 0) % shapesArray.length])\n\t\t\t\t\t.attr('fill', '#4b5563')\n\t\t\t\t\t.attr('fill-opacity', hidden ? 0.35 : 0.9)\n\t\t\t\ticon.on('click', (event: any) => openShapeMenu(event, name))\n\t\t\t\trow\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.text(name)\n\t\t\t\t\t.style('text-decoration', hidden ? 'line-through' : 'none')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.on('click', (event: any) => openShapeMenu(event, name))\n\t\t\t}\n\t\t}\n\n\t\tif (shapeMode === 'assayType') {\n\t\t\tdrawShapeLegend(assayNames, assayShapes)\n\t\t} else if (shapeMode === 'cohort') {\n\t\t\tdrawShapeLegend(cohortNames, cohortShapes)\n\t\t} else if (shapeMode === 'proteinAccession') {\n\t\t\tdrawShapeLegend(proteinAccessions, proteinShapes)\n\t\t}\n\t}\n\n\trenderColorLegend()\n\n\tconst sizeLegendRow = legend\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'flex-start')\n\t\t.style('gap', '8px')\n\t\t.style('margin-top', '8px')\n\n\tsizeLegendRow.append('span').style('display', 'inline-block').style('margin-top', '42px').text('Tested sample size')\n\n\tconst legendSvg = sizeLegendRow.append('svg').attr('width', 190).attr('height', 110).style('display', 'block')\n\n\tnew LegendCircleReference({\n\t\tg: legendSvg.append('g').attr('transform', 'translate(12, 8)'),\n\t\tinputMax: 12,\n\t\tinputMin: 4,\n\t\tmaxLabel: maxTestedN || minTestedN,\n\t\tmaxRadius: radiusScale(Math.max(minTestedN + 1, maxTestedN || minTestedN)),\n\t\tminLabel: minTestedN,\n\t\tminRadius: radiusScale(minTestedN),\n\t\ttitle: '',\n\t\tmenu: {\n\t\t\tminMaxLabel: 'pixels',\n\t\t\tcallback: async (obj: { min: number; max: number }) => {\n\t\t\t\tradiusScale.range([obj.min, obj.max])\n\t\t\t\tupdateDots()\n\t\t\t}\n\t\t}\n\t})\n}\n\n/*\nfunction renderFCSummary(holder: any, data: any, self: ProteinView) {\n\tholder.selectAll('*').remove()\n\n\t// data.nonPTMAssays store the fold change for each nonPTM assay type, data.PTMs store the PTM data (including fold change) for each PTM assay type\n\tconst nonPTMAssays = data?.nonPTMAssays || []\n\n\tlet maxAbs = 0\n\tfor (const assay of nonPTMAssays) {\n\t\tfor (const c of assay.nonPTMCohorts || []) {\n\t\t\tconst log2ratio = getLog2Ratio(c.value)\n\t\t\tif (log2ratio !== null) maxAbs = Math.max(maxAbs, Math.abs(log2ratio))\n\t\t}\n\t}\n\tif (maxAbs < 0.05) maxAbs = 0.05 // set a minimum scale for better visualization of small fold changes\n\n\tfor (const assay of nonPTMAssays) {\n\t\tconst assayName = assay.assayName\n\t\tconst section = holder.append('div').style('margin-bottom', '18px')\n\t\tsection.append('div').style('font-weight', 600).style('margin-bottom', '8px').text(`${assayName}`)\n\n\t\tconst header = section\n\t\t\t.append('div')\n\t\t\t.style('display', 'grid')\n\t\t\t.style('grid-template-columns', '220px 30% 100px')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '8px')\n\t\t\t.style('margin', '0 0 6px 0')\n\t\t\t.style('font-size', '.75em')\n\t\t\t.style('font-weight', 600)\n\t\t\t.style('color', '#495057')\n\n\t\theader.append('div').text('Cohort')\n\t\tconst scaleHeader = header.append('div').style('position', 'relative').style('height', '14px')\n\n\t\tscaleHeader.append('div').style('position', 'absolute').style('left', 0).style('top', 0).text((-maxAbs).toFixed(2))\n\n\t\tscaleHeader\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('left', '50%')\n\t\t\t.style('top', 0)\n\t\t\t.style('transform', 'translateX(-50%)')\n\t\t\t.text('0')\n\n\t\tscaleHeader.append('div').style('position', 'absolute').style('right', 0).style('top', 0).text(maxAbs.toFixed(2))\n\n\t\theader.append('div').text('log2 fold change')\n\n\t\tfor (const c of assay.nonPTMCohorts || []) {\n\t\t\tconst cohortName = c.cohortName\n\t\t\tconst log2ratio = getLog2Ratio(c.value)\n\t\t\tconst row = section\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'grid')\n\t\t\t\t.style('grid-template-columns', '220px 30% 100px')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '8px')\n\t\t\t\t.style('margin', '4px 0')\n\n\t\t\trow.append('div').style('font-size', '.9em').text(cohortName)\n\n\t\t\tconst track = row\n\t\t\t\t.append('div')\n\t\t\t\t.style('height', '14px')\n\t\t\t\t.style('background', '#f1f3f4')\n\t\t\t\t.style('border-radius', '7px')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('overflow', 'hidden')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.attr('title', 'Click to show violin plot')\n\t\t\t\t.on('click', () => launchViolinPlot(self, assayName, cohortName))\n\n\t\t\ttrack\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('left', '50%')\n\t\t\t\t.style('top', 0)\n\t\t\t\t.style('bottom', 0)\n\t\t\t\t.style('width', '1px')\n\t\t\t\t.style('transform', 'translateX(-0.5px)')\n\t\t\t\t.style('background', '#868e96')\n\t\t\t\t.style('opacity', 0.7)\n\n\t\t\tconst value = Number.isFinite(log2ratio) ? log2ratio : 0\n\t\t\tconst ratio = maxAbs > 0 ? Math.abs(value as number) / maxAbs : 0\n\t\t\tconst widthPct = Math.max(0, Math.min(50, ratio * 50))\n\t\t\tif (log2ratio !== null && widthPct > 0) {\n\t\t\t\ttrack\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('position', 'absolute')\n\t\t\t\t\t.style('left', log2ratio >= 0 ? '50%' : `${50 - widthPct}%`)\n\t\t\t\t\t.style('top', 0)\n\t\t\t\t\t.style('bottom', 0)\n\t\t\t\t\t.style('width', `${widthPct}%`)\n\t\t\t\t\t.style('background', log2ratio >= 0 ? '#2b8a3e' : '#c92a2a')\n\t\t\t\t\t.style('opacity', 1)\n\t\t\t}\n\n\t\t\trow\n\t\t\t\t.append('div')\n\t\t\t\t.style('font-family', 'monospace')\n\t\t\t\t.style('font-size', '.85em')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.attr('title', 'Click to show violin plot')\n\t\t\t\t.on('click', () => launchViolinPlot(self, assayName, cohortName))\n\t\t\t\t.text(log2ratio !== null ? log2ratio.toFixed(3) : 'NA')\n\t\t}\n\t}\n}\n*/\n\nfunction launchViolinPlot(self: ProteinView, assayName: string, cohortName: string, isoform: string) {\n\tconst selectedProtein = self.state.config?.tw?.term\n\tif (!selectedProtein) throw new Error('proteinView: selected protein term is missing')\n\n\tconst action: any = {\n\t\ttype: 'plot_create',\n\t\tconfig: {\n\t\t\tchartType: 'summary'\n\t\t}\n\t}\n\n\taction.config.assayCohortTitle = `${assayName}: ${cohortName}`\n\taction.config.proteomeDetails = { assay: assayName, cohort: cohortName }\n\n\tconst termdbConfig = self.app.vocabApi.termdbConfig\n\tconst proteomeOverlayTerm = termdbConfig?.queries?.proteome?.overlayTerm\n\tconst t = structuredClone(selectedProtein)\n\tt.name = `${t.name}: ${isoform}`\n\tt.proteomeDetails = { assay: assayName, cohort: cohortName }\n\taction.config.term = { term: t, q: { mode: NumericModes.continuous } }\n\n\tif (proteomeOverlayTerm) {\n\t\taction.config.term2 = { term: structuredClone(proteomeOverlayTerm), q: {} }\n\t}\n\n\tself.app.dispatch(action)\n}\n\nasync function renderPTMLollipop(holder: any, ptmCohorts: any, self: ProteinView, isoform: string) {\n\tif (!ptmCohorts?.length) return\n\n\tconst custom_variants: any[] = []\n\tconst mergedMclassOverride: any = {}\n\tconst gm = await getGmForPTM(ptmCohorts[0].geneName, self.app.opts.genome.name, isoform)\n\tfor (const ptm of ptmCohorts) {\n\t\t//use default gene model to get coordinates for all PTM sites, which is sufficient for most cases\n\t\t//and avoids the complexity of mapping between different isoforms. TODO:support isoform-specific mapping.\n\t\tif (!gm) continue\n\t\tconst logValue = getLog2Ratio(ptm.foldChange)\n\n\t\tif (ptm.mclassOverride && typeof ptm.mclassOverride == 'object') {\n\t\t\tObject.assign(mergedMclassOverride, ptm.mclassOverride)\n\t\t}\n\n\t\tconst site = parsePTMModSites(ptm.modSites)\n\t\tif (!site) continue\n\t\tconst pos = aa2gmcoord(site, gm)\n\t\tif (!Number.isInteger(pos)) continue\n\t\tconst ptmClass = Object.keys(ptm.mclassOverride || {})[0]\n\t\tcustom_variants.push({\n\t\t\tchr: gm.chr,\n\t\t\tpos,\n\t\t\tmname: `${ptm.modSites}: ${ptm.cohortName}`,\n\t\t\tclass: ptmClass,\n\t\t\tdt: 1,\n\t\t\tlogValue\n\t\t})\n\t}\n\tif (!custom_variants.length) return\n\n\tconst mclassOverride = {\n\t\tclassName: 'PTMs',\n\t\tclasses: mergedMclassOverride\n\t}\n\n\t// apply mclass override to global mclass, which will be used by the mds3 track to display the PTM sites.\n\t// this is necessary because the lollipop plot relies on mclass for variant\n\t// TODO: find a better way (such as defining PTM-specific class keys) to pass mclass override to the track\n\t// without modifying global mclass, which can have unintended side effects on other plots.\n\tfor (const key in mclassOverride.classes) {\n\t\tif (mclass[key]) Object.assign(mclass[key], mclassOverride.classes[key])\n\t}\n\n\t// create mds3 custom track using numeric mode with logValue on y-axis\n\tconst tk = {\n\t\ttype: 'mds3',\n\t\tname: 'PTMs',\n\t\tcustom_variants: custom_variants,\n\t\tskewerModes: [\n\t\t\t{\n\t\t\t\ttype: 'numeric',\n\t\t\t\tbyAttribute: 'logValue',\n\t\t\t\tlabel: 'Log2FC Disease vs Control',\n\t\t\t\tinuse: true,\n\t\t\t\taxisheight: 100\n\t\t\t}\n\t\t],\n\t\tmclassOverride\n\t}\n\n\t// launch block in protein mode with custom track\n\tconst arg = {\n\t\tholder: holder.append('div'),\n\t\tgenome: self.app.opts.genome,\n\t\tnobox: true,\n\t\ttklst: [tk],\n\t\tmclassOverride,\n\t\tdebugmode: self.app.opts.debug,\n\t\tquery: gm.isoform\n\t}\n\n\tconst _ = await import('#src/block.init')\n\tawait _.default(arg)\n}\n\n// return the first valid modification site parsed from the modSites string, which is expected to be in the format like \"S10\", or \"S10,T11\"\n// for now return the first valid site for simplicity. TODO: parse and display multiple sites if available.\nfunction parsePTMModSites(modSites: string) {\n\tif (!modSites) return null\n\tconst regex = /([A-Za-z])(\\d+)/g\n\tlet m\n\twhile ((m = regex.exec(modSites)) !== null) {\n\t\tconst position = Number(m[2])\n\t\tif (!Number.isInteger(position) || position < 1) continue\n\t\treturn position\n\t}\n\treturn null\n}\n\nasync function getGmForPTM(geneName: string, genomeName: string, isoform: string) {\n\tif (!geneName) return null\n\tconst d = await dofetch3('genelookup', {\n\t\tbody: {\n\t\t\tdeep: 1,\n\t\t\tgenome: genomeName,\n\t\t\tinput: geneName\n\t\t}\n\t})\n\n\tif (d.error || !Array.isArray(d.gmlst) || !d.gmlst.length) return null\n\n\tconst normalizedIsoform = isoform?.trim().toUpperCase()\n\tconst gm =\n\t\td.gmlst.find((i: any) => i.isoform && normalizedIsoform && i.isoform.toUpperCase() == normalizedIsoform) ||\n\t\td.gmlst.find((i: any) => i.isdefault) ||\n\t\td.gmlst[0]\n\treturn gm\n}\n\nfunction getLog2Ratio(foldChange: number) {\n\tif (!Number.isFinite(foldChange) || foldChange <= 0) return null\n\treturn Math.log2(foldChange)\n}\n\nexport async function getPlotConfig(opts: any) {\n\tconst config = structuredClone(defaultConfig)\n\tif (!opts.tw) throw new Error('proteinView requires opts.tw')\n\treturn copyMerge(config, opts)\n}\n\nexport function makeChartBtnMenu(holder: any, chartsInstance: any) {\n\tconst row = holder.append('div').style('padding', '5px')\n\trow.append('span').style('font-weight', 'bold').text('Enter a gene name:')\n\n\tconst geneSearch = addGeneSearchbox({\n\t\trow,\n\t\tgenome: chartsInstance.app.opts.genome,\n\t\ttip: new Menu({ padding: '0px' }),\n\t\tsearchOnly: 'gene',\n\t\tcallback: async () => {\n\t\t\tif (!geneSearch.geneSymbol) throw new Error('A valid gene selection is required')\n\t\t\tchartsInstance.dom.tip.hide()\n\t\t\tchartsInstance.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'proteinView',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\tgene: geneSearch.geneSymbol,\n\t\t\t\t\t\t\tname: geneSearch.geneSymbol,\n\t\t\t\t\t\t\ttype: TermTypes.PROTEOME_ABUNDANCE\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t})\n}\n\nexport const proteinViewInit = getCompInit(ProteinView)\nexport const componentInit = proteinViewInit\n"],
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-  "names": []
-}

package/dist/proteomeAbundance-3UZIGZWO.js

@@ -1,21 +0,0 @@
-import {
-  makeChartBtnMenu,
-  renderAssayAndCohortRadios,
-  toTvslstFilter
-} from "./chunk-QPYRMBI5.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  makeChartBtnMenu,
-  renderAssayAndCohortRadios,
-  toTvslstFilter
-};
-//# sourceMappingURL=proteomeAbundance-3UZIGZWO.js.map

package/dist/proteomeAbundance-6QXRHIJD.js

@@ -1,63 +0,0 @@
-import {
-  renderAssayAndCohortRadios
-} from "./chunk-QPYRMBI5.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/proteomeAbundance.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.opts = opts;
-    this.dom = {};
-    opts.holder.style("padding", "5px 10px 10px 25px");
-    this.assays = this.opts.app.vocabApi.termdbConfig?.queries?.proteome?.assays || {};
-    const assayKeys = Object.keys(this.assays);
-    if (!assayKeys.length) throw "No proteome assays available";
-    const initialProteomeDetails = opts.usecase?.proteomeDetails || {};
-    const selectedAssay = initialProteomeDetails.assay && this.assays[initialProteomeDetails.assay] ? initialProteomeDetails.assay : assayKeys[0];
-    const cohortKeys = Object.keys(this.assays[selectedAssay]?.cohorts || {});
-    if (!cohortKeys.length) throw "No cohorts available for selected assay";
-    const selectedCohort = initialProteomeDetails.cohort && this.assays[selectedAssay]?.cohorts?.[initialProteomeDetails.cohort] ? initialProteomeDetails.cohort : cohortKeys[0];
-    this.proteomeDetails = { assay: selectedAssay, cohort: selectedCohort };
-    this.dom.typeSettingDiv = opts.holder.append("div");
-    renderAssayAndCohortRadios({
-      holder: this.dom.typeSettingDiv,
-      assays: this.assays,
-      selectedProteomeDetails: this.proteomeDetails,
-      onChange: (proteomeDetails) => {
-        const { assay, cohort } = proteomeDetails;
-        this.proteomeDetails = { assay, cohort };
-        void this.updateUsecase();
-      }
-    });
-    await this.updateUsecase();
-  }
-  async updateUsecase() {
-    const { assay, cohort } = this.proteomeDetails;
-    const state = this.opts.app.getState();
-    await this.opts.app.dispatch({
-      type: "app_refresh",
-      state: {
-        tree: {
-          ...state.tree,
-          usecase: {
-            ...state.tree.usecase,
-            proteomeDetails: { assay, cohort }
-          }
-        }
-      }
-    });
-  }
-};
-export {
-  SearchHandler
-};
-//# sourceMappingURL=proteomeAbundance-6QXRHIJD.js.map

package/dist/qualitative-7XEX7QZP.js

@@ -1,220 +0,0 @@
-import {
-  HandlerBase,
-  require_debounce
-} from "./chunk-LSEFWW72.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termsetting/handlers/qualitative.ts
-var import_debounce = __toESM(require_debounce(), 1);
-var GroupSet = class extends HandlerBase {
-  constructor(opts) {
-    super(opts);
-    this.defaultMaxGrpNum = 5;
-    this.minGrpNum = 3;
-    //{groups: any[], values: any[]}
-    this.dom = {};
-    this.termsetting = opts.termsetting;
-    this.tw = opts.termsetting.tw;
-    this.dom.holder = opts.holder || this.termsetting.dom.tip.d;
-    this.data = { groups: [], values: [], filters: [] };
-  }
-  getPillStatus() {
-    return this.tw.getStatus(this.termsetting.usecase);
-  }
-  async showEditMenu() {
-    const self = this.termsetting;
-    const holder = this.dom.holder;
-    this.dom.loadingDiv = holder.append("div").style("margin", "15px").text("Getting categories...");
-    this.dom.menuWrapper = holder.append("div");
-    const body = self.opts.getBodyParams?.() || {};
-    const data = await self.vocabApi.getCategories(self.term, self.filter, body);
-    this.dom.loadingDiv.style("display", "none");
-    this.category2samplecount = data.lst;
-    this.data = this.tw.getGroups(this.category2samplecount);
-    await this.initGrpSetUI();
-  }
-  async initGrpSetUI() {
-    const self = this.termsetting;
-    this.maxGrpNum = this.data.values.length >= this.defaultMaxGrpNum ? this.defaultMaxGrpNum + 1 : this.data.values.length;
-    self.dom.tip.showunder(self.dom.holder.node());
-    await this.showDraggables();
-  }
-  async showDraggables() {
-    const self = this.termsetting;
-    this.dom.menuWrapper.style("padding", "10px");
-    this.dom.actionDiv = this.dom.menuWrapper.append("div").attr("class", "sjpp-group-actions").style("padding", "0px 10px 10px 0px");
-    const findNewGrps = this.data.groups.filter((g) => g.name.startsWith("New Group"));
-    let newGrpNum = findNewGrps.length > 0 ? findNewGrps[findNewGrps.length - 1].name.replace(`New Group `, "") : 0;
-    const q = this.tw.q;
-    this.dom.actionDiv.addGroup = this.dom.actionDiv.append("button").classed("sjpp_grpset_addGrp_btn", true).style("display", "inline-block").style("text-align", "center").style("cursor", q.mode == "binary" ? "default" : "pointer").property("disabled", q.mode == "binary" ? true : this.data.groups.length >= this.maxGrpNum).text("Add Group").on("click", async () => {
-      newGrpNum++;
-      this.data.groups.push({
-        currentIdx: this.data.groups.length,
-        type: "values",
-        name: `New Group${newGrpNum != 1 ? ` ${newGrpNum}` : ""}`
-      });
-      const group = this.data.groups[this.data.groups.length - 1];
-      await this.initGroupDiv(group);
-      await this.update();
-    });
-    this.dom.actionDiv.applyBtn = this.dom.actionDiv.append("button").classed("sjpp_grpset_apply_btn", true).style("display", self.opts.hideApply ? "none" : "inline-block").style("text-align", "center").style("float", "right").style("cursor", "pointer").text("Apply").on("click", () => {
-      this.processDraggables();
-      self.dom.tip.hide();
-      self.api.runCallback();
-    });
-    this.dom.menuWrapper.append("div").style("display", "block").style("margin", "5px 2px").style("font-size", ".6em").style("color", "#999").text("Drag-and-drop to assign categories to groups.");
-    this.dom.grpsWrapper = this.dom.menuWrapper.append("div").classed("sjpp-groups-wrapper", true);
-    this.dom.includedWrapper = this.dom.grpsWrapper.append("div").classed("sjpp-groups-include", true).classed("sjpp-group-edit-div", true).style("display", "flex");
-    this.dom.excludedWrapper = this.dom.grpsWrapper.append("div").classed("sjpp-groups-exclude", true).classed("sjpp-group-edit-div", true).classed("sjpp-drag-drop-div", true);
-    const excludedGroup = this.data.groups.find((d) => d.currentIdx === 0);
-    delete excludedGroup.wrapper;
-    await this.initGroupDiv(excludedGroup);
-    const handler = this;
-    await this.dom.includedWrapper.selectAll("div").data(this.data.groups.filter((d) => d.currentIdx != 0)).enter().append("div").classed("sjpp-drag-drop-div", true).style("border", "1px solid #efefef").style("display", "block").style("padding", "10px").style("vertical-align", "top").each(async function(group) {
-      group.wrapper = select_default(this);
-      await handler.initGroupDiv(group);
-    });
-  }
-  processDraggables() {
-    const self = this.termsetting;
-    const editedGrpset = this.draggedItem || this.editedName || this.removedGrp;
-    if (!editedGrpset) return;
-    const customset = { groups: [] };
-    for (const group of this.data.groups) {
-      if (group.type != "values" && group.type != "QualTWValues" && group.type != "QualTWValues")
-        throw `group.type='${group.type}' is not recognized`;
-      const customgroup = { name: group.name, type: "values", uncomputable: group.uncomputable };
-      const groupValues = this.data.values.filter((v) => v.group == group.currentIdx).map((v) => {
-        return { key: v.key, label: v.label, samplecount: v.samplecount };
-      });
-      customgroup.values = groupValues;
-      customset.groups.push(customgroup);
-    }
-    Object.assign(self.q, {
-      type: "custom-groupset",
-      customset
-    });
-  }
-  async initGroupDiv(group) {
-    const wrapper = group.currentIdx === 0 ? this.dom.excludedWrapper : this.dom.includedWrapper;
-    if (!group.type) group.type = "values";
-    if (!group.wrapper)
-      group.wrapper = wrapper.append("div").classed("sjpp-drag-drop-div", true).style("border", "1px solid #efefef").style("display", "block").style("padding", "10px").style("vertical-align", "top");
-    group.wrapper.on("drop", (event) => {
-      const itemData = this.draggedItem.node().__data__;
-      if (itemData.group === group.currentIdx) return;
-      group.draggables.node().appendChild(this.draggedItem.node());
-      this.draggedItem.style("transition-property", "background-color").style("transition-duration", "1s").style("background-color", "#fff2cc");
-      this.data.values.find((v) => v === itemData).group = group.currentIdx;
-      event.preventDefault();
-      event.stopPropagation();
-    }).on("dragleave", (event) => {
-      event.preventDefault();
-      event.stopPropagation();
-      group.wrapper.style("background-color", "#fff");
-    }).on("dragend", (event) => {
-      event.preventDefault();
-      event.stopPropagation();
-      group.wrapper.style("background-color", "#fff");
-    }).on("dragover", (event) => {
-      event.preventDefault();
-      event.stopPropagation();
-      group.wrapper.style(
-        "background-color",
-        group.currentIdx !== this.draggedItem.node().__data__.group ? "#cfe2f3" : "#fff"
-      );
-    }).on("dragenter", (event) => {
-      if (this.draggedItem.node().__data__.group === group.currentIdx) return;
-      event.preventDefault();
-      event.stopPropagation();
-      group.wrapper.style(
-        "background-color",
-        group.currentIdx !== this.draggedItem.node().__data__.group ? "#cfe2f3" : "#fff"
-      );
-    });
-    if (group.currentIdx === 0) {
-      group.title = group.wrapper.append("div").style("display", "inline-block").style("padding", "3px 10px").style("text-align", "left").style("font-size", ".6em").style("text-transform", "uppercase").style("color", "#999").text(group.name);
-    } else {
-      group.dragActionDiv = group.wrapper.append("div").style("display", "flex").style("align-items", "center");
-      group.input = group.dragActionDiv.append("input").attr("size", 12).attr("value", group.name).style("margin", "5px").style("margin-left", "8px").style("display", "inline-block").style("font-size", ".8em").style("width", "87%").on("keyup", () => {
-        (0, import_debounce.debounce)(this.onKeyUp(group), 1e3);
-      });
-      group.inputMessage = group.dragActionDiv.append("span").style("color", "red").style("font-size", "0.7em").text("NOT unique").style("display", "none");
-      group.destroyBtn = group.dragActionDiv.append("button").style("display", "inline-block").style("padding", "0px 4px").property("disabled", this.data.groups.length <= this.minGrpNum).text("x").on("click", async () => {
-        if (this.data.groups.length <= this.minGrpNum) return;
-        this.data.groups = this.data.groups.filter((d) => d.currentIdx != group.currentIdx);
-        await this.removeGroup(group);
-      });
-    }
-    group.draggables = group.wrapper.append("div").classed("sjpp-drag-list-div", true);
-    await this.addItems(group);
-  }
-  async addItems(group) {
-    const handler = this;
-    await group.draggables.selectAll("div").data(this.data.values.filter((d) => d.group == group.currentIdx)).enter().append("div").attr("draggable", "true").attr("class", "sjpp-drag-item").style("margin", "3px").style("cursor", "default").style("padding", "3px 10px").style("border-radius", "5px").style("color", (d) => d.samplecount == 0 ? "#777" : "black").text((d) => `${d.label}${d.samplecount !== void 0 ? ` (n=${d.samplecount})` : ""}`).style("background-color", "#eee").each(function() {
-      const itemNode = select_default(this).on("dragstart", function() {
-        itemNode.style("background-color", "#fff2cc");
-        handler.draggedItem = itemNode;
-      }).on("mouseenter", function() {
-        itemNode.style("background-color", "#fff2cc");
-      }).on("mouseleave", function() {
-        itemNode.style("background-color", "#eee");
-      });
-    });
-  }
-  async removeGroup(group) {
-    this.removedGrp = true;
-    const itemsNum = group.wrapper.selectAll(".sjpp-drag-item").nodes();
-    if (itemsNum.length === 0) {
-      group.wrapper.remove();
-    } else {
-      group.input.remove();
-      group.destroyBtn.remove();
-      group.wrapper.remove();
-      for (const v of this.data.values) {
-        if (v.group == group.currentIdx) v.group = 0;
-      }
-    }
-    await this.update();
-  }
-  async update() {
-    this.dom.actionDiv.addGroup.property("disabled", this.data.groups.length >= this.maxGrpNum);
-    for (const [i, grp] of this.data.groups.entries()) {
-      if (i === 0) continue;
-      if (grp.currentIdx != i) {
-        this.data.values.filter((v) => v.group == grp.currentIdx).forEach((v) => v.group = i);
-        this.data.filters.filter((f) => f.group == grp.currentIdx).forEach((f) => f.group = i);
-        grp.currentIdx = i;
-      }
-    }
-    this.dom.grpsWrapper.selectAll(".sjpp-drag-drop-div").data(this.data.groups).each(async (group) => {
-      if (group.currentIdx !== 0) {
-        group.input.node().value = group.name;
-        group.destroyBtn.property("disabled", this.data.groups.length <= this.minGrpNum);
-      }
-      await this.addItems(group);
-    });
-  }
-  async onKeyUp(group) {
-    if (group.name == group.input.node().value) return;
-    this.editedName = true;
-    const match = this.data.groups.filter((g) => g.name == group.input.node().value);
-    if (match.length > 0) {
-      this.dom.actionDiv.applyBtn.property("disabled", true);
-      group.inputMessage.style("display", "block");
-    } else {
-      this.dom.actionDiv.applyBtn.property("disabled", false);
-      group.inputMessage.style("display", "none");
-      this.data.groups[group.currentIdx].name = group.input.node().value.trim();
-    }
-  }
-};
-export {
-  GroupSet
-};
-//# sourceMappingURL=qualitative-7XEX7QZP.js.map

package/dist/qualitative-MESSRM45.js

@@ -1,41 +0,0 @@
-import {
-  QualCustomGS,
-  QualPredefinedGS,
-  QualValues,
-  QualitativeBase
-} from "./chunk-KBYRXJ6Y.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-Y7S3EY6T.js";
-import "./chunk-RCYTUKAJ.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-B2F23ESD.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-JOT4WDJE.js";
-import "./chunk-OTCYJP7G.js";
-import "./chunk-GXINX3WK.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  QualCustomGS,
-  QualPredefinedGS,
-  QualValues,
-  QualitativeBase
-};
-//# sourceMappingURL=qualitative-MESSRM45.js.map

package/dist/regression-XIHVK4ZG.js

@@ -1,54 +0,0 @@
-import {
-  componentInit,
-  getPlotConfig,
-  get_defaultQ4fillTW,
-  makeChartBtnMenu,
-  regressionInit
-} from "./chunk-TRXU2NWS.js";
-import "./chunk-MFLKXGQC.js";
-import "./chunk-KLV7RCJM.js";
-import "./chunk-762BT2DY.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-VEXSAWKT.js";
-import "./chunk-JKDUB36U.js";
-import "./chunk-ODEZHSWS.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-EWSI62JW.js";
-import "./chunk-7OYOC7XY.js";
-import "./chunk-KBYRXJ6Y.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-Y7S3EY6T.js";
-import "./chunk-RCYTUKAJ.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-B2F23ESD.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-JOT4WDJE.js";
-import "./chunk-OTCYJP7G.js";
-import "./chunk-GXINX3WK.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  componentInit,
-  getPlotConfig,
-  get_defaultQ4fillTW,
-  makeChartBtnMenu,
-  regressionInit
-};
-//# sourceMappingURL=regression-XIHVK4ZG.js.map

package/dist/regression.inputs-GI6FWC5D.js

@@ -1,46 +0,0 @@
-import {
-  RegressionInputs
-} from "./chunk-TRXU2NWS.js";
-import "./chunk-MFLKXGQC.js";
-import "./chunk-KLV7RCJM.js";
-import "./chunk-762BT2DY.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-VEXSAWKT.js";
-import "./chunk-JKDUB36U.js";
-import "./chunk-ODEZHSWS.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-EWSI62JW.js";
-import "./chunk-7OYOC7XY.js";
-import "./chunk-KBYRXJ6Y.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-Y7S3EY6T.js";
-import "./chunk-RCYTUKAJ.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-B2F23ESD.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-JOT4WDJE.js";
-import "./chunk-OTCYJP7G.js";
-import "./chunk-GXINX3WK.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  RegressionInputs
-};
-//# sourceMappingURL=regression.inputs-GI6FWC5D.js.map

package/dist/regression.inputs.term-FEK2O6DJ.js

@@ -1,46 +0,0 @@
-import {
-  InputTerm
-} from "./chunk-TRXU2NWS.js";
-import "./chunk-MFLKXGQC.js";
-import "./chunk-KLV7RCJM.js";
-import "./chunk-762BT2DY.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-VEXSAWKT.js";
-import "./chunk-JKDUB36U.js";
-import "./chunk-ODEZHSWS.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-EWSI62JW.js";
-import "./chunk-7OYOC7XY.js";
-import "./chunk-KBYRXJ6Y.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-Y7S3EY6T.js";
-import "./chunk-RCYTUKAJ.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-B2F23ESD.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-JOT4WDJE.js";
-import "./chunk-OTCYJP7G.js";
-import "./chunk-GXINX3WK.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  InputTerm
-};
-//# sourceMappingURL=regression.inputs.term-FEK2O6DJ.js.map