@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/Violin-VA6FBRUQ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/violin/violin.renderer.ts", "../plots/violin/violin.interactivity.ts", "../plots/violin/Violin.ts"],
+  "sourcesContent": ["import { axisLeft, axisTop } from 'd3-axis'\nimport { scaleLinear, scaleLog } from 'd3-scale'\nimport { curveBasis, line } from 'd3-shape'\nimport { brushX, brushY } from 'd3-brush'\nimport { renderTable, getMaxLabelWidth, table2col, getChartTitle } from '#dom'\nimport { rgb } from 'd3-color'\nimport { format as d3format } from 'd3-format'\nimport { isSingleCellTerm } from '#shared'\nimport type { TermWrapper, ViolinResponse, ViolinResponseChart } from '#types'\nimport { getValueConversionFactor, toUserUnit } from '#shared/helpers.js'\n\n// const minSampleSize = 5 // a group below cutoff will not render a violin plot\n\ntype ViolinDensityBin = {\n\tx0: number\n\tdensity: number\n}\n\ntype LegendItem = {\n\ttext: string\n\tnoIcon: boolean\n\tisHidden?: boolean\n\tisClickable?: boolean\n\thiddenOpacity?: number\n}\n\ntype LegendGroup = {\n\tname: string\n\titems: LegendItem[]\n}\n\n// const minSampleSize = 5 // a group below cutoff will not render a violin plot\n\n/* the term whose values the numeric axis is of. a term with valueConversion{} stores its values in\none unit (e.g. day) and is read by users in another (e.g. year), so everything a user reads off this\naxis is converted. the scale that maps a value to a pixel is not: the violin marks, the median line\nand the range a brush turns into a filter all stay in the stored unit */\nfunction getNumericTerm(t1: TermWrapper, t2?: TermWrapper) {\n\treturn (t2 as any)?.q?.mode === 'continuous' ? (t2 as any).term : (t1 as any)?.term\n}\n\nexport default function setViolinRenderer(self: any) {\n\tself.render = function () {\n\t\tconst settings = self.config.settings.violin\n\t\tconst isH = settings.orientation === 'horizontal'\n\t\tconst t1 = self.config.term\n\t\tconst t2 = self.config.term2\n\n\t\t//termsetting.js 'set_hiddenvalues()' adds uncomputable values from term.values to q.hiddenValues object. Since it will show up on the legend, delete that key-value pair from t2.q.hiddenValues object.\n\t\tconst termNum: TermWrapper =\n\t\t\tt2?.term.type === 'condition' ||\n\t\t\tt2?.term.type === 'samplelst' ||\n\t\t\tt2?.term.type === 'categorical' ||\n\t\t\t((t2?.term.type === 'float' || t2?.term.type === 'integer') && t1.q.mode === 'continuous')\n\t\t\t\t? t2\n\t\t\t\t: t1\n\t\tif (!(termNum as any)?.q.hiddenValues) (termNum as any).q.hiddenValues = {}\n\n\t\tif ((termNum as any)?.term?.values) {\n\t\t\tfor (const [k, val] of Object.entries((termNum as any).term.values)) {\n\t\t\t\tconst v = val as { label: string; uncomputable?: boolean }\n\t\t\t\tif (v.uncomputable) {\n\t\t\t\t\tif ((termNum as any).q.hiddenValues[k]) {\n\t\t\t\t\t\t;(termNum as any).q.hiddenValues[v.label] = 1\n\t\t\t\t\t\tdelete (termNum as any).q.hiddenValues[k]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t//filter out hidden values and only keep plots which are not hidden in term2.q.hiddenvalues\n\t\tself.dom.violinDiv.selectAll('*').remove()\n\t\tconst data: ViolinResponse = self.data\n\t\tconst chartKeys = Object.keys(data.charts)\n\t\tif (!chartKeys?.length) {\n\t\t\tself.dom.banner.html(`<span>No visible violin plot data to render</span>`).style('display', 'block')\n\t\t\tself.dom.legendDiv.selectAll('*').remove()\n\t\t\treturn\n\t\t}\n\t\tfor (const chartKey of chartKeys) {\n\t\t\tconst chart: ViolinResponseChart & { chartDiv?: any } = data.charts[chartKey]\n\t\t\tconst plots = chart.plots.filter(p => !termNum?.q?.hiddenValues?.[p.label || p.seriesId])\n\t\t\tif (settings.orderByMedian == true) {\n\t\t\t\tplots.sort((a, b) => a.summaryStats.median.value - b.summaryStats.median.value)\n\t\t\t}\n\t\t\tif (self.legendRenderer) self.legendRenderer(getLegendGrps(termNum, self))\n\n\t\t\tconst chartDiv = self.dom.violinDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-vp-chartDiv')\n\t\t\t\t.style('padding', Object.keys(self.data.charts).length > 1 ? '20px 20px 0px 0px' : '0px')\n\t\t\tchart.chartDiv = chartDiv\n\t\t\tif (plots.length === 0) {\n\t\t\t\tchartDiv.html(\n\t\t\t\t\t` <span style=\"opacity:.6;font-size:1em;margin-left:90px;\">No visible violin plot data to render</span>`\n\t\t\t\t)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// append the svg object to the body of the page\n\t\t\tchartDiv.select('.sjpp-violin-plot').remove()\n\n\t\t\t//Fix for centering the chart title over the chart,\n\t\t\t//not the entire div.\n\t\t\tconst chartWrapper = chartDiv.append('div').style('display', 'inline-block')\n\t\t\t// render chart title\n\t\t\tif (chart.chartId) {\n\t\t\t\tconst totalCount = chart.plots.reduce((acc, plot) => acc + plot.plotValueCount, 0)\n\t\t\t\tchartWrapper\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'pp-chart-title')\n\t\t\t\t\t.style('display', 'block')\n\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t.style('font-size', '1.1em')\n\t\t\t\t\t.style('margin-bottom', '5px')\n\t\t\t\t\t.text(self.getChartTitle(chart.chartId, totalCount))\n\t\t\t}\n\n\t\t\t// render chart data\n\t\t\tconst svgData = renderSvg(t1, plots, chartWrapper, self, isH, settings)\n\t\t\trenderScale(t1, t2, settings, isH, svgData, self)\n\t\t\tlet y = 0\n\t\t\tconst thickness = self.settings.plotThickness || self.getAutoThickness()\n\t\t\tfor (const plot of plots) {\n\t\t\t\t//R x values are not the same as the plot values, so we need to use a scale to map them to the plot values\n\t\t\t\t// The scale uses half of the plotThickness as the maximum value as the image is symmetrical\n\t\t\t\t// Only one half of the image is computed and the other half is mirrored\n\t\t\t\tconst wScale = scaleLinear()\n\t\t\t\t\t.domain([plot.density.densityMax, plot.density.densityMin])\n\t\t\t\t\t.range([thickness / 2, 0])\n\t\t\t\tlet areaBuilder\n\t\t\t\t//when doing this interpolation, the violin plot will be smoother and some padding may be added\n\t\t\t\t//between the plot and the axis\n\t\t\t\tif (isH) {\n\t\t\t\t\tareaBuilder = line<ViolinDensityBin>()\n\t\t\t\t\t\t.curve(curveBasis)\n\t\t\t\t\t\t.x(d => svgData.axisScale(d.x0))\n\t\t\t\t\t\t.y(d => wScale(d.density))\n\t\t\t\t} else {\n\t\t\t\t\tareaBuilder = line<ViolinDensityBin>()\n\t\t\t\t\t\t.curve(curveBasis)\n\t\t\t\t\t\t.x(d => wScale(d.density))\n\t\t\t\t\t\t.y(d => svgData.axisScale(d.x0))\n\t\t\t\t}\n\t\t\t\t//if only one plot pass area builder to calculate the exact height of the plot\n\t\t\t\tconst { violinG, height } = renderViolinPlot(svgData, plot, isH, wScale, areaBuilder, y)\n\t\t\t\ty += height\n\t\t\t\tif (self.opts.mode != 'minimal') renderLabels(t1, t2, violinG, plot, isH, settings)\n\n\t\t\t\tif (isSingleCellTerm(self.config.term.term)) {\n\t\t\t\t\t// is sc data, disable brushing for now because 1) no use 2) avoid bug of listing cells\n\t\t\t\t} else {\n\t\t\t\t\t// enable brushing\n\t\t\t\t\tif (self.opts.mode != 'minimal') renderBrushing(t1, t2, violinG, settings, plot, isH, svgData)\n\t\t\t\t}\n\n\t\t\t\tself.labelHideLegendClicking(t2, plot) // FIXME\n\t\t\t}\n\n\t\t\t// render p-value table\n\t\t\tif (self.settings.showAssociationTests) self.renderPvalueTable(chartDiv, chart)\n\t\t}\n\t}\n\n\tself.displaySummaryStats = function (\n\t\tdata: { summaryStats: { key: string; label: string; value: number }[] },\n\t\tevent: MouseEvent\n\t) {\n\t\tconst d = data as { summaryStats: { key: string; label: string; value: number }[] }\n\t\tif (!d.summaryStats) return\n\t\tself.dom.hovertip.clear().show(event.clientX, event.clientY)\n\t\tconst table = table2col({ holder: self.dom.hovertip.d.append('div') })\n\t\t/* stats are computed on the stored values, so read them in the term's user-facing unit.\n\t\tevery stat getDescrStats() reports scales with the unit (min, quartiles, median, max, mean,\n\t\tstandard deviation) except the sample count, which is not a value of the term at all */\n\t\tconst term = getNumericTerm(self.config.term, self.config.term2)\n\t\tfor (const { key, label, value } of Object.values(d.summaryStats))\n\t\t\ttable.addRow(label, key == 'total' ? value : toUserUnit(value, term))\n\t}\n\tself.getAutoThickness = function () {\n\t\tlet maxPlotCount = 0\n\t\tfor (const k of Object.keys(this.data.charts)) {\n\t\t\tconst chart = this.data.charts[k]\n\t\t\tmaxPlotCount = Math.max(maxPlotCount, chart.plots.length)\n\t\t}\n\t\tif (maxPlotCount == 1) return 150\n\t\treturn Math.min(100, Math.max(40, 600 / maxPlotCount)) //clamp between 60 and 130\n\t}\n\n\tself.getPlotThicknessWithPadding = function () {\n\t\tconst plotThickness = self.settings.plotThickness || self.getAutoThickness()\n\t\treturn plotThickness + self.settings.rowSpace\n\t}\n\n\tself.renderPvalueTable = function (chartDiv: any, chart: any) {\n\t\tif (!chart.pvalues) return\n\t\tconst tableHolder = chartDiv\n\t\t\t.append('div')\n\t\t\t.classed('sjpp-tableHolder', true)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '10px')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin-left', '0px')\n\t\t\t.style('margin-top', '30px')\n\t\t\t.style('margin-right', '30px')\n\n\t\tconst t1 = self.config.term\n\t\tconst t2 = self.config.term2\n\n\t\tif (!t2) {\n\t\t\t// no term2, no table to show\n\t\t\ttableHolder.style('display', 'none')\n\t\t\treturn\n\t\t}\n\n\t\tconst termNum =\n\t\t\tt2?.term.type === 'condition' ||\n\t\t\tt2?.term.type === 'samplelst' ||\n\t\t\tt2?.term.type === 'categorical' ||\n\t\t\t((t2?.term.type === 'float' || t2?.term.type === 'integer') && t1.q.mode === 'continuous')\n\t\t\t\t? t2\n\t\t\t\t: t1\n\n\t\t//hide p-values for categories that are hidden\n\t\tconst pvalues = chart.pvalues.filter(arr => {\n\t\t\tfor (let i = 0; i < arr.length; i++) {\n\t\t\t\tif (typeof arr[i].value === 'string') {\n\t\t\t\t\tif (termNum.q?.hiddenValues && arr[i].value in termNum.q.hiddenValues) {\n\t\t\t\t\t\treturn false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn true\n\t\t})\n\n\t\ttableHolder\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.append('div')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text(pvalues.length > 0 ? \"Group comparisons (Wilcoxon's rank sum test)\" : '')\n\n\t\tconst columns = [{ label: 'Group 1' }, { label: 'Group 2' }, { label: 'P-value' }]\n\t\tconst rows = pvalues\n\t\tconst isH = this.settings.orientation === 'horizontal'\n\t\tconst maxHeight = isH\n\t\t\t? self.getPlotThicknessWithPadding() * chart.plots.length + 10 //add axes height\n\t\t\t: this.settings.svgw + this.config.term.term.name.length\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv: tableHolder,\n\t\t\tshowLines: false,\n\t\t\tmaxWidth: '27vw',\n\t\t\tmaxHeight: `${maxHeight}px`,\n\t\t\tresize: true\n\t\t})\n\t}\n\n\tself.getChartTitle = function (chartId: string, totalCount?:number) {\n\t\treturn getChartTitle(self.config, chartId, totalCount)\n\t}\n\n\tfunction createMargins(labelsize: number, settings: any, isH: boolean, isMinimal: boolean) {\n\t\tlet margins\n\n\t\tif (isMinimal) {\n\t\t\tmargins = isH\n\t\t\t\t? { left: 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 }\n\t\t\t\t: { left: settings.axisHeight, top: 30, right: settings.rightMargin, bottom: 10 }\n\t\t} else {\n\t\t\tmargins = isH\n\t\t\t\t? { left: labelsize + 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 }\n\t\t\t\t: { left: settings.axisHeight, top: 50, right: settings.rightMargin, bottom: labelsize }\n\t\t}\n\t\treturn margins\n\t}\n\n\tfunction renderSvg(t1: TermWrapper, plots: any[], chartDiv: any, self: any, isH: boolean, settings: any) {\n\t\tconst violinDiv = chartDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', self.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t.style('overflow', 'auto')\n\t\t\t.style('scrollbar-width', 'none')\n\n\t\tconst violinSvg = violinDiv.append('svg')\n\n\t\tconst labelsize = getMaxLabelWidth(\n\t\t\tviolinSvg,\n\t\t\tplots.map(plot => `${plot.label}, n=${plot.plotValueCount}`)\n\t\t)\n\n\t\tconst margin = createMargins(labelsize, settings, isH, self.opts.mode == 'minimal')\n\t\tconst plotThickness = self.getPlotThicknessWithPadding()\n\t\tconst width = margin.left + margin.top + (isH ? settings.svgw : plotThickness * plots.length + t1.term.name.length)\n\t\tconst height =\n\t\t\tmargin.bottom + margin.top + (isH ? plotThickness * plots.length : settings.svgw + t1.term.name.length)\n\n\t\tviolinSvg\n\t\t\t.attr('width', width)\n\t\t\t.attr('height', height)\n\t\t\t.classed('sjpp-violin-plot', true)\n\t\t\t.attr('data-testid', 'sja_violin_plot')\n\n\t\t// a <g> in which everything is rendered into\n\t\tconst svgG = violinSvg.append('g').attr('transform', 'translate(' + margin.left + ',' + margin.top + ')')\n\n\t\treturn { margin: margin, svgG: svgG, axisScale: createNumericScale(self, settings, isH), violinSvg: violinSvg }\n\t}\n\n\tfunction renderScale(t1: TermWrapper, t2: TermWrapper | undefined, settings: any, isH: boolean, svg: any, self: any) {\n\t\t// <g>: holder of numeric axis\n\t\tconst g = svg.svgG\n\t\t\t.append('g')\n\t\t\t.style('font-size', '12')\n\t\t\t.classed(settings.isLogScale ? 'sjpp-logscale' : 'sjpp-linearscale', true)\n\n\t\t/* tick labels are read by the user, so they are in the term's user-facing unit. the scale is a\n\t\tcopy with a converted domain over the same pixel range, so a tick still lands where its value does */\n\t\tconst f = getValueConversionFactor(getNumericTerm(t1, t2))\n\t\tconst uiScale = f == 1 ? svg.axisScale : svg.axisScale.copy().domain(svg.axisScale.domain().map(v => v * f))\n\n\t\tconst ticks = settings.isLogScale\n\t\t\t? uiScale.ticks(15)\n\t\t\t: // svg.axisScale.ticks().filter(tick => tick > 0 || tick < 0)\n\t\t\t  uiScale.ticks()\n\n\t\tg.call(\n\t\t\t(isH ? axisTop : axisLeft)(uiScale)\n\t\t\t\t.scale(uiScale)\n\t\t\t\t.tickFormat((d, i) => {\n\t\t\t\t\tconst value = Number(d)\n\t\t\t\t\tif (settings.isLogScale) {\n\t\t\t\t\t\tif (self.app.vocabApi.termdbConfig.logscaleBase2) {\n\t\t\t\t\t\t\tif (ticks.length > 10 && i % 2 !== 0) return ''\n\t\t\t\t\t\t\tif (value < 0.1) return d3format('.3f')(value)\n\t\t\t\t\t\t\treturn d3format('.1f')(value)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (ticks.length >= 12 && i % 5 !== 0) return ''\n\t\t\t\t\t\t\tif (value < 50) return String(value)\n\t\t\t\t\t\t\treturn d3format('.1s')(value)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (ticks.length >= 12 && i % 2 !== 0) return ''\n\t\t\t\t\treturn String(value)\n\t\t\t\t})\n\t\t\t\t.tickValues(ticks)\n\t\t)\n\n\t\tif (self.opts.mode != 'minimal') {\n\t\t\t// TODO need to add term2 label onto the svg\n\t\t\tconst numTerm = getNumericTerm(t1, t2)\n\t\t\t// name the unit the ticks are in, when it is not the one the values are stored in\n\t\t\tconst n = numTerm.valueConversion ? `${numTerm.name} (${numTerm.valueConversion.toUnit}s)` : numTerm.name\n\t\t\t/*const lab = */ svg.svgG\n\t\t\t\t.append('text')\n\t\t\t\t.text(n)\n\t\t\t\t.classed('sjpp-numeric-term-label', true)\n\t\t\t\t.attr('data-testid', `sjpp-violin-label-${n}`)\n\t\t\t\t.style('font-weight', 600)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('x', isH ? settings.svgw / 2 : -settings.svgw / 2)\n\t\t\t\t.attr('y', isH ? -30 : -45)\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.attr('transform', isH ? null : 'rotate(-90)')\n\t\t\t\t// .transition()\n\t\t\t\t// .delay(self.opts.mode == 'minimal' ? 0 : 100)\n\t\t\t\t// .duration(self.opts.mode == 'minimal' ? 0 : 200)\n\t\t\t\t.style('opacity', 1)\n\t\t}\n\t}\n\n\tfunction renderViolinPlot(svgData: any, plot: any, isH: boolean, wScale: any, areaBuilder: any, y: number) {\n\t\tconst label = plot.label?.split(',')[0]\n\t\tconst catTerm = self.config.term.q.mode == 'discrete' ? self.config.term : self.config.term2\n\t\tconst category = catTerm?.term.values\n\t\t\t? (Object.values(catTerm.term.values as Record<string, { label: string; color?: string }>).find(\n\t\t\t\t\to => o.label == label\n\t\t\t  ) as { label: string; color?: string } | undefined) ?? null\n\t\t\t: null\n\t\tlet color\n\t\tif (catTerm) {\n\t\t\tif (catTerm.q.type == 'predefined-groupset' || catTerm.q.type == 'custom-groupset') {\n\t\t\t\tconst groupset =\n\t\t\t\t\tcatTerm.q.type == 'predefined-groupset'\n\t\t\t\t\t\t? catTerm.term.groupsetting.lst[catTerm.q.predefined_groupset_idx]\n\t\t\t\t\t\t: catTerm.q.customset\n\t\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\t\tconst group = groupset.groups.find(g => g.name == label)\n\t\t\t\tif (group?.color) color = group.color\n\t\t\t} else {\n\t\t\t\tcolor = category?.color\n\t\t\t}\n\t\t}\n\n\t\tif (!color) color = self.config.settings.violin.defaultColor\n\n\t\tif (!plot.color) plot.color = color\n\t\tif (category && !category.color) category.color = color\n\t\t// <g> of one plot\n\t\t// adding .5 to plotIdx allows to anchor each plot <g> to the middle point\n\t\tconst svg = svgData.svgG\n\t\tconst violinG = svg.append('g').datum(plot).attr('class', 'sjpp-violinG')\n\t\trenderArea(violinG, plot, areaBuilder)\n\t\t//render symmetrical violin plot\n\t\trenderArea(violinG, plot, isH ? areaBuilder.y(d => -wScale(d.density)) : areaBuilder.x(d => -wScale(d.density)))\n\n\t\trenderSymbolImage(self, violinG, plot, isH)\n\t\tif (self.opts.mode != 'minimal') renderMedian(violinG, isH, plot, svgData, self)\n\t\trenderLines(violinG, isH, self.config.settings.violin.lines, svgData)\n\t\tif ('value' in self.state.config) {\n\t\t\tconst value = svgData.axisScale(self.state.config.value)\n\t\t\tconst s = self.config.settings.violin\n\t\t\tviolinG\n\t\t\t\t.append('line')\n\t\t\t\t.style('stroke', 'black')\n\t\t\t\t.style('stroke-width', s.medianThickness)\n\t\t\t\t.attr('x1', 200)\n\t\t\t\t.attr('x2', 200)\n\t\t\t\t.attr('x1', isH ? value : -s.medianLength)\n\t\t\t\t.attr('x2', isH ? value : s.medianLength)\n\t\t\t\t.attr('y1', isH ? -s.medianLength : value)\n\t\t\t\t.attr('y2', isH ? s.medianLength : value)\n\t\t}\n\t\tconst height = self.getPlotThicknessWithPadding()\n\t\tconst translate = isH ? `translate(0, ${y + height / 2}) ` : `translate(${y + height / 2}, 0)`\n\t\tviolinG.attr('transform', translate)\n\n\t\treturn { violinG, height }\n\t}\n\n\t// label for each violin (on left when horizontal)\n\tfunction renderLabels(t1: any, t2: any, violinG: any, plot: any, isH: boolean, settings: any) {\n\t\tviolinG\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'sjpp-violin-label')\n\t\t\t.text(`${plot.label}, n=${plot.plotValueCount}`)\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.on('click', function (event: MouseEvent) {\n\t\t\t\tif (!event) return\n\t\t\t\tself.displayLabelClickMenu(t1, t2, plot, event)\n\t\t\t})\n\t\t\t.on('mouseover', function (event: MouseEvent, d: any) {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tif (!event) return\n\t\t\t\tself.displaySummaryStats(d, event)\n\t\t\t})\n\t\t\t.on('mouseout', function () {\n\t\t\t\tself.dom.hovertip.hide()\n\t\t\t})\n\t\t\t.style('opacity', 0)\n\t\t\t.style('opacity', 1)\n\t\t\t.attr('x', isH ? -5 : 0 - settings.svgw - 5)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('transform', isH ? null : 'rotate(-90)')\n\t}\n\n\tfunction renderArea(violinG: any, plot: any, areaBuilder: any) {\n\t\tif (plot.density.densityMax == 0) return\n\t\tviolinG\n\t\t\t.append('path')\n\t\t\t.attr('class', 'sjpp-vp-path')\n\t\t\t.style('fill', self.opts.mode === 'minimal' ? rgb(221, 221, 221) : plot.color)\n\t\t\t.style('opacity', 0)\n\t\t\t.attr('stroke', rgb(plot.color).darker())\n\t\t\t.attr('stroke-width', 1)\n\t\t\t.attr('stroke-linejoin', 'round')\n\t\t\t.style('opacity', '0.8')\n\t\t\t.attr('d', areaBuilder(plot.density.bins))\n\t}\n\n\tfunction renderSymbolImage(self: any, violinG: any, plot: any, isH: boolean) {\n\t\tconst i = violinG\n\t\t\t.append('image')\n\t\t\t.style('opacity', 0)\n\t\t\t.classed(self.config.settings.violin.datasymbol === 'rug' ? 'sjpp-rug-img' : 'sjpp-beans-img', true)\n\t\t\t.style('opacity', 1)\n\t\t\t.attr('xlink:href', plot.src)\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\tisH ? `translate(0, -${self.settings.radius / 2})` : `translate(-${self.settings.radius / 2}, 0)`\n\t\t\t)\n\t\t// set image dimension for crisp look\n\t\tif (self.settings.orientation == 'horizontal') {\n\t\t\ti.attr('width', self.settings.svgw)\n\t\t} else if (self.settings.orientation == 'vertical') {\n\t\t\ti.attr('height', self.settings.svgw)\n\t\t}\n\t}\n\n\tfunction renderMedian(violinG: any, isH: boolean, plot: any, svgData: any, self: any) {\n\t\tconst s = self.config.settings.violin\n\t\t//render median values on plots\n\t\tconst median = svgData.axisScale(plot.summaryStats.median.value)\n\t\tif (plot.plotValueCount >= 2) {\n\t\t\tviolinG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', 'sjpp-median-line')\n\t\t\t\t.style('stroke-width', s.medianThickness)\n\t\t\t\t.style('stroke', s.medianColor)\n\t\t\t\t.style('opacity', '0.5')\n\t\t\t\t.attr('y1', isH ? -s.medianLength : median)\n\t\t\t\t.attr('y2', isH ? s.medianLength : median)\n\t\t\t\t.attr('x1', isH ? median : -s.medianLength)\n\t\t\t\t.attr('x2', isH ? median : s.medianLength)\n\t\t} else return\n\t}\n\n\tfunction renderLines(violinG: any, isH: boolean, lines: number[] | undefined, svgData: any) {\n\t\t// render straight lines on plot\n\t\tconst plotThickness = self.settings.plotThickness\n\n\t\tviolinG.selectAll('.sjpp-vp-line').remove()\n\t\tif (!lines?.length) return\n\t\tfor (const line of lines) {\n\t\t\tviolinG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', 'sjpp-vp-line')\n\t\t\t\t.style('stroke', self.opts.mode == 'minimal' ? 'red' : 'black') // if not minimal, then red median line will also appear\n\t\t\t\t.attr('y1', isH ? -(plotThickness / 2) : svgData.axisScale(line))\n\t\t\t\t.attr('y2', isH ? plotThickness / 2 : svgData.axisScale(line))\n\t\t\t\t.attr('x1', isH ? svgData.axisScale(line) : -(plotThickness / 2))\n\t\t\t\t.attr('x2', isH ? svgData.axisScale(line) : plotThickness / 2)\n\t\t}\n\t}\n\n\tfunction renderBrushing(t1: any, t2: any, violinG: any, settings: any, plot: any, isH: boolean, svgData: any) {\n\t\t//brushing on data points\n\t\tif (settings.datasymbol === 'rug' || settings.datasymbol === 'bean') {\n\t\t\tconst br = isH\n\t\t\t\t? brushX()\n\t\t\t\t\t\t.extent([\n\t\t\t\t\t\t\t[0, -20],\n\t\t\t\t\t\t\t[settings.svgw, 20]\n\t\t\t\t\t\t])\n\t\t\t\t\t\t.on('end', event => {\n\t\t\t\t\t\t\tif (!event.selection) return\n\t\t\t\t\t\t\tself.displayBrushMenu(t1, t2, self, plot, event, svgData.axisScale, isH)\n\t\t\t\t\t\t\tdocument.body.addEventListener('pointerdown', onClickOut, true)\n\t\t\t\t\t\t})\n\t\t\t\t: brushY()\n\t\t\t\t\t\t.extent([\n\t\t\t\t\t\t\t[-20, 0],\n\t\t\t\t\t\t\t[20, settings.svgw]\n\t\t\t\t\t\t])\n\t\t\t\t\t\t.on('end', event => {\n\t\t\t\t\t\t\tif (!event.selection) return\n\t\t\t\t\t\t\tself.displayBrushMenu(t1, t2, self, plot, event, svgData.axisScale, isH)\n\t\t\t\t\t\t\tdocument.body.addEventListener('pointerdown', onClickOut, true)\n\t\t\t\t\t\t})\n\n\t\t\tconst brushG = violinG.append('g').classed('sjpp-brush', true).call(br)\n\n\t\t\t// clear brush when clicking outside of it\n\t\t\tconst onClickOut = (e: PointerEvent) => {\n\t\t\t\tif (!brushG || !br) return\n\t\t\t\tif (!brushG.node().contains(e.target)) br.clear(brushG)\n\t\t\t\tdocument.body.removeEventListener('pointerdown', onClickOut, true)\n\t\t\t}\n\t\t}\n\t}\n}\n\n// creates numeric axis\nexport function createNumericScale(self, settings, isH) {\n\tlet axisScale\n\tif (settings.isLogScale) {\n\t\taxisScale = scaleLog()\n\t\t\t.base(self.app.vocabApi.termdbConfig.logscaleBase2 ? 2 : 10)\n\t\t\t.domain([self.data.min, self.data.max])\n\t\t\t.range(isH ? [0, settings.svgw] : [settings.svgw, 0])\n\t} else {\n\t\taxisScale = scaleLinear()\n\t\t\t.domain([self.data.min, self.data.max])\n\t\t\t.range(isH ? [0, settings.svgw] : [settings.svgw, 0])\n\t}\n\treturn axisScale\n}\n\nfunction getLegendGrps(termNum: TermWrapper, self: any) {\n\tconst legendGrps: LegendGroup[] = [],\n\t\tt1 = self.config.term,\n\t\tt2 = self.config.term2,\n\t\t// changed color from #aaa to address Section 508 contrast issue\n\t\theadingStyle = 'color: #555; font-weight: 400'\n\tif (self.settings.showStats) {\n\t\taddDescriptiveStats(t1, legendGrps, headingStyle, self)\n\t\tif (t2?.q.descrStats) addDescriptiveStats(t2, legendGrps, headingStyle, self)\n\t}\n\n\taddUncomputableValues(\n\t\tt1?.q.mode === 'continuous' && t1?.q.hiddenValues && Object.keys(t1?.q.hiddenValues).length > 0\n\t\t\t? t1\n\t\t\t: t2?.q.mode === 'continuous' && t2?.q.hiddenValues && Object.keys(t2?.q.hiddenValues).length > 0\n\t\t\t? t2\n\t\t\t: null,\n\t\tlegendGrps,\n\t\theadingStyle,\n\t\tself\n\t)\n\n\tif (t2) {\n\t\tif (termNum.q.hiddenValues && Object.entries(termNum.q.hiddenValues).length != 0) {\n\t\t\taddHiddenValues(termNum, legendGrps, headingStyle)\n\t\t}\n\t}\n\treturn legendGrps\n}\n\nfunction addDescriptiveStats(term: TermWrapper, legendGrps: LegendGroup[], headingStyle: string, self: any) {\n\tconst descrStats = (term as any)?.q?.descrStats as\n\t\t| Record<string, { label: string; value: number | string }>\n\t\t| undefined\n\tif (descrStats) {\n\t\tconst items: LegendItem[] = Object.values(descrStats).map(stat => {\n\t\t\treturn {\n\t\t\t\ttext: `${stat.label}: ${stat.value}`,\n\t\t\t\tnoIcon: true\n\t\t\t}\n\t\t})\n\n\t\t\tconst title = self.config.term2?.q.descrStats\n\t\t\t\t? `Descriptive statistics: ${term.term.name}`\n\t\t\t\t: `Descriptive statistics`\n\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\tlegendGrps.push({ name, items })\n\t}\n}\n\nfunction addUncomputableValues(term: TermWrapper | null, legendGrps: LegendGroup[], headingStyle: string, self: any) {\n\tif (term?.term.values) {\n\t\tconst items: LegendItem[] = []\n\t\tconst values = term.term.values as Record<string, { label?: string }>\n\t\tfor (const k in values) {\n\t\t\tconst label = values[k]?.label\n\t\t\tif (!label) continue\n\t\t\tif (self.data.uncomputableValues?.[label]) {\n\t\t\t\titems.push({\n\t\t\t\t\ttext: `${label}, n = ${self.data.uncomputableValues[label]}`,\n\t\t\t\t\tnoIcon: true,\n\t\t\t\t\t/** Need to specify that this is a hidden value for\n\t\t\t\t\t * text styling in the legend but not a plot to avoid\n\t\t\t\t\t * rendering a tooltip or click events.\n\t\t\t\t\t */\n\t\t\t\t\tisHidden: true,\n\t\t\t\t\tisClickable: false,\n\t\t\t\t\thiddenOpacity: 1\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (items.length) {\n\t\t\tconst name =\n\t\t\t\tself.config.term2?.term.type === 'float' || self.config.term2?.term.type === 'integer'\n\t\t\t\t\t? `<span style=\"${headingStyle}\">${term.term.name}</span>`\n\t\t\t\t\t: `<span style=\"${headingStyle}\">Other categories</span>`\n\t\t\tlegendGrps.push({ name, items })\n\t\t}\n\t}\n}\n\nfunction addHiddenValues(term: TermWrapper, legendGrps: LegendGroup[], headingStyle: string) {\n\tconst items: LegendItem[] = []\n\tfor (const key of Object.keys(term.q.hiddenValues || {})) {\n\t\titems.push({\n\t\t\ttext: `${key}`,\n\t\t\tnoIcon: true,\n\t\t\t/** Need to specify that this is a hidden value for\n\t\t\t * text styling in the legend and  a plot for\n\t\t\t * rendering a tooltip or click events.\n\t\t\t */\n\t\t\tisHidden: true,\n\t\t\tisClickable: true,\n\t\t\thiddenOpacity: 1\n\t\t})\n\t}\n\tconst title = `${term.term.name}`\n\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\tlegendGrps.push({ name, items })\n}\n", "import { filterJoin, getFilterItemByTag } from '#filter'\nimport { DownloadMenu, niceNumLabels, ListSamples, renderTable } from '#dom'\nimport { isSingleCellTerm } from '#shared'\n\ntype MenuOption = {\n\tlabel: string\n\ttestid?: string\n\tcallback: () => void | Promise<void>\n}\n\nexport function setInteractivity(self: any) {\n\tself.getChartImages = function () {\n\t\tconst charts: Array<{ name: string; svg: any }> = []\n\n\t\tfor (const chart of Object.values(self.data.charts as Record<string, any>)) {\n\t\t\tconst title = self.getChartTitle(chart.chartId)\n\t\t\tconst name = `${self.config.term.term.name}  ${title}`\n\t\t\tconst chartDiv = chart.chartDiv\n\t\t\tcharts.push({ name, svg: chartDiv.select('svg') })\n\t\t}\n\t\treturn charts\n\t}\n\n\tself.download = function (event: MouseEvent) {\n\t\tif (!self.state) return\n\t\tconst name2svg = self.getChartImages()\n\t\tconst dm = new DownloadMenu(name2svg, self.config.term.term.name)\n\t\tdm.show(event.clientX, event.clientY, undefined)\n\t}\n\n\tself.displayLabelClickMenu = function (t1: any, t2: any, plot: any, event: MouseEvent) {\n\t\tif (!t2) return // when no term 2 do not show options on the sole violin label\n\t\tif (isSingleCellTerm(self.config.term.term)) return // is sc data, none of the options below work, thus disable\n\n\t\tconst label = t1.q.mode === 'continuous' ? 'term2' : 'term'\n\t\tconst options: MenuOption[] = []\n\t\tif (this.app.getState().nav.header_mode !== 'only_buttons')\n\t\t\toptions.push({\n\t\t\t\tlabel: `Add filter: ${plot.label.split(',')[0]}`,\n\t\t\t\ttestid: 'sjpp-violinLabOpt-addf',\n\t\t\t\tcallback: getAddFilterCallback(self, plot)\n\t\t\t})\n\n\t\toptions.push({\n\t\t\tlabel: `Hide: ${plot.label}`,\n\t\t\ttestid: 'sjpp-violinLabOpt-hide',\n\t\t\tcallback: () => {\n\t\t\t\tconst config = structuredClone(self.config)\n\t\t\t\tconst term = config[label]\n\t\t\t\tif (!term.q.hiddenValues) term.q.hiddenValues = {}\n\t\t\t\tterm.q.hiddenValues[plot.label || plot.seriesId] = 1\n\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\tconst { samples } = self.config.controlLabels\n\t\tif (self.state.displaySampleIds && self.state.hasVerifiedToken) {\n\t\t\toptions.push({\n\t\t\t\tlabel: `List ${samples}`,\n\t\t\t\ttestid: 'sjpp-violinLabOpt-list',\n\t\t\t\tcallback: async () => {\n\t\t\t\t\t/** self.data.max * 2 appears to be a workaround for a\n\t\t\t\t\t * previous bug in the list samples logic. Since that logic\n\t\t\t\t\t * has been refined, this appears to be no longer necessary.\n\t\t\t\t\t * Commenting out for now, but leaving in place in case.*/\n\t\t\t\t\t// const [start, end] = [self.data.min, self.data.max * 2]\n\t\t\t\t\tconst [start, end] = [self.data.min, self.data.max]\n\t\t\t\t\tawait self.callListSamples(event, plot, start, end)\n\t\t\t\t}\n\t\t\t})\n\n\t\t\tif (self.opts.allow2selectSamples) {\n\t\t\t\tconst ss = self.opts.allow2selectSamples\n\t\t\t\toptions.push({\n\t\t\t\t\tlabel: ss.buttonText,\n\t\t\t\t\tcallback: async () => {\n\t\t\t\t\t\tconst [start, end] = [self.data.min, self.data.max]\n\t\t\t\t\t\tawait self.selectSamples(plot, start, end, ss)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tself.displayMenu(event, options)\n\t}\n\n\tself.displayBrushMenu = function (t1: any, t2: any, self: any, plot: any, event: any, scale: any, isH: boolean) {\n\t\tconst selection = event.selection\n\t\tconst [start, end] = isH\n\t\t\t? [scale.invert(selection[0]), scale.invert(selection[1])]\n\t\t\t: [scale.invert(selection[1]), scale.invert(selection[0])]\n\n\t\tconst options: MenuOption[] = []\n\n\t\tif (this.app.getState().nav.header_mode === 'with_tabs')\n\t\t\toptions.push({\n\t\t\t\tlabel: `Add filter`,\n\t\t\t\ttestid: 'sjpp-violinBrushOpt-addf',\n\t\t\t\tcallback: getAddFilterCallback(self, plot, start, end)\n\t\t\t})\n\n\t\tconst { samples } = self.config.controlLabels\n\t\tif (self.state.displaySampleIds && self.state.hasVerifiedToken) {\n\t\t\toptions.push({\n\t\t\t\tlabel: `List ${samples}`,\n\t\t\t\ttestid: 'sjpp-violinBrushOpt-list',\n\t\t\t\tcallback: async () => self.callListSamples(event.sourceEvent, plot, start, end)\n\t\t\t})\n\n\t\t\tif (self.opts.allow2selectSamples) {\n\t\t\t\tconst ss = self.opts.allow2selectSamples\n\t\t\t\toptions.push({\n\t\t\t\t\tlabel: ss.buttonText,\n\t\t\t\t\tcallback: async () => {\n\t\t\t\t\t\tawait self.selectSamples(plot, start, end, ss)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tself.displayMenu(event.sourceEvent, options, start, end)\n\t}\n\n\tself.displayMenu = function (event: MouseEvent, options: MenuOption[], start?: number, end?: number) {\n\t\tconst tip = self.dom.clicktip.clear().show(event.clientX, event.clientY)\n\n\t\tconst isBrush = start != null && end != null\n\n\t\tif (isBrush) {\n\t\t\tconst [niceStart, niceEnd] =\n\t\t\t\tself.config.term.term.type == 'integer' ? [Math.round(start), Math.round(end)] : niceNumLabels([start, end])\n\n\t\t\ttip.d.append('div').style('margin', '10px').text(`From ${niceStart} to ${niceEnd}`)\n\t\t}\n\t\t//show menu options for label clicking and brush selection\n\t\ttip.d\n\t\t\t.append('div')\n\t\t\t.selectAll('div')\n\t\t\t.data(options)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.attr('data-testid', d => d.testid)\n\t\t\t.text(d => d.label)\n\t\t\t.on('click', async (event, d: MenuOption) => {\n\t\t\t\tconst target = event.target as HTMLElement & { _clicked?: boolean }\n\t\t\t\tif (target._clicked) return\n\t\t\t\ttarget._clicked = true\n\t\t\t\ttarget.textContent = 'Loading...'\n\t\t\t\ttry {\n\t\t\t\t\tawait d.callback()\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\t// menu callbacks are fire-and-forget, so a request that was canceled by app.destroy()\n\t\t\t\t\t// or a superseding action must be swallowed here, or it surfaces as an unhandled rejection.\n\t\t\t\t\t// a rethrown abort reason may be rewrapped as an Error, so also test the message.\n\t\t\t\t\tif (self.app.isAbortError(e) || self.app.isAbortError(e?.message)) {\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tthrow e\n\t\t\t\t}\n\t\t\t\ttip.hide()\n\t\t\t})\n\t}\n\n\tself.selectSamples = async function (plot: any, start: number, end: number, ss: any) {\n\t\tconst ls = self.getSampleList(plot, start, end)\n\t\tconst data = await ls.getData()\n\t\tconst table = ls.setTableData(data)\n\t\tconst samples = table[2]\n\t\tss.callback({\n\t\t\tsamples: await self.app.vocabApi.convertSampleId(samples, ss.attributes),\n\t\t\tsource: ss.defaultSelectionLabel || `Selected from violin`\n\t\t})\n\t}\n\n\t//get sample list for menu option callbacks\n\tself.getSampleList = function (plot: any, start?: number, end?: number) {\n\t\tconst { term, term2, term0 } = self.config\n\t\tconst bins = self.data.bins\n\t\tconst rangeStart = start !== undefined ? start : null\n\t\tconst rangeStop = end !== undefined ? end : null\n\n\t\tconst ls = new ListSamples({\n\t\t\tapp: self.app,\n\t\t\ttermfilter: self.state.termfilter,\n\t\t\tterm,\n\t\t\tterm2,\n\t\t\tterm0,\n\t\t\tplot,\n\t\t\tbins,\n\t\t\tstart: rangeStart,\n\t\t\tend: rangeStop\n\t\t})\n\t\treturn ls\n\t}\n\n\tself.callListSamples = async function (event: MouseEvent, plot: any, start: number, end: number) {\n\t\tconst ls = self.getSampleList(plot, start, end)\n\t\t// aborted requests are handled by the menu option click handler in self.displayMenu()\n\t\tconst data = await ls.getData()\n\t\tconst [rows, columns] = ls.setTableData(data)\n\n\t\tconst tip = self.dom.sampletabletip\n\t\ttip.clear().show(event.clientX, event.clientY, false)\n\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv: tip.d,\n\t\t\tshowLines: true,\n\t\t\tmaxHeight: '40vh',\n\t\t\tresize: true,\n\t\t\tdataTestId: 'sjpp-listsampletable'\n\t\t})\n\t}\n\n\tself.labelHideLegendClicking = function (t2: any) {\n\t\t// whoever wrote this tangled mess needs to be fired\n\t\tself.dom.legendDiv\n\t\t\t.selectAll('.sjpp-htmlLegend')\n\t\t\t.on('click', event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tconst d = (event.target as HTMLElement & { __data__?: any }).__data__\n\t\t\t\tconst termNum =\n\t\t\t\t\tt2?.term.type === 'condition' ||\n\t\t\t\t\tt2?.term.type === 'samplelst' ||\n\t\t\t\t\tt2?.term.type === 'categorical' ||\n\t\t\t\t\t((t2?.term.type === 'float' || t2?.term.type === 'integer') && self.config.term?.q.mode === 'continuous')\n\t\t\t\t\t\t? 'term2'\n\t\t\t\t\t\t: 'term'\n\t\t\t\tconst config = structuredClone(self.config)\n\t\t\t\tconst term = config[termNum]\n\t\t\t\tif (t2) {\n\t\t\t\t\tfor (const key of Object.keys(term.q.hiddenValues || {})) {\n\t\t\t\t\t\tif (d.text === key) {\n\t\t\t\t\t\t\tdelete term.q.hiddenValues[key]\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('mouseover', event => {\n\t\t\t\tconst q = (event.target as HTMLElement & { __data__?: any }).__data__\n\t\t\t\tif (q === undefined) return\n\t\t\t\tif (q.isHidden === true && q.isClickable === true) {\n\t\t\t\t\tself.dom.hovertip.clear().show(event.clientX, event.clientY).d.append('span').text('Click to unhide plot')\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('mouseout', function () {\n\t\t\t\tself.dom.hovertip.hide()\n\t\t\t})\n\t}\n}\n\nfunction getAddFilterCallback(self: any, plot: any, rangeStart?: number, rangeStop?: number) {\n\tconst ls = self.getSampleList(plot, rangeStart, rangeStop)\n\n\treturn () => {\n\t\tconst filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, 'filterUiRoot')\n\t\tconst filter = filterJoin([filterUiRoot, ls.tvslst])\n\t\tfilter.tag = 'filterUiRoot'\n\t\tself.app.dispatch({\n\t\t\ttype: 'filter_replace',\n\t\t\tfilter\n\t\t})\n\t}\n}\n\n", "import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { controlsInit, renderTerm1Label } from '../controls'\nimport { getT0T2defaultQ } from '../summaryQ.ts'\nimport setViolinRenderer from './violin.renderer'\nimport { htmlLegend, Menu, setDescrStatsByTerm } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\nimport { setInteractivity } from './violin.interactivity'\nimport { isNumericTw } from '#shared/terms.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\nimport { getSingleCellSpecialCase } from '#plots/sc/utils/specialCase.ts'\nimport { getDefaultViolinSettings } from './settings/defaults'\nimport type { ViolinSettings } from './settings/Settings'\nimport type { ViolinRequest } from '#types'\n/*\nwhen opts.mode = 'minimal', a minimal violin plot will be rendered that \nwill have a single term and minimal features (i.e. no controls, legend, \nlabels, brushing, transitions, etc.)\n*/\n\nclass ViolinPlot extends PlotBase implements RxComponent{\n\tstatic type = 'violin'\n\n\ttype: string\n\tdom!: { \n\t\thovertip: Menu\n\t\tclicktip: Menu\n\t\tsampletabletip: Menu\n\t\theader: any\n\t\tcontrols: any\n\t\tbanner: any\n\t\terrdiv: any\n\t\tloadingDiv: any\n\t\trenderedData: any\n\t\tviolinDiv: any\n\t\tlegendDiv: any\n\t}\n\tsettings!: ViolinSettings\n\tlegendRenderer!: any\n\trender!: () => void\n\trenderPvalueTable!: (chartDiv: any, chart: any) => void\n\tgetChartTitle!: (chartId: string, totalNum?: number) => string\n\tdata!: any\n\tconfig!: any\n\tdisplayLabelClickMenu!: (...args: any[]) => void\n\tdisplayBrushMenu!: (...args: any[]) => void\n\tdisplayMenu!: (...args: any[]) => void\n\tselectSamples!: (...args: any[]) => Promise<void>\n\tgetSampleList!: (...args: any[]) => any[]\n\tcallListSamples!: (...args: any[]) => Promise<void>\n\tlabelHideLegendClicking!: (...args: any[]) => void\n\tdownload!: (arg?: any) => void\n\tgetChartImages!: () => any\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = ViolinPlot.type\n\t}\n\n\tasync init() {\n\t\t// const config = appState.plots.find(p => p.id === this.id)\n\t\tconst holder = this.opts.holder\n\t\t\t.append('div')\n\t\t\t//.style('display', 'inline-block')\n\t\t\t//.style('padding', this.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t//.style('padding-left', this.opts.mode != 'minimal' ? '20px' : '0px')\n\t\t\t.attr('id', 'sjpp-vp-holder')\n\n\t\tconst { controls, errdiv, loadingDiv, banner, renderedData, charts, legendDiv } = this.getStandardDomLayout(\n\t\t\tholder,\n\t\t\tthis.opts\n\t\t)\n\n\t\tthis.dom = {\n\t\t\thovertip: new Menu({ padding: '3px' }), // separate tips for hover & click on violin labels to avoid interfering\n\t\t\tclicktip: new Menu({ padding: '0px' }),\n\t\t\tsampletabletip: new Menu({ padding: '3px' }), // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..\n\t\t\theader: this.opts.header,\n\t\t\tcontrols: controls.attr('class', 'sjpp-plot-controls').style('display', 'inline-block'),\n\t\t\tbanner: banner.attr('data-testid', 'sjpp-violin-banner'),\n\t\t\terrdiv,\n\t\t\tloadingDiv: loadingDiv\n\t\t\t\t.attr('data-testid', 'sjpp-violin-loading-div')\n\t\t\t\t.style('display', this.opts.mode != 'minimal' ? 'inline-block' : 'none'),\n\t\t\trenderedData,\n\t\t\tviolinDiv: charts\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-vp-violinDiv')\n\t\t\t\t.attr('data-testid', 'sjpp-violin-div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('flex-direction', 'row')\n\t\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t\t.style('max-width', '100vw'),\n\t\t\tlegendDiv: legendDiv\n\t\t\t\t.classed('sjpp-vp-legend', true)\n\t\t\t\t.attr('data-testid', 'sjpp-violin-legend')\n\t\t\t\t.style('margin-left', '-15px')\n\t\t\t\t.style('padding-top', '20px')\n\t\t}\n\n\t\tsetViolinRenderer(this)\n\t\tsetInteractivity(this)\n\n\t\tif (this.opts.mode != 'minimal') {\n\t\t\tthis.legendRenderer = htmlLegend(this.dom.legendDiv, {\n\t\t\t\tsettings: {\n\t\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t\t},\n\t\t\t\thandlers: {}\n\t\t\t})\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t\treturn true\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\n\t\tapi.getChartImages = () => this.getChartImages()\n\t}\n\n\tasync setControls() {\n\t\t// do not replace this.components.controls on every re-render,\n\t\t// that could lead to missing control.state if there are errors\n\t\t// with config.terms filling, etc. Better to set getDisplayStyle()\n\t\t// option for an input that doesn't have to be rendered for a given\n\t\t// term/term2/term0 combination.\n\t\tif (this.components.controls) return\n\t\tthis.dom.controls.selectAll('*').remove()\n\t\tconst controlLabels = this.state.config.controlLabels\n\t\tif (!controlLabels) throw 'controls labels not found'\n\t\tthis.components = {}\n\t\tif (this.opts.mode == 'minimal') return\n\n\t\tconst specialCase = getSingleCellSpecialCase(this.config)\n\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term' },\n\t\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tmenuOptions: 'edit'\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term2',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term2', specialCase },\n\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ(),\n\t\t\t\tgetDisplayStyle: plot => (plot.config?.term?.term?.type === 'termCollection' ? 'none' : '')\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term0',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term0', specialCase },\n\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t// by default, do not allow continuous mode for divide-by term, since\n\t\t\t\t// it will create a separate violin-overlay group per unique float or integer value\n\t\t\t\t// and there will nonsensical tens/hundreds of these charts based on the cohort size\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion || ['discrete'],\n\t\t\t\tdefaultQ4fillTW: getT0T2defaultQ(),\n\t\t\t\tgetDisplayStyle: plot => (plot.config?.term?.term?.type === 'termCollection' ? 'none' : '')\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Orientation',\n\t\t\t\ttitle: 'Orientation of the chart',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orientation',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Data symbol',\n\t\t\t\ttitle: 'Symbol type',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'datasymbol',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Ticks', value: 'rug' },\n\t\t\t\t\t{ label: 'Circles', value: 'bean' },\n\t\t\t\t\t{ label: 'Off', value: 'none' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Scale',\n\t\t\t\ttitle: 'Axis scale',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'isLogScale',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Linear', value: false },\n\t\t\t\t\t{ label: 'Log10', value: true }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Order by',\n\t\t\t\ttitle: 'Order violin plots by parameters',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orderByMedian',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Default', value: false },\n\t\t\t\t\t{ label: 'Median', value: true }\n\t\t\t\t],\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\tlet style = 'none'\n\t\t\t\t\tconst charts = this.data?.charts || {}\n\t\t\t\t\tfor (const k of Object.keys(charts)) {\n\t\t\t\t\t\tconst chart = charts[k]\n\t\t\t\t\t\tif (chart?.plots.length > 1) style = ''\n\t\t\t\t\t}\n\t\t\t\t\treturn style\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Symbol size',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'radius',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 30,\n\t\t\t\tmin: 4\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Bins',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'ticks',\n\t\t\t\ttitle: 'Number of bins used to build the plot',\n\t\t\t\tmin: 1,\n\t\t\t\tmax: 50\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot length',\n\t\t\t\ttitle: 'Length of the plot',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 1000,\n\t\t\t\tmin: 200,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot thickness',\n\t\t\t\ttitle: 'If not specified, the plot thickness is calculated based on the number of categories',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'plotThickness',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 200,\n\t\t\t\tmin: 20,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot padding',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'rowSpace',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 20,\n\t\t\t\tmin: 0,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median length',\n\t\t\t\ttitle: 'Length of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianLength',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 50,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median color',\n\t\t\t\ttitle: 'color of median',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median thickness',\n\t\t\t\ttitle: 'Width of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianThickness',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 10,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 100\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Default violin color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show stats',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showStats',\n\t\t\t\tboxLabel: 'Yes'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show association tests',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showAssociationTests',\n\t\t\t\tboxLabel: 'Yes',\n\t\t\t\tgetDisplayStyle: plot => (plot.term2 ? 'table-row' : 'none')\n\t\t\t}\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,\n\t\t\tinputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.violin', this.download)\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermfilter,\n\t\t\tconfig,\n\t\t\tdisplaySampleIds: appState.termdbConfig.displaySampleIds,\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken()\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config)\n\t\tthis.settings = this.config.settings.violin\n\t\tawait this.setControls()\n\n\t\tif (this.config.chartType != this.type && this.config.childType != this.type) return\n\t\tif (this.dom.header)\n\t\t\tthis.dom.header.html(\n\t\t\t\tthis.config.term.term.name + ` <span style=\"opacity:.6;font-size:1em;margin-left:10px;\">Violin Plot</span>`\n\t\t\t)\n\n\t\t//Fix for rm'ing error message when plot re-renders\n\t\t//Leave in main() so the message doesn't linger whilst\n\t\t//the plot is rendering\n\t\tconst existingMsg = this.dom.banner.style('display', 'none').select('span')\n\t\tif (!existingMsg.empty()) existingMsg.remove()\n\n\t\tconst args: any = this.validateArgs()\n\t\tlet data\n\t\ttry {\n\t\t\tthis.toggleLoadingDiv('block', 'block')\n\t\t\tdata = await this.app.vocabApi.getViolinBox(args, null, this.api?.getAbortSignal())\n\t\t} catch (e) {\n\t\t\tthis.toggleLoadingDiv('none', 'none')\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthrow e\n\t\t}\n\n\t\tthis.data = data\n\t\tif (this.data.error) {\n\t\t\tthis.toggleLoadingDiv('none', 'none')\n\t\t\tthrow this.data.error\n\t\t}\n\t\tsetDescrStatsByTerm([this.config.term, this.config.term2], this.data.descrStats)\n\t\t//this.toggleLoadingDiv(this.opts.mode == 'minimal' ? 'none' : '')\n\t\tsetTimeout(\n\t\t\t() => {\n\t\t\t\tthis.render()\n\t\t\t\tthis.toggleLoadingDiv('none')\n\t\t\t},\n\t\t\tthis.opts.mode == 'minimal' ? 0 : 500\n\t\t)\n\t}\n\n\tvalidateArgs(): ViolinRequest {\n\t\tconst { term, term2, term0, /*settings*/ } = this.config\n\t\tconst s = this.settings\n\t\tconst isNumericTermCollection =\n\t\t\tterm.term?.type === 'termCollection' &&\n\t\t\tterm.term?.memberType === 'numeric' &&\n\t\t\tterm.type !== 'TermCollectionTWFraction'\n\t\t// dslabel and genome are injected by vocabApi.getViolinBox\n\t\tconst arg: any = {\n\t\t\tplotType: 'violin',\n\t\t\tsvgw: s.svgw,\n\t\t\torientation: s.orientation,\n\t\t\tdevicePixelRatio: window.devicePixelRatio,\n\t\t\tdatasymbol: s.datasymbol,\n\t\t\tradius: s.radius,\n\t\t\taxisHeight: s.axisHeight,\n\t\t\trightMargin: s.rightMargin,\n\t\t\tisLogScale: s.isLogScale,\n\t\t\tticks: s.ticks,\n\t\t\torderByMedian: s.orderByMedian,\n\t\t\tfilter: this.state.termfilter.filter\n\t\t}\n\n\t\tif (this.opts.mode == 'minimal') {\n\t\t\targ.tw = term\n\t\t\t// assume a single term for minimal plot\n\t\t\tif (term2 || term0) throw 'only a single term allowed for minimal plot'\n\t\t\tif (term.q.mode == 'spline') {\n\t\t\t\t/** FIXME bad design; should not modify setting or even plot state in runtime, \n\t\t\t\tinstead supply this in constructor arg and generalize it beyond spline\n\t\t\t\t// term may be cubic spline from regression analysis\n\t\t\t\t// render knot values as vertical lines on the plot\n\t\t\t\t*/\n\t\t\t\ts.lines = term.q.knots.map(x => Number(x.value))\n\t\t\t} else {\n\t\t\t\ts.lines = []\n\t\t\t}\n\t\t\tif (term.q.scale) {\n\t\t\t\t// term may be scaled from regression analysis\n\t\t\t\t// scale the data on the server-side\n\t\t\t\targ.scale = term.q.scale\n\t\t\t}\n\t\t} else if (isNumericTermCollection) {\n\t\t\t// numeric termCollection: server-side expandNumericTermCollection creates a\n\t\t\t// synthetic overlay from member terms, so don't send term2/term0\n\t\t\targ.tw = term\n\t\t} else if (isNumericTw(term) && term.q.mode === 'continuous') {\n\t\t\targ.tw = term\n\t\t\tif (term2) arg.overlayTw = term2\n\t\t} else if (isNumericTw(term2) && term2.q.mode === 'continuous') {\n\t\t\targ.tw = term2\n\t\t\targ.overlayTw = term\n\t\t} else {\n\t\t\tthrow 'both term1 and term2 are not numeric/continuous'\n\t\t}\n\n\t\tif (term0 && !isNumericTermCollection) arg.divideTw = term0\n\t\treturn arg satisfies ViolinRequest ? arg : (arg as any)\n\t}\n}\n\nexport const violinInit = getCompInit(ViolinPlot)\nexport const componentInit = violinInit\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'violin getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tthrow `${e} [violin getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\t// common: {\n\t\t\t// \tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t// \tuse_percentage: false,\n\t\t\t// \tbarheight: 300, // maximum bar length\n\t\t\t// \tbarwidth: 20, // bar thickness\n\t\t\t// \tbarspace: 2 // space between two bars\n\t\t\t// },\n\t\t\tviolin: getDefaultViolinSettings(app)\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n"],
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+}