@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-OCC5HEPR.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/violin.renderer.js"],
+  "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 } from '#dom'\nimport { rgb } from 'd3'\nimport { format as d3format } from 'd3-format'\nimport { SINGLECELL_GENE_EXPRESSION } from '#types'\nimport { getValueConversionFactor, toUserUnit } from '#shared/helpers.js'\n\nconst 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, t2) {\n\treturn t2?.q?.mode === 'continuous' ? t2.term : t1?.term\n}\n\nexport default function setViolinRenderer(self) {\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 =\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\tif (termNum && termNum.term?.values) {\n\t\t\tfor (const [k, v] of Object.entries(termNum.term.values)) {\n\t\t\t\tif (v.uncomputable) {\n\t\t\t\t\tif (termNum.q.hiddenValues[k]) {\n\t\t\t\t\t\ttermNum.q.hiddenValues[v.label] = 1\n\t\t\t\t\t\tdelete termNum.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 chartKeys = Object.keys(self.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 = self.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(\n\t\t\t\t\t(a, b) =>\n\t\t\t\t\t\ta.summaryStats.find(x => x.id === 'median').value - b.summaryStats.find(x => x.id === 'median').value\n\t\t\t\t)\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.html(`${self.getChartTitle(chart.chartId)} (n=${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 [plotIdx, plot] of plots.entries()) {\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()\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()\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 (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) {\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 (d, event) {\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, chart) {\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: `${maxHeight}px`,\n\t\t\tresize: true\n\t\t})\n\t}\n\n\tself.getChartTitle = function (chartId) {\n\t\tif (!self.config.term0) return chartId\n\t\treturn self.config.term0.term.values && chartId in self.config.term0.term.values\n\t\t\t? self.config.term0.term.values[chartId].label\n\t\t\t: chartId\n\t}\n\n\tfunction createMargins(labelsize, settings, isH, isMinimal) {\n\t\tlet margins\n\n\t\tif (isMinimal) {\n\t\t\tmargins = isH\n\t\t\t\t? { left: 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 }\n\t\t\t\t: { left: settings.axisHeight, top: 30, right: settings.rightMargin, bottom: 10 }\n\t\t} else {\n\t\t\tmargins = isH\n\t\t\t\t? { left: labelsize + 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 }\n\t\t\t\t: { left: settings.axisHeight, top: 50, right: settings.rightMargin, bottom: labelsize }\n\t\t}\n\t\treturn margins\n\t}\n\n\tfunction renderSvg(t1, plots, chartDiv, self, isH, settings) {\n\t\tconst violinDiv = chartDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', self.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t.style('overflow', 'auto')\n\t\t\t.style('scrollbar-width', 'none')\n\n\t\tconst violinSvg = violinDiv.append('svg')\n\n\t\tconst labelsize = getMaxLabelWidth(\n\t\t\tviolinSvg,\n\t\t\tplots.map(plot => `${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, t2, settings, isH, svg, self) {\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)()\n\t\t\t\t.scale(uiScale)\n\t\t\t\t.tickFormat((d, i) => {\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 (d < 0.1) return d3format('.3f')(d)\n\t\t\t\t\t\t\treturn d3format('.1f')(d)\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 (d < 50) return d\n\t\t\t\t\t\t\treturn d3format('.1s')(d)\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 d\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} (${numTerm.valueConversion.toUnit}s)` : numTerm.name\n\t\t\tconst lab = svg.svgG\n\t\t\t\t.append('text')\n\t\t\t\t.text(n)\n\t\t\t\t.classed('sjpp-numeric-term-label', true)\n\t\t\t\t.attr('data-testid', `sjpp-violin-label-${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, plot, isH, wScale, areaBuilder, y) {\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 ? Object.values(catTerm.term.values).find(o => o.label == label) : 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\tlet 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, t2, violinG, plot, isH, settings) {\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) {\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, d) {\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, plot, areaBuilder) {\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, violinG, plot, isH) {\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, isH, plot, svgData, self) {\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, isH, lines, svgData) {\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, t2, violinG, settings, plot, isH, svgData) {\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 => {\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\tsettings.isLogScale\n\t\t? (axisScale = scaleLog()\n\t\t\t\t.base(self.app.vocabApi.termdbConfig.logscaleBase2 ? 2 : 10)\n\t\t\t\t.domain([self.data.min, self.data.max])\n\t\t\t\t.range(isH ? [0, settings.svgw] : [settings.svgw, 0]))\n\t\t: (axisScale = scaleLinear()\n\t\t\t\t.domain([self.data.min, self.data.max])\n\t\t\t\t.range(isH ? [0, settings.svgw] : [settings.svgw, 0]))\n\treturn axisScale\n}\n\nfunction getLegendGrps(termNum, self) {\n\tconst legendGrps = [],\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) addDescriptiveStats(t1, legendGrps, headingStyle, self)\n\tif (t2?.term.type === 'float' || t2?.q.mode === 'continuous' || t2?.term.type === 'integer')\n\t\taddDescriptiveStats(t2, legendGrps, headingStyle, self)\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, legendGrps, headingStyle, self) {\n\tif (term?.q.descrStats) {\n\t\tconst items = Object.values(term.q.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\tconst title =\n\t\t\tself.config.term2?.term.type === 'float' || self.config.term2?.term.type === 'integer'\n\t\t\t\t? `Descriptive statistics: ${term.term.name}`\n\t\t\t\t: `Descriptive statistics`\n\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\tlegendGrps.push({ name, items })\n\t}\n}\n\nfunction addUncomputableValues(term, legendGrps, headingStyle, self) {\n\tif (term?.term.values) {\n\t\tconst items = []\n\t\tfor (const k in term.term.values) {\n\t\t\tif (self.data.uncomputableValues?.[term.term.values[k]?.label]) {\n\t\t\t\titems.push({\n\t\t\t\t\ttext: `${term.term.values[k].label}, n = ${self.data.uncomputableValues[term.term.values[k].label]}`,\n\t\t\t\t\tnoIcon: true,\n\t\t\t\t\t/** Need to specify that this is a hidden value for\n\t\t\t\t\t * text styling in the legend but not a plot to avoid\n\t\t\t\t\t * rendering a tooltip or click events.\n\t\t\t\t\t */\n\t\t\t\t\tisHidden: true,\n\t\t\t\t\tisClickable: false,\n\t\t\t\t\thiddenOpacity: 1\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (items.length) {\n\t\t\tconst name =\n\t\t\t\tself.config.term2?.term.type === 'float' || self.config.term2?.term.type === 'integer'\n\t\t\t\t\t? `<span style=\"${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, legendGrps, headingStyle) {\n\tconst items = []\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"],
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+  "names": ["self"]
+}

package/dist/chunk-OMIUJ7JT.js

@@ -0,0 +1,448 @@
+import {
+  setViolinRenderer
+} from "./chunk-OCC5HEPR.js";
+import {
+  setInteractivity
+} from "./chunk-RL3IRMOA.js";
+import {
+  PlotBase,
+  controlsInit,
+  defaultUiLabels,
+  fillTermWrapper,
+  getCombinedTermFilter,
+  getSingleCellSpecialCase,
+  getT0T2defaultQ,
+  htmlLegend,
+  renderTerm1Label
+} from "./chunk-73PFJ2VF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  isNumericTw
+} from "./chunk-X6VTVZY7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-H6INPPUC.js";
+import {
+  plotColor
+} from "./chunk-GEQUQ3GG.js";
+
+// plots/violin.js
+var ViolinPlot = class _ViolinPlot extends PlotBase {
+  static type = "violin";
+  constructor(opts) {
+    super(opts);
+    this.type = _ViolinPlot.type;
+  }
+  async init(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    const holder = this.opts.holder.append("div").attr("id", "sjpp-vp-holder");
+    const { controls, errdiv, loadingDiv, banner, renderedData, charts, legendDiv } = this.getStandardDomLayout(
+      holder,
+      this.opts
+    );
+    this.dom = {
+      hovertip: new Menu({ padding: "3px" }),
+      // separate tips for hover & click on violin labels to avoid interfering
+      clicktip: new Menu({ padding: "0px" }),
+      sampletabletip: new Menu({ padding: "3px" }),
+      // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..
+      header: this.opts.header,
+      controls: controls.attr("class", "sjpp-plot-controls").style("display", "inline-block"),
+      banner: banner.attr("data-testid", "sjpp-violin-banner"),
+      errdiv,
+      loadingDiv: loadingDiv.attr("data-testid", "sjpp-violin-loading-div").style("display", this.opts.mode != "minimal" ? "inline-block" : "none"),
+      renderedData,
+      violinDiv: charts.append("div").attr("class", "sjpp-vp-violinDiv").attr("data-testid", "sjpp-violin-div").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
+      legendDiv: legendDiv.classed("sjpp-vp-legend", true).attr("data-testid", "sjpp-violin-legend").style("margin-left", "-15px").style("padding-top", "20px")
+    };
+    setViolinRenderer(this);
+    setInteractivity(this);
+    if (this.opts.mode != "minimal") {
+      this.legendRenderer = htmlLegend(this.dom.legendDiv, {
+        settings: {
+          legendOrientation: "vertical"
+        },
+        handlers: {}
+      });
+    }
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("plot_")) {
+      return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
+    }
+    return true;
+  }
+  preApiFreeze(api) {
+    api.download = this.download;
+    api.getChartImages = () => this.getChartImages();
+  }
+  async setControls() {
+    if (this.components.controls) return;
+    this.dom.controls.selectAll("*").remove();
+    const controlLabels = this.state.config.controlLabels;
+    if (!controlLabels) throw "controls labels not found";
+    this.components = {};
+    if (this.opts.mode == "minimal") return;
+    const specialCase = getSingleCellSpecialCase(this.config);
+    const inputs = [
+      {
+        type: "term",
+        configKey: "term",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term" },
+        label: controlLabels.term1?.label || renderTerm1Label,
+        vocabApi: this.app.vocabApi,
+        menuOptions: "edit"
+      },
+      {
+        type: "term",
+        configKey: "term2",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term2", specialCase },
+        title: controlLabels.term2.title || controlLabels.term2.label,
+        label: controlLabels.term2.label,
+        vocabApi: this.app.vocabApi,
+        numericEditMenuVersion: this.opts.numericEditMenuVersion,
+        defaultQ4fillTW: getT0T2defaultQ(),
+        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
+      },
+      {
+        type: "term",
+        configKey: "term0",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term0", specialCase },
+        title: controlLabels.term0.title || controlLabels.term0.label,
+        label: controlLabels.term0.label,
+        vocabApi: this.app.vocabApi,
+        // by default, do not allow continuous mode for divide-by term, since
+        // it will create a separate violin-overlay group per unique float or integer value
+        // and there will nonsensical tens/hundreds of these charts based on the cohort size
+        numericEditMenuVersion: this.opts.numericEditMenuVersion || ["discrete"],
+        defaultQ4fillTW: getT0T2defaultQ(),
+        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
+      },
+      {
+        label: "Orientation",
+        title: "Orientation of the chart",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "orientation",
+        options: [
+          { label: "Vertical", value: "vertical" },
+          { label: "Horizontal", value: "horizontal" }
+        ]
+      },
+      {
+        label: "Data symbol",
+        title: "Symbol type",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "datasymbol",
+        options: [
+          { label: "Ticks", value: "rug" },
+          { label: "Circles", value: "bean" },
+          { label: "Off", value: "none" }
+        ]
+      },
+      {
+        label: "Scale",
+        title: "Axis scale",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "isLogScale",
+        options: [
+          { label: "Linear", value: false },
+          { label: "Log10", value: true }
+        ]
+      },
+      {
+        label: "Order by",
+        title: "Order violin plots by parameters",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "orderByMedian",
+        options: [
+          { label: "Default", value: false },
+          { label: "Median", value: true }
+        ],
+        getDisplayStyle: () => {
+          let style = "none";
+          const charts = this.data?.charts || {};
+          for (const k of Object.keys(charts)) {
+            const chart = charts[k];
+            if (chart?.plots.length > 1) style = "";
+          }
+          return style;
+        }
+      },
+      {
+        label: "Symbol size",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "radius",
+        step: 1,
+        max: 30,
+        min: 4
+      },
+      {
+        label: "Bins",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "ticks",
+        title: "Number of bins used to build the plot",
+        min: 1,
+        max: 50
+      },
+      {
+        label: "Plot length",
+        title: "Length of the plot",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "svgw",
+        step: 10,
+        max: 1e3,
+        min: 200,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Plot thickness",
+        title: "If not specified, the plot thickness is calculated based on the number of categories",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "plotThickness",
+        step: 10,
+        max: 200,
+        min: 20,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Plot padding",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "rowSpace",
+        step: 1,
+        max: 20,
+        min: 0,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Median length",
+        title: "Length of median",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "medianLength",
+        step: 1,
+        max: 50,
+        min: 3,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Median color",
+        title: "color of median",
+        type: "color",
+        chartType: "violin",
+        settingsKey: "medianColor"
+      },
+      {
+        label: "Median thickness",
+        title: "Width of median",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "medianThickness",
+        step: 1,
+        max: 10,
+        min: 3,
+        debounceInterval: 100
+      },
+      {
+        label: "Default violin color",
+        type: "color",
+        chartType: "violin",
+        settingsKey: "defaultColor"
+      },
+      {
+        label: "Show stats",
+        type: "checkbox",
+        chartType: "violin",
+        settingsKey: "showStats",
+        boxLabel: "Yes"
+      },
+      {
+        label: "Show association tests",
+        type: "checkbox",
+        chartType: "violin",
+        settingsKey: "showAssociationTests",
+        boxLabel: "Yes",
+        getDisplayStyle: (plot) => plot.term2 ? "table-row" : "none"
+      }
+    ];
+    this.components.controls = await controlsInit({
+      app: this.app,
+      id: this.id,
+      holder: this.dom.controls,
+      inputs
+    });
+    this.components.controls.on("downloadClick.violin", this.download);
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
+    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
+    return {
+      termfilter,
+      config,
+      displaySampleIds: appState.termdbConfig.displaySampleIds,
+      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken()
+    };
+  }
+  async main() {
+    this.config = structuredClone(this.state.config);
+    this.settings = this.config.settings.violin;
+    await this.setControls();
+    if (this.config.chartType != this.type && this.config.childType != this.type) return;
+    if (this.dom.header)
+      this.dom.header.html(
+        this.config.term.term.name + ` <span style="opacity:.6;font-size:1em;margin-left:10px;">Violin Plot</span>`
+      );
+    const existingMsg = this.dom.banner.style("display", "none").select("span");
+    if (!existingMsg.empty()) existingMsg.remove();
+    const args = this.validateArgs();
+    let data;
+    try {
+      this.toggleLoadingDiv("block", "block");
+      data = await this.app.vocabApi.getViolinBox(args, null, this.api.getAbortSignal());
+    } catch (e) {
+      this.toggleLoadingDiv("none", "none");
+      if (this.app.isAbortError(e)) return;
+      throw e;
+    }
+    this.data = data;
+    if (this.data.error) {
+      this.toggleLoadingDiv("none", "none");
+      throw this.data.error;
+    }
+    args.tw.q.descrStats = this.data.descrStats;
+    setTimeout(
+      () => {
+        this.render();
+        this.toggleLoadingDiv("none");
+      },
+      this.opts.mode == "minimal" ? 0 : 500
+    );
+  }
+  validateArgs() {
+    const { term, term2, term0, settings } = this.config;
+    const s = this.settings;
+    const arg = {
+      plotType: "violin",
+      svgw: s.svgw,
+      orientation: s.orientation,
+      devicePixelRatio: window.devicePixelRatio,
+      datasymbol: s.datasymbol,
+      radius: s.radius,
+      axisHeight: s.axisHeight,
+      rightMargin: s.rightMargin,
+      isLogScale: s.isLogScale,
+      ticks: s.ticks,
+      orderByMedian: s.orderByMedian,
+      filter: this.state.termfilter.filter
+    };
+    if (this.opts.mode == "minimal") {
+      arg.tw = term;
+      if (term2 || term0) throw "only a single term allowed for minimal plot";
+      if (term.q.mode == "spline") {
+        s.lines = term.q.knots.map((x) => Number(x.value));
+      } else {
+        s.lines = [];
+      }
+      if (term.q.scale) {
+        arg.scale = term.q.scale;
+      }
+    } else if (term.term?.type === "termCollection" && term.term?.memberType === "numeric" && term.type !== "TermCollectionTWFraction") {
+      arg.tw = term;
+    } else if (isNumericTw(term) && term.q.mode === "continuous") {
+      arg.tw = term;
+      if (term2) arg.overlayTw = term2;
+    } else if (isNumericTw(term2) && term2.q.mode === "continuous") {
+      arg.tw = term2;
+      arg.overlayTw = term;
+    } else {
+      throw "both term1 and term2 are not numeric/continuous";
+    }
+    if (term0) arg.divideTw = term0;
+    return arg;
+  }
+};
+var violinInit = getCompInit(ViolinPlot);
+var componentInit = violinInit;
+function getDefaultViolinSettings(app, overrides = {}) {
+  const defaults = {
+    orientation: "horizontal",
+    rowlabelw: 250,
+    brushRange: null,
+    //object with start and end if there is a brush selection
+    svgw: 500,
+    // span length of a plot/svg, not including margin
+    datasymbol: "rug",
+    radius: 10,
+    axisHeight: 60,
+    rightMargin: 50,
+    lines: [],
+    isLogScale: false,
+    // false: linear scale, true: log scale
+    rowSpace: 10,
+    medianLength: 7,
+    medianColor: "#FF0000",
+    medianThickness: 3,
+    ticks: 15,
+    defaultColor: plotColor,
+    method: 0,
+    orderByMedian: false,
+    showStats: true,
+    showAssociationTests: true
+  };
+  return Object.assign(defaults, overrides);
+}
+async function getPlotConfig(opts, app) {
+  if (!opts.term) throw "violin getPlotConfig: opts.term{} missing";
+  try {
+    await fillTermWrapper(opts.term, app.vocabApi);
+    if (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi);
+    if (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi);
+  } catch (e) {
+    throw `${e} [violin getPlotConfig()]`;
+  }
+  const config = {
+    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
+    settings: {
+      controls: {
+        term2: null,
+        // the previous overlay value may be displayed as a convenience for toggling
+        term0: null
+      },
+      // common: {
+      // 	use_logscale: false, // flag for y-axis scale type, 0=linear, 1=log
+      // 	use_percentage: false,
+      // 	barheight: 300, // maximum bar length
+      // 	barwidth: 20, // bar thickness
+      // 	barspace: 2 // space between two bars
+      // },
+      violin: getDefaultViolinSettings(app)
+    }
+  };
+  return copyMerge(config, opts);
+}
+
+export {
+  violinInit,
+  componentInit,
+  getDefaultViolinSettings,
+  getPlotConfig
+};
+//# sourceMappingURL=chunk-OMIUJ7JT.js.map