@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/chunk-YEYC4PLD.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/boxplot/model/Model.ts", "../plots/boxplot/viewModel/LegendDataMapper.ts", "../plots/boxplot/viewModel/ViewModel.ts", "../plots/boxplot/view/BoxPlotToolTips.ts", "../plots/boxplot/view/BoxPlotLabelMenu.ts", "../plots/boxplot/view/View.ts", "../plots/boxplot/interactions/ListSamples.ts", "../plots/boxplot/interactions/BoxPlotInteractions.ts", "../plots/boxplot/view/LegendRender.ts", "../plots/boxplot/view/AssociationTableRender.ts", "../plots/boxplot/BoxPlot.ts"],
+  "sourcesContent": ["import type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { BoxPlotSettings, BoxPlotConfig } from '../BoxPlotTypes'\nimport type { TdbBoxplot } from '../BoxPlot.ts'\nimport type { BoxPlotResponse } from '#types'\nimport { isNumericTerm } from '#shared/terms.js'\n\n/**\n * Requests data for the boxplots.\n * Add more methods for formating the request opts and api requests.\n */\nexport class Model {\n\tboxplot: TdbBoxplot\n\tconfig: BoxPlotConfig\n\tstate: MassState\n\tapp: MassAppApi\n\tsettings: BoxPlotSettings\n\n\tconstructor(boxplot: TdbBoxplot, config: BoxPlotConfig) {\n\t\tthis.boxplot = boxplot\n\t\tthis.config = config\n\t\tthis.state = boxplot.state\n\t\tthis.app = boxplot.app\n\t\tthis.settings = config.settings.boxplot\n\t}\n\n\tasync getData() {\n\t\tconst boxPlotDataArgs = this.setRequestOpts()\n\t\tconst data: BoxPlotResponse = await this.app.vocabApi.getBoxPlotData(\n\t\t\tboxPlotDataArgs,\n\t\t\tthis.boxplot.api.getAbortSignal()\n\t\t)\n\t\treturn data\n\t}\n\n\tsetRequestOpts() {\n\t\tconst opts: { [index: string]: any } = {\n\t\t\ttw: this.getContinousTerm(),\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0: this.state.termfilter.filter0,\n\t\t\torderByMedian: this.settings.orderByMedian,\n\t\t\tisLogScale: this.settings.isLogScale,\n\t\t\tremoveOutliers: this.settings.removeOutliers,\n\t\t\tshowAssocTests: this.settings.showAssocTests\n\t\t}\n\t\tif (this.config.term2)\n\t\t\topts.overlayTw = this.getContinousTerm() == this.config.term ? this.config.term2 : this.config.term\n\n\t\tif (this.config.term0) opts.divideTw = this.config.term0\n\n\t\treturn opts\n\t}\n\n\tgetContinousTerm() {\n\t\tif (!this.config?.term2) return this.config.term\n\t\treturn isNumericTerm(this.config.term.term) && this.config.term.q.mode == 'continuous'\n\t\t\t? this.config.term\n\t\t\t: this.config.term2\n\t}\n}\n", "import type { FormattedPlotEntry, LegendData, LegendItemEntry, BoxPlotConfig } from '../BoxPlotTypes'\nimport type { BoxPlotChartEntry, DescrStats } from '#types'\n\nexport class LegendDataMapper {\n\tlegendData: LegendData = []\n\tconstructor(config: BoxPlotConfig, data: BoxPlotChartEntry, plots: FormattedPlotEntry[]) {\n\t\tconst isTerm2 = config?.term2\n\t\tif (config.term.q?.descrStats) {\n\t\t\tthis.legendData.push({\n\t\t\t\tlabel: `Descriptive Statistics${isTerm2 ? `: ${config.term.term.name}` : ''}`,\n\t\t\t\titems: this.getDescrStatItems(config.term.q.descrStats)\n\t\t\t})\n\t\t}\n\t\tif (isTerm2 && isTerm2.q?.descrStats) {\n\t\t\tthis.legendData.push({\n\t\t\t\tlabel: `Descriptive Statistics: ${config.term2.term.name}`,\n\t\t\t\titems: this.getDescrStatItems(isTerm2.q.descrStats)\n\t\t\t})\n\t\t}\n\t\tconst hiddenPlots =\n\t\t\tplots\n\t\t\t\t.filter(p => p.isHidden)\n\t\t\t\t?.map(p => {\n\t\t\t\t\tconst total = p.descrStats.total\n\t\t\t\t\tif (!total || !total.value) throw `Missing total value for ${p.key}`\n\t\t\t\t\treturn { key: p.key, text: p.key, n: total.value, isHidden: true, isPlot: true }\n\t\t\t\t}) || []\n\t\tif (config.term.term?.values) {\n\t\t\tconst term1Label = config.term2 ? config.term.term.name : 'Other categories'\n\t\t\tconst term1Data = this.setHiddenCategoryItems(config.term, term1Label, hiddenPlots, data.uncomputableValues || [])\n\t\t\tif (term1Data) this.legendData.push(term1Data)\n\t\t}\n\n\t\tif (config.term2?.term?.values) {\n\t\t\tconst term2Data = this.setHiddenCategoryItems(\n\t\t\t\tconfig.term2,\n\t\t\t\tconfig.term2.term.name,\n\t\t\t\thiddenPlots,\n\t\t\t\tdata.uncomputableValues || []\n\t\t\t)\n\t\t\tif (term2Data) this.legendData.push(term2Data)\n\t\t}\n\t}\n\n\tgetDescrStatItems(stats: DescrStats) {\n\t\treturn Object.values(stats).map(s => ({\n\t\t\tkey: s.key,\n\t\t\ttext: `${s.label}: ${s.value}`,\n\t\t\tisHidden: false,\n\t\t\tisPlot: false\n\t\t}))\n\t}\n\n\tsetHiddenCategoryItems(\n\t\ttw: any,\n\t\tlabel: string,\n\t\thiddenPlots: LegendItemEntry[],\n\t\tuncomputableValues?: { label: string; value: number }[]\n\t) {\n\t\tconst termData: { label: string; items: LegendItemEntry[] } = { label, items: [] }\n\n\t\tif (hiddenPlots.length) {\n\t\t\tfor (const key of Object.keys(tw.q.hiddenValues || {})) {\n\t\t\t\tconst plot = hiddenPlots.find(p => p.key === key)\n\t\t\t\tif (plot) termData.items.push(plot)\n\t\t\t}\n\t\t}\n\t\tif (uncomputableValues && uncomputableValues.length) {\n\t\t\tfor (const v of Object.values((tw.term.values || {}) as { label: string }[])) {\n\t\t\t\tconst uncomputableItem = uncomputableValues.find(u => u.label === v.label)\n\t\t\t\tif (uncomputableItem) {\n\t\t\t\t\ttermData.items.push({\n\t\t\t\t\t\tkey: uncomputableItem.label,\n\t\t\t\t\t\ttext: `${uncomputableItem.label}, n=${uncomputableItem.value}`,\n\t\t\t\t\t\tisHidden: true,\n\t\t\t\t\t\tisPlot: false\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn termData.items.length ? termData : null\n\t}\n}\n", "import { format } from 'd3-format'\nimport { decimalPlacesUntilFirstNonZero } from '#shared/roundValue.js'\nimport { rgb } from 'd3-color'\nimport type { BoxPlotChartEntry } from '#types'\nimport type { BoxPlotSettings, PlotDimensions, ViewData, BoxPlotConfig } from '../BoxPlotTypes'\nimport { LegendDataMapper } from './LegendDataMapper'\n\nexport class ViewModel {\n\t/** Top padding for the svg */\n\treadonly topPad = 20\n\t/** Bottom padding for the svg */\n\treadonly bottomPad = 40\n\t/** Horizontal, or right and left padding */\n\treadonly horizPad = 120\n\t/** For outliers, set a radius rather than using the default. */\n\treadonly outRadius = 5\n\t/** Increasing padding to space out the boxplots and determine position */\n\tincrPad = 40\n\t/** Range is 20 - 50 */\n\trowHeight: number\n\t/** Range is 10 -20 */\n\trowSpace: number\n\t/** Total size of the labels. May reflect height or width depending on orientation */\n\tprivate totalLabelSize: number\n\t/** Total size of each box plot. May reflect height or width depending on orientation */\n\tprivate totalRowSize: number\n\tviewData: ViewData\n\tconstructor(\n\t\tconfig: BoxPlotConfig,\n\t\tdata: BoxPlotChartEntry,\n\t\tsettings: BoxPlotSettings,\n\t\tmaxLabelLgth: number,\n\t\tuseDefaultSettings: boolean\n\t) {\n\t\t/** As requested, adjust the size of each plot based on the number of boxplots\n\t\t * Manages rendering very large svgs. */\n\t\tconst numOfPlots = data.plots.filter(p => !p.isHidden).length\n\t\tif (useDefaultSettings) {\n\t\t\tconst isLargePlotCount = numOfPlots > 20\n\t\t\tthis.rowHeight = numOfPlots > 10 ? (isLargePlotCount ? 20 : 35) : 50\n\t\t\tthis.rowSpace = numOfPlots > 10 ? (isLargePlotCount ? 10 : 12) : 15\n\t\t} else {\n\t\t\tthis.rowHeight = settings.rowHeight\n\t\t\tthis.rowSpace = settings.rowSpace\n\t\t}\n\n\t\tthis.totalLabelSize = maxLabelLgth + settings.labelPad\n\t\tthis.totalRowSize = this.rowHeight + this.rowSpace\n\n\t\tconst plotDim = this.setPlotDimensions(data, config, settings)\n\t\t//20 for the axis offset (above), 10 more for the first boxplot\n\t\tthis.incrPad += 30\n\n\t\tconst plots = this.setPlotData(data, config, settings)\n\n\t\tthis.viewData = {\n\t\t\tplotDim: plotDim as PlotDimensions,\n\t\t\tplots: plots.filter(p => !p.isHidden),\n\t\t\tlegend: new LegendDataMapper(config, data, plots).legendData\n\t\t}\n\t}\n\n\tsetPlotDimensions(data: BoxPlotChartEntry, config: any, settings: BoxPlotSettings) {\n\t\tconst svg = this.setSvgDimensions(settings, data)\n\t\tconst plotDim = {\n\t\t\t//Add 1 to the max is big enough so the upper line to boxplot isn't cutoff\n\t\t\t//Note: ts is complaining absMax could be null. Ignore. Error in server request.\n\t\t\tdomain: [data.absMin, data.absMax! <= 1 ? data.absMax : data.absMax! + 1],\n\t\t\trange: [0, settings.plotLength],\n\t\t\tsvg,\n\t\t\tchartTitle: getChartTitle(config, data.chartId),\n\t\t\ttitle: this.setTitleDimensions(config, settings, svg.height),\n\t\t\taxis: {\n\t\t\t\tx: settings.isVertical ? this.horizPad / 2 + this.incrPad + this.topPad : this.totalLabelSize,\n\t\t\t\ty: this.topPad + (settings.isVertical ? settings.labelPad : this.incrPad + 20),\n\t\t\t\tvalues: (ticks: number[]) => {\n\t\t\t\t\tif (settings.isLogScale) return this.filterTickValues(ticks)\n\t\t\t\t\treturn ticks\n\t\t\t\t},\n\t\t\t\tformat: (d: number) => {\n\t\t\t\t\tif (settings.isLogScale) {\n\t\t\t\t\t\tif (Number.isInteger(d)) return format('.0f')(d)\n\t\t\t\t\t\tconst dec = decimalPlacesUntilFirstNonZero(d)\n\t\t\t\t\t\tif (dec > 1) return format(`.${dec + 1}f`)(d)\n\t\t\t\t\t\treturn format('.2f')(d)\n\t\t\t\t\t}\n\t\t\t\t\treturn d.toString()\n\t\t\t\t}\n\t\t\t},\n\t\t\tbackgroundColor: settings.displayMode == 'dark' ? 'black' : 'white',\n\t\t\ttextColor: settings.displayMode == 'dark' ? 'white' : 'black'\n\t\t}\n\t\treturn plotDim\n\t}\n\n\tfilterTickValues(ticks: number[]) {\n\t\tconst signifcantLessThanOne = ticks.filter(t => t < 1).length / ticks.length\n\t\tconst range = ticks[ticks.length - 1] - ticks[0]\n\t\tconst spread = range > 1000 ? 4 : range > 100 ? 3 : 2\n\t\tconst formattedTicks = ticks.filter((t, i) => {\n\t\t\tif (t === 0 || (i == ticks.length - 1 && i % spread !== 0)) return t\n\t\t\telse if (t <= 1 && signifcantLessThanOne > 0.5) {\n\t\t\t\t/** Scales with a significant number of values under 1\n\t\t\t\t * require more space. Show every fifth value if under 1 */\n\t\t\t\tif (i % 5 === 0) return t\n\t\t\t} else if (i % spread === 0) return t\n\t\t})\n\t\treturn formattedTicks\n\t}\n\n\tsetSvgDimensions(settings: BoxPlotSettings, data: BoxPlotChartEntry) {\n\t\tconst plotsSpace =\n\t\t\tdata.plots.filter(p => !p.isHidden).length * this.totalRowSize + this.topPad + this.bottomPad + this.incrPad\n\t\tconst depth = settings.plotLength + this.totalLabelSize + this.horizPad / 2\n\t\treturn {\n\t\t\twidth: settings.isVertical ? plotsSpace + this.horizPad : depth,\n\t\t\theight: settings.isVertical ? depth : plotsSpace\n\t\t}\n\t}\n\n\tsetTitleDimensions(config: any, settings: BoxPlotSettings, height: number) {\n\t\tconst depth = this.totalLabelSize + settings.plotLength / 2\n\t\treturn {\n\t\t\tx: settings.isVertical ? this.horizPad / 2 : depth,\n\t\t\ty: settings.isVertical ? height - depth - this.horizPad / 2 : this.topPad + this.incrPad / 2,\n\t\t\ttext: config.term.q.mode == 'continuous' ? config.term.term.name : config.term2.term.name\n\t\t}\n\t}\n\n\tsetPlotData(data: any, config: any, settings: BoxPlotSettings) {\n\t\tconst plots = structuredClone(data.plots)\n\t\tfor (const plot of plots) {\n\t\t\t/** Set rendering properties for the plot */\n\n\t\t\t//Set the color for all plots\n\t\t\tlet color\n\t\t\tconst term2 = config.term2\n\t\t\tif (term2) {\n\t\t\t\tif (term2.q.type == 'predefined-groupset' || term2.q.type == 'custom-groupset') {\n\t\t\t\t\tconst groupset =\n\t\t\t\t\t\tterm2.q.type == 'predefined-groupset'\n\t\t\t\t\t\t\t? term2.term.groupsetting.lst[term2.q.predefined_groupset_idx]\n\t\t\t\t\t\t\t: term2.q.customset\n\t\t\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\t\t\tconst group = groupset.groups.find(g => g.name == plot.seriesId)\n\t\t\t\t\tif (group?.color) color = group.color\n\t\t\t\t} else {\n\t\t\t\t\tcolor = term2.term.values?.[plot.seriesId]?.color\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!color) color = settings.color\n\n\t\t\tif (!plot.color) plot.color = color\n\t\t\t//Brighten the colors in dark mode for better visibility\n\t\t\tif (settings.displayMode == 'dark') plot.color = rgb(plot.color).brighter(0.75)\n\t\t\t//Ignore if hidden after the color is set\n\t\t\tif (plot.isHidden) continue\n\t\t\tif (plot.boxplot.out.length) {\n\t\t\t\tconst maxOut = plot.boxplot.out.reduce((a: { value: number }, b: { value: number }) =>\n\t\t\t\t\tMath.max(a.value, b.value)\n\t\t\t\t)\n\t\t\t\tif (maxOut && maxOut.value > data.absMax) data.absMax = maxOut.value\n\t\t\t\tplot.boxplot.radius = this.outRadius\n\t\t\t}\n\t\t\tplot.labColor = settings.displayMode == 'dark' ? 'white' : 'black'\n\t\t\tplot.boxplot.rectFill =\n\t\t\t\tsettings.displayMode == 'dark' ? 'black' : settings.displayMode == 'filled' ? color : 'white'\n\t\t\tplot.x = settings.isVertical ? this.horizPad / 2 + this.incrPad : this.totalLabelSize\n\t\t\tplot.y = this.topPad + (settings.isVertical ? settings.plotLength + settings.labelPad : this.incrPad)\n\t\t\tthis.incrPad += this.totalRowSize\n\t\t}\n\t\treturn plots\n\t}\n}\n\nexport function getChartTitle(config, chartId) {\n\tif (!config.term0) return chartId\n\treturn config.term0.term.values && chartId in config.term0.term.values\n\t\t? config.term0.term.values[chartId].label\n\t\t: chartId\n}\n", "import type { Menu, RenderedBoxPlot } from '#dom'\nimport type { SvgG } from 'types/d3'\nimport type { RenderedPlot } from './RenderedPlot'\nimport { select } from 'd3-selection'\n\nexport class BoxPlotToolTips {\n\tboxplot: RenderedBoxPlot\n\tg: SvgG\n\tplot: RenderedPlot\n\tisVertical: boolean\n\ttip: Menu\n\treadonly tablePadding = '3px'\n\tconstructor(plot: any, g: SvgG, tip: Menu, isVertical: boolean) {\n\t\tthis.plot = plot\n\t\tthis.g = g\n\t\tthis.boxplot = plot.boxplot\n\t\tthis.isVertical = isVertical\n\t\tthis.tip = tip\n\n\t\tthis.addLabelTooltip()\n\t\t// this.addLineToolTips()\n\t\tthis.addOutliersTooltip()\n\t}\n\n\t//Add rendering preferences here to maintain styles\n\t//across all tooltip instances\n\taddText(text: string) {\n\t\tthis.tip.d.append('div').text(text)\n\t}\n\n\taddLabelTooltip() {\n\t\tif (Object.keys(this.plot.descrStats).length < 2) return\n\t\tthis.boxplot.labelG.on('mouseover', (event: MouseEvent) => {\n\t\t\tthis.tip.clear()\n\t\t\tif (this.isVertical) this.tip.show(event.clientX, event.clientY)\n\t\t\telse this.tip.showunder(this.boxplot.labelG.node())\n\t\t\tconst table = this.tip.d.append('table').attr('class', 'sja_simpletable')\n\t\t\ttable\n\t\t\t\t.append('tr')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.append('td')\n\t\t\t\t.attr('colspan', 2)\n\t\t\t\t.style('padding', this.tablePadding)\n\t\t\t\t.text(this.plot.key)\n\t\t\tfor (const stat of Object.values(this.plot.descrStats)) {\n\t\t\t\tconst row = table.append('tr')\n\t\t\t\trow.append('td').style('padding', this.tablePadding).style('opacity', 0.5).text(stat.label)\n\t\t\t\trow.append('td').style('padding', this.tablePadding).style('text-align', 'center').text(stat.value)\n\t\t\t}\n\t\t})\n\t\tthis.boxplot.labelG.on('mouseout', () => {\n\t\t\tthis.tip.hide()\n\t\t})\n\t}\n\n\t// addLineToolTips() {\n\t// \tconst addToolTips = (elem, text: string) => {\n\t// \t\tconst elemBBox = elem.node().getBBox()\n\t// \t\t//Add an expanded area for the tooltip\n\t// \t\t//Easier for user to hover over\n\t// \t\tthis.g\n\t// \t\t\t.append('rect')\n\t// \t\t\t.attr('x', elemBBox.x - 10)\n\t// \t\t\t.attr('y', elemBBox.y - 10)\n\t// \t\t\t.attr('width', elemBBox.width + 20)\n\t// \t\t\t.attr('height', elemBBox.height + 20)\n\t// \t\t\t.attr('fill', 'transparent')\n\t// \t\t\t.style('pointer-events', 'all')\n\t// \t\t\t.on('mouseover', () => {\n\t// \t\t\t\tthis.tip.clear().showunder(elem.node())\n\t// \t\t\t\tthis.addText(text)\n\t// \t\t\t})\n\t// \t\t\t.on('mouseout', () => {\n\t// \t\t\t\tthis.tip.hide()\n\t// \t\t\t})\n\t// \t}\n\n\t// \tif (this.boxplot.linep50) {\n\t// \t\tconst median = this.plot.descrStats.find((d: any) => d.id == 'median')\n\t// \t\tif (!median) throw `Missing median value for ${this.plot.key}`\n\t// \t\taddToolTips(this.boxplot.linep50, `Median: ${median.value}`)\n\t// \t}\n\t// \tif (this.boxplot.linew1) {\n\t// \t\taddToolTips(this.boxplot.linew1, `${this.boxplot.w1}`)\n\t// \t}\n\t// \tif (this.boxplot.linew2) {\n\t// \t\taddToolTips(this.boxplot.linew2, `${this.boxplot.w2}`)\n\t// \t}\n\t// }\n\n\taddOutliersTooltip() {\n\t\tthis.g\n\t\t\t.selectAll('circle')\n\t\t\t.data(this.boxplot.out)\n\t\t\t.each((d: any, i, nodes) => {\n\t\t\t\tconst circle = select(nodes[i])\n\t\t\t\tcircle.on('mouseover', () => {\n\t\t\t\t\tthis.tip.clear().showunder(circle.node())\n\t\t\t\t\tthis.addText(d.value)\n\t\t\t\t})\n\t\t\t\tcircle.on('mouseout', () => {\n\t\t\t\t\tthis.tip.hide()\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n", "import type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\nimport type { RenderedPlot } from './RenderedPlot'\nimport { renderTable, type Menu } from '#dom'\nimport { rgb } from 'd3-color'\n\n/** Menu is available when more than one boxplot is rendered. */\nexport class BoxPlotLabelMenu {\n\tconstructor(plot: RenderedPlot, app: MassAppApi, interactions: BoxPlotInteractions, tip: Menu, isVertical: boolean) {\n\t\tconst options = [\n\t\t\t{\n\t\t\t\ttext: `Add filter: ${plot.key}`,\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: () => interactions.addFilter(plot)\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: `Hide ${plot.key}`,\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: () => interactions.hidePlot(plot)\n\t\t\t},\n\t\t\t{\n\t\t\t\ttext: `List samples`,\n\t\t\t\tisVisible: (state: MassState) => state.termdbConfig.displaySampleIds && app.vocabApi.hasVerifiedToken(),\n\t\t\t\tcallback: async (event: MouseEvent) => {\n\t\t\t\t\tif (isVertical) tip.clear().show(event.clientX, event.clientY)\n\t\t\t\t\telse tip.clear().showunder(plot.boxplot.labelG.node())\n\t\t\t\t\tconst rows = await interactions.listSamples(plot)\n\n\t\t\t\t\tconst tableDiv = tip.d.append('div')\n\t\t\t\t\tconst columns = [{ label: 'Sample' }, { label: 'Value' }]\n\n\t\t\t\t\trenderTable({\n\t\t\t\t\t\trows,\n\t\t\t\t\t\tcolumns,\n\t\t\t\t\t\tdiv: tableDiv,\n\t\t\t\t\t\tmaxWidth: '30vw',\n\t\t\t\t\t\tmaxHeight: '25vh',\n\t\t\t\t\t\tresize: true,\n\t\t\t\t\t\tshowLines: true\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t\tplot.boxplot.labelG.on('click', (event: MouseEvent) => {\n\t\t\ttip.clear()\n\t\t\tif (isVertical) tip.show(event.clientX, event.clientY)\n\t\t\telse tip.showunder(plot.boxplot.labelG.node())\n\t\t\tconst state = app.getState()\n\t\t\tfor (const opt of options) {\n\t\t\t\t//Adds all the menu options before the color picker\n\t\t\t\tif (!opt.isVisible(state)) continue\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.classed('sja_menuoption', true)\n\t\t\t\t\t.text(opt.text)\n\t\t\t\t\t.on('click', (event: MouseEvent) => {\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\topt.callback(event)\n\t\t\t\t\t})\n\t\t\t}\n\t\t\tif (plot.color) {\n\t\t\t\ttip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.text('Color:')\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.property('value', rgb(plot.color).formatHex())\n\t\t\t\t\t.on('change', event => {\n\t\t\t\t\t\tinteractions.updatePlotColor(plot, event.target.value)\n\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n}\n", "import { drawBoxplot, Menu } from '#dom'\nimport { scaleLinear, scaleLog, type ScaleLinear } from 'd3-scale'\nimport { axisstyle } from '#src/client'\nimport { axisTop, axisLeft } from 'd3-axis'\nimport type { BoxPlotSettings, ViewData, PlotDimensions } from '../BoxPlotTypes'\nimport type { MassAppApi } from '#mass/types/mass'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\nimport type { RenderedPlot } from './RenderedPlot'\nimport { BoxPlotToolTips } from './BoxPlotToolTips'\nimport { BoxPlotLabelMenu } from './BoxPlotLabelMenu'\n\n/** Handles all the rendering logic for the boxplot. */\nexport class View {\n\tapp: MassAppApi\n\tdom: any\n\tinteractions: BoxPlotInteractions\n\tsettings: BoxPlotSettings\n\tconstructor(data: ViewData, settings: BoxPlotSettings, dom: any, app: MassAppApi, interactions: BoxPlotInteractions) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.interactions = interactions\n\t\tthis.settings = settings\n\t\tif (!data || !data.plots.length) return\n\n\t\tconst plotDim = data.plotDim\n\n\t\tdom.div.style('background-color', plotDim.backgroundColor)\n\n\t\tdom.svg\n\t\t\t.transition()\n\t\t\t.attr('width', plotDim.svg.width)\n\t\t\t.attr('height', plotDim.svg.height)\n\t\t\t//Fix for white background when downloading dark mode image.\n\t\t\t.style('fill', plotDim.backgroundColor)\n\n\t\tconst setScaleFunc = settings.isLogScale ? scaleLog().base(10) : scaleLinear()\n\t\tconst scale = setScaleFunc.domain(plotDim.domain).range(plotDim.range)\n\n\t\tthis.renderTitle(plotDim, dom)\n\t\tthis.renderBoxPlots(dom, data, scale, settings)\n\t\tthis.renderAxis(plotDim, dom, scale, settings)\n\t}\n\n\trenderTitle(plotDim: PlotDimensions, dom: any) {\n\t\t//Title of the chart\n\t\tdom.chartTitle.text(plotDim.chartTitle)\n\n\t\t//Title of the plot\n\t\tconst transformStr = `translate(${plotDim.title.x}, ${plotDim.title.y})${\n\t\t\tthis.settings.isVertical ? `,rotate(-90)` : ''\n\t\t}`\n\t\tdom.plotTitle\n\t\t\t.attr('class', 'sjpp-boxplot-title')\n\t\t\t.style('font-weight', 600)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('transform', transformStr)\n\t\t\t.attr('fill', plotDim.textColor)\n\t\t\t.text(plotDim.title.text.length > 80 ? plotDim.title.text.slice(0, 80) + '...' : plotDim.title.text)\n\t}\n\n\t//Fix for the axis rendering min -> max when the plot is vertical\n\trenderAxis(plotDim: PlotDimensions, dom: any, scale: ScaleLinear<number, number, never>, settings: BoxPlotSettings) {\n\t\t/** draw_boxplot renders the boxplot from min-max but the scale\n\t\t * renders the axis from max - min. Render the box plots, then change\n\t\t * the scale vector to match. */\n\t\tif (settings.isVertical) scale.range([scale.range()[1], scale.range()[0]])\n\t\tconst ticks = scale.ticks()\n\t\tconst tickValues = plotDim.axis.values(ticks)\n\t\tdom.axis\n\t\t\t.attr('class', 'sjpp-boxplot-axis')\n\t\t\t.attr('transform', `translate(${plotDim.axis.x}, ${plotDim.axis.y})`)\n\t\t\t.transition()\n\t\t\t.call(\n\t\t\t\tthis.settings.isVertical\n\t\t\t\t\t? axisLeft(scale)\n\t\t\t\t\t\t\t.tickValues(tickValues)\n\t\t\t\t\t\t\t.tickFormat(d => plotDim.axis.format(d as number))\n\t\t\t\t\t\t\t.tickPadding(8)\n\t\t\t\t\t: axisTop(scale)\n\t\t\t\t\t\t\t.tickValues(tickValues)\n\t\t\t\t\t\t\t.tickFormat(d => plotDim.axis.format(d as number))\n\t\t\t)\n\n\t\taxisstyle({\n\t\t\taxis: dom.axis,\n\t\t\tshowline: true,\n\t\t\tfontsize: 12,\n\t\t\tcolor: plotDim.textColor\n\t\t})\n\t}\n\n\trenderBoxPlots(dom: any, data: ViewData, scale: ScaleLinear<number, number, never>, settings: BoxPlotSettings) {\n\t\t/** Draw boxplots, incrementing by the total row height */\n\t\tfor (const plot of data.plots) {\n\t\t\tconst g = dom.boxplots.append('g').attr('class', 'sjpp-boxplot-plot').attr('padding', '5px')\n\n\t\t\tdrawBoxplot({\n\t\t\t\tbp: plot.boxplot,\n\t\t\t\tg,\n\t\t\t\tcolor: settings.displayMode == 'filled' ? 'black' : plot.color,\n\t\t\t\tscale: scale,\n\t\t\t\trowheight: settings.rowHeight,\n\t\t\t\tlabpad: settings.labelPad,\n\t\t\t\tlabColor: plot.labColor\n\t\t\t})\n\n\t\t\tconst transformStr = `translate(${plot.x}, ${plot.y})${settings.isVertical ? `, rotate(-90)` : ''}`\n\t\t\tg.attr('transform', transformStr)\n\n\t\t\tif (settings.isVertical) {\n\t\t\t\t//Rotate the text slightly in veritcal orientation\n\t\t\t\tg.select('text').attr('transform', 'rotate(45)')\n\t\t\t}\n\n\t\t\tnew BoxPlotToolTips(plot, g, this.dom.tip, settings.isVertical)\n\t\t\tif (data.plots.length > 1) {\n\t\t\t\t//Do not try to use the same tip for the menu as the tooltips.\n\t\t\t\t//When the boxplots are rendered close together, the menu\n\t\t\t\t//disappears to show the tooltip for the next boxplot.\n\t\t\t\t//The user can't make a selection in time.\n\t\t\t\tconst labelMenuTip = new Menu({ padding: '' })\n\t\t\t\tnew BoxPlotLabelMenu(\n\t\t\t\t\tplot as unknown as RenderedPlot,\n\t\t\t\t\tthis.app,\n\t\t\t\t\tthis.interactions,\n\t\t\t\t\tlabelMenuTip,\n\t\t\t\t\tsettings.isVertical\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n}\n", "import type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { RenderedPlot } from '../view/RenderedPlot'\nimport type { TermWrapper } from '#types'\nimport type { AnnotatedSampleData } from '../../../types/termdb'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { getSamplelstFilter } from '../../../mass/groups.js'\n\nexport class ListSamples {\n\tapp: MassAppApi\n\tdataOpts: {\n\t\tterms: any[]\n\t\tfilter: any\n\t}\n\tplot: RenderedPlot\n\tterm: any\n\ttvslst: any\n\tconstructor(app: MassAppApi, state: MassState, id: string, plot: RenderedPlot, getRange = true) {\n\t\tthis.app = app\n\t\tthis.plot = plot\n\n\t\tconst plotConfig = state.plots.find((p: { id: string }) => p.id === id)\n\t\tif (!plotConfig) throw 'Box plot not found [ListSamples]'\n\n\t\ttry {\n\t\t\t//ids 'min' and 'max' are always present in the descrStats{}\n\t\t\tconst min = plot.descrStats.min.value\n\t\t\tconst max = plot.descrStats.max.value\n\t\t\tthis.tvslst = this.getTvsLst(min, max, getRange, plotConfig.term, plotConfig.term2)\n\t\t} catch (e: any) {\n\t\t\tconsole.error(e.message || e)\n\t\t}\n\n\t\tthis.term = plotConfig.term.q?.mode === 'continuous' ? plotConfig.term : plotConfig.term2\n\n\t\tconst filter = {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tlst: [state.termfilter.filter, this.tvslst],\n\t\t\tin: true\n\t\t}\n\t\tthis.dataOpts = {\n\t\t\tterms: [this.term],\n\t\t\tfilter\n\t\t}\n\t}\n\n\tasync getData() {\n\t\treturn await this.app.vocabApi.getAnnotatedSampleData(this.dataOpts)\n\t}\n\n\tsetRows(data: AnnotatedSampleData) {\n\t\tconst rows: [{ value: string }, { value: number }][] = []\n\t\tfor (const [c, k] of Object.entries(data.samples))\n\t\t\trows.push([\n\t\t\t\t{ value: data.refs.bySampleId[c].label },\n\t\t\t\t{ value: Number(roundValueAuto((k as Record<string, { value: number }>)[this.term.$id].value)) }\n\t\t\t])\n\t\treturn rows\n\t}\n\n\tcreateTvsTerm(tw: TermWrapper, tvslst: any) {\n\t\ttvslst.lst.push({\n\t\t\ttype: 'tvs',\n\t\t\ttvs: {\n\t\t\t\tterm: tw.term\n\t\t\t}\n\t\t})\n\t}\n\n\tcreateTvsLstValues(tw: any, tvslst: any, lstIdx: number) {\n\t\tthis.createTvsTerm(tw, tvslst)\n\t\tif (tw.term.type === 'samplelst') {\n\t\t\tconst key: any = this.plot.seriesId\n\t\t\tconst ids = tw.term.values[key].list.map(s => s.sampleId)\n\t\t\tconst tvs = getSamplelstFilter(ids).lst[0] // tvslst is an array of 1 tvs\n\t\t\ttvslst.lst[lstIdx] = tvs\n\t\t} else tvslst.lst[lstIdx].tvs.values = [{ key: this.plot.seriesId, label: this.plot.key }]\n\n\t\tif (tw.term.type === 'condition') {\n\t\t\tObject.assign(tvslst.lst[lstIdx].tvs, {\n\t\t\t\tbar_by_grade: tw.q?.bar_by_grade || null,\n\t\t\t\tvalue_by_max_grade: tw.q.value_by_max_grade\n\t\t\t})\n\t\t}\n\t}\n\n\tcreateTvsLstRanges(tw: TermWrapper, tvslst: any, rangeStart: number, rangeStop: number, lstIdx: number) {\n\t\tthis.createTvsTerm(tw, tvslst)\n\n\t\ttvslst.lst[lstIdx].tvs.ranges = [\n\t\t\t{\n\t\t\t\t//Only show integers for integer terms\n\t\t\t\tstart: tw.term.type == 'integer' ? Math.round(rangeStart) : rangeStart,\n\t\t\t\tstop: tw.term.type == 'integer' ? Math.round(rangeStop) : rangeStop,\n\t\t\t\tstartinclusive: true,\n\t\t\t\tstopinclusive: true,\n\t\t\t\tstartunbounded: false,\n\t\t\t\tstopunbounded: false\n\t\t\t}\n\t\t]\n\t}\n\n\tassignPlotRangeRanges() {\n\t\tconst { start, stop, startinclusive, stopinclusive, startunbounded, stopunbounded } = this.plot.overlayBins || {}\n\t\treturn [\n\t\t\t{\n\t\t\t\tstart: start ?? null,\n\t\t\t\tstop: stop ?? null,\n\t\t\t\tstartinclusive: startinclusive ?? true,\n\t\t\t\tstopinclusive: stopinclusive ?? false,\n\t\t\t\tstartunbounded: startunbounded ?? null,\n\t\t\t\tstopunbounded: stopunbounded ?? null\n\t\t\t}\n\t\t]\n\t}\n\n\tisContinuousOrBinned(tw2: TermWrapper) {\n\t\tif (!('mode' in tw2.q)) return\n\t\treturn (\n\t\t\ttw2.q?.mode === 'continuous' || (['float', 'integer'].includes(tw2.term?.type) && this.plot.overlayBins != null)\n\t\t)\n\t}\n\n\tgetTvsLst(rangeStart: number, rangeStop: number, getRange = true, tw1: TermWrapper, tw2: TermWrapper) {\n\t\tconst tvslst: {\n\t\t\ttype: string\n\t\t\tin: boolean\n\t\t\tjoin: string\n\t\t\tlst: any[]\n\t\t} = {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t}\n\t\tconst isTw1CategoricalOrCondition = ['categorical', 'condition'].includes(tw1.term.type)\n\t\tif (tw2) {\n\t\t\tif (isTw1CategoricalOrCondition) {\n\t\t\t\tthis.createTvsLstValues(tw1, tvslst, 0)\n\t\t\t\tif (getRange) this.createTvsLstRanges(tw2, tvslst, rangeStart, rangeStop, 1)\n\t\t\t} else if (this.isContinuousOrBinned(tw2)) {\n\t\t\t\tthis.createTvsTerm(tw2, tvslst)\n\t\t\t\ttvslst.lst[0].tvs.ranges = this.assignPlotRangeRanges()\n\t\t\t\tif (getRange) this.createTvsLstRanges(tw1, tvslst, rangeStart, rangeStop, 1)\n\t\t\t} else {\n\t\t\t\tthis.createTvsLstValues(tw2, tvslst, 0)\n\t\t\t\tif (getRange) this.createTvsLstRanges(tw1, tvslst, rangeStart, rangeStop, 1)\n\t\t\t}\n\t\t} else {\n\t\t\tif (getRange) this.createTvsLstRanges(tw1, tvslst, rangeStart, rangeStop, 0)\n\t\t}\n\n\t\treturn tvslst\n\t}\n}\n", "import type { BoxPlotDom, LegendItemEntry, BoxPlotConfig } from '../BoxPlotTypes'\nimport type { MassAppApi } from '#mass/types/mass'\nimport type { RenderedPlot } from '../view/RenderedPlot'\nimport { ListSamples } from './ListSamples'\nimport { filterJoin, getFilterItemByTag } from '#filter'\n\nexport class BoxPlotInteractions {\n\tapp: MassAppApi\n\tdom: BoxPlotDom\n\tid: string\n\tconstructor(app: MassAppApi, dom: BoxPlotDom, id: string) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.id = id\n\t}\n\n\thelp() {\n\t\t//May add more options in the future\n\t\twindow.open('https://github.com/stjude/proteinpaint/wiki/Box-plot')\n\t}\n\n\t/** Option to add a global filter from the box plot label menu. */\n\taddFilter(plot: RenderedPlot) {\n\t\tconst config = this.app.getState()\n\t\tconst sampleList = new ListSamples(this.app, config, this.id, plot, false)\n\t\tconst filterUiRoot = getFilterItemByTag(config.termfilter.filter, 'filterUiRoot')\n\t\tconst filter = filterJoin([filterUiRoot, sampleList.tvslst])\n\t\tfilter.tag = 'filterUiRoot'\n\t\tthis.app.dispatch({\n\t\t\ttype: 'filter_replace',\n\t\t\tfilter\n\t\t})\n\t}\n\n\t/** Option to hide a plot from the box plot label menu. */\n\thidePlot(plot: RenderedPlot) {\n\t\tconst plotConfig = this.app.getState().plots.find((p: BoxPlotConfig) => p.id === this.id)\n\t\t//Don't try to modify a frozen object\n\t\tconst config = structuredClone(plotConfig)\n\t\tconst contTerm = config.term.q.mode == 'continuous' ? 'term2' : 'term'\n\t\tif (!config[contTerm].q.hiddenValues) config[contTerm].q.hiddenValues = {}\n\t\tconfig[contTerm].q.hiddenValues[plot.key] = 1\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: config\n\t\t})\n\t}\n\n\t/** Trigger when clicking on a hidden plot in the legend */\n\tunhidePlot(item: LegendItemEntry) {\n\t\tconst plotConfig = this.app.getState().plots.find((p: BoxPlotConfig) => p.id === this.id)\n\t\tconst config = structuredClone(plotConfig)\n\t\tconst contTerm = config.term.q.mode == 'continuous' ? 'term2' : 'term'\n\t\tdelete config[contTerm].q.hiddenValues[item.key]\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig\n\t\t})\n\t}\n\n\t/** Option from box plot label to show the samples in a table within the tooltip. */\n\tasync listSamples(plot: RenderedPlot) {\n\t\tconst config = this.app.getState()\n\t\tconst sampleList = new ListSamples(this.app, config, this.id, plot)\n\t\tconst data = await sampleList.getData()\n\t\tconst rows = sampleList.setRows(data)\n\t\treturn rows\n\t}\n\n\t/** Callback for color picker in plot(s) label menu */\n\tupdatePlotColor(plot: RenderedPlot, color: string) {\n\t\tif (!plot.seriesId) return\n\t\tconst plotConfig = this.app.getState().plots.find((p: BoxPlotConfig) => p.id === this.id)\n\t\tconst config = structuredClone(plotConfig)\n\t\tconfig.term2.term.values[plot.seriesId].color = color\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig\n\t\t})\n\t}\n\n\tclearDom() {\n\t\tthis.dom.error.style('padding', '').text('')\n\t\tthis.dom.charts.selectAll('*').remove()\n\t\tthis.dom.legend.selectAll('*').remove()\n\t}\n}\n", "import type { LegendData, LegendItemEntry } from '../BoxPlotTypes'\nimport type { BoxPlotInteractions } from '../interactions/BoxPlotInteractions'\nimport type { Div } from '../../../types/d3'\n\nexport class LegendRenderer {\n\tinteractions: BoxPlotInteractions\n\ttextColor: string\n\tconstructor(legendDiv: Div, legendData: LegendData, interactions: BoxPlotInteractions, textColor: string) {\n\t\tthis.interactions = interactions\n\t\tthis.textColor = textColor\n\t\tthis.renderLegend(legendDiv, legendData)\n\t}\n\n\trenderLegend(legendDiv: Div, legendData: LegendData) {\n\t\tlegendDiv.attr('id', 'sjpp-boxplot-legend')\n\t\tfor (const section of legendData) {\n\t\t\tlegendDiv.append('div').style('opacity', '0.5').style('color', this.textColor).text(section.label)\n\t\t\tconst sectionDiv = legendDiv.append('div').style('padding-left', '10px')\n\t\t\tfor (const item of section.items) {\n\t\t\t\tthis.addItem(item, sectionDiv)\n\t\t\t}\n\t\t}\n\t}\n\n\taddItem(item: LegendItemEntry, sectionDiv: Div) {\n\t\tconst legendItem = sectionDiv.append('div')\n\t\tif (item.isPlot) {\n\t\t\tlegendItem\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin-right', '3px')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('vertical-align', 'middle')\n\t\t\t\t.html(`<svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"${this.textColor}\" class=\"bi bi-arrow-counterclockwise\" viewBox=\"0 0 16 16\" style=\"vertical-align: middle; display: block; margin: auto;\">\n                <path stroke=\"#000\" stroke-width=\"0.25\" fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z\"/>\n                <path d=\"M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z\"/>\n                </svg>`)\n\t\t}\n\t\tlegendItem\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', this.textColor)\n\t\t\t.style('text-decoration', item.isHidden ? 'line-through' : '')\n\t\t\t.text(item.text)\n\n\t\tif (item.isPlot) {\n\t\t\t//Do not apply to uncomputable values, only items with plot data\n\t\t\tlegendItem.attr('aria-label', `Click to unhide plot`).on('click', () => {\n\t\t\t\tthis.interactions.unhidePlot(item)\n\t\t\t})\n\t\t}\n\t}\n}\n", "import { renderTable } from '#dom'\n\nexport class AssociationTableRender {\n\tconstructor(div, data) {\n\t\tconst wrapper = div.style('vertical-align', 'top').style('margin-top', '30px')\n\n\t\t//Title div\n\t\twrapper\n\t\t\t.append('div')\n\t\t\t.text(\"Group comparisons (Wilcoxon's rank sum test)\")\n\t\t\t.style('font-weight', '600')\n\t\t\t.style('text-align', 'center')\n\n\t\tconst tableDiv = wrapper.append('div').style('margin-top', '5px')\n\t\trenderTable({\n\t\t\tdiv: tableDiv,\n\t\t\tcolumns: [{ label: 'Group 1' }, { label: 'Group 2' }, { label: 'P-Value' }],\n\t\t\trows: data\n\t\t})\n\t}\n}\n", "import { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { fillTermWrapper } from '#termsetting'\nimport { controlsInit, term0_term2_defaultQ, renderTerm1Label } from '../controls'\nimport { plotColor } from '#shared/common.js'\nimport { Menu, getMaxLabelWidth, DownloadMenu } from '#dom'\nimport type { Elem } from '../../types/d3'\nimport type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { TdbBoxPlotOpts, BoxPlotSettings, BoxPlotDom, BoxPlotConfigOpts } from './BoxPlotTypes'\nimport { Model } from './model/Model'\nimport { ViewModel, getChartTitle } from './viewModel/ViewModel'\nimport { View } from './view/View'\nimport { BoxPlotInteractions } from './interactions/BoxPlotInteractions'\nimport { LegendRenderer } from './view/LegendRender'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.ts'\nimport { AssociationTableRender } from './view/AssociationTableRender'\n\nexport class TdbBoxplot extends PlotBase implements RxComponent {\n\tstatic type = 'boxplot'\n\ttype: string\n\tcomponents: { controls: any }\n\tdom: BoxPlotDom\n\tdata: any\n\tinteractions?: BoxPlotInteractions\n\tprivate useDefaultSettings = true\n\tparentId?: string\n\tapi: any\n\n\tconstructor(opts: TdbBoxPlotOpts, api: MassAppApi) {\n\t\tsuper(opts)\n\t\tthis.opts = opts\n\t\tthis.api = api\n\t\tthis.type = TdbBoxplot.type\n\t\tthis.components = {\n\t\t\tcontrols: {}\n\t\t}\n\n\t\tconst holder = opts.holder.classed('sjpp-boxplot-main', true)\n\t\tconst controls = opts.controls ? holder : holder.append('div')\n\t\tconst div = holder.append('div')\n\t\tconst errorDiv = div.append('div').attr('class', 'sjpp-boxplot-error').style('opacity', 0.75)\n\t\tconst chartsDiv = div\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-boxplot-charts')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-direction', 'row')\n\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t.style('max-width', '100vw')\n\t\tthis.dom = {\n\t\t\tcontrols: controls as Elem,\n\t\t\tdiv,\n\t\t\terror: errorDiv,\n\t\t\tcharts: chartsDiv,\n\t\t\tlegend: div.append('div').attr('class', 'sjpp-boxplot-legend').style('margin-top', '25px'),\n\t\t\ttip: new Menu()\n\t\t}\n\t\tif (opts.header) this.dom.header = opts.header.html('Box plot')\n\t}\n\n\tasync setControls() {\n\t\tconst state = this.getState(this.app.getState())\n\t\tconst controlLabels = state.config.controlLabels\n\t\tif (!controlLabels) throw new Error('controls labels not found')\n\t\tconst inputs: { [index: string]: any }[] = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tusecase: { target: 'boxplot', 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: 'boxplot',\n\t\t\t\tusecase: { target: 'boxplot', detail: 'term2' },\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 || ['continuous', 'discrete'],\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\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: 'boxplot',\n\t\t\t\tusecase: { target: 'boxplot', detail: 'term0' },\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\tnumericEditMenuVersion: this.opts.numericEditMenuVersion || ['continuous', 'discrete'],\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Order by',\n\t\t\t\ttitle: 'Order box plots by parameters',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'boxplot',\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 values', 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\tfor (const k of Object.keys(this.data.charts)) {\n\t\t\t\t\t\tconst chart = this.data.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: 'Scale',\n\t\t\t\ttitle: 'Change the axis scale',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'boxplot',\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: 'Orientation',\n\t\t\t\ttitle: 'Change the orientation of the box plots',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'isVertical',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Vertical', value: true },\n\t\t\t\t\t{ label: 'Horizontal', value: false }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot length',\n\t\t\t\ttitle: 'Set the plot length of the entire plot in pixels, >=200',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'plotLength',\n\t\t\t\tdebounceInterval: 500,\n\t\t\t\tmin: 200,\n\t\t\t\tstep: 10\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot height',\n\t\t\t\ttitle: 'Set the height of each box plot between 20 and 50',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'rowHeight',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 50,\n\t\t\t\tmin: 20,\n\t\t\t\tdebounceInterval: 500,\n\t\t\t\tprocessInput: (val: number) => {\n\t\t\t\t\t/**TODO: This is a hack. */\n\t\t\t\t\tif (this.useDefaultSettings == true) this.useDefaultSettings = false\n\t\t\t\t\treturn val\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot padding',\n\t\t\t\ttitle: 'Set the space between each box plot. Number must be between 10 and 20',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'rowSpace',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 20,\n\t\t\t\tmin: 10,\n\t\t\t\tdebounceInterval: 500,\n\t\t\t\tprocessInput: (val: number) => {\n\t\t\t\t\t/**TODO: This is a hack. */\n\t\t\t\t\tif (this.useDefaultSettings == true) this.useDefaultSettings = false\n\t\t\t\t\treturn val\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Default color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'color',\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\tlet style = ''\n\t\t\t\t\tfor (const k of Object.keys(this.data.charts)) {\n\t\t\t\t\t\tconst chart = this.data.charts[k]\n\t\t\t\t\t\tif (chart.plots.length > 1) style = 'none'\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: 'Display mode',\n\t\t\t\ttitle: 'Apply a dark theme to the plot',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'displayMode',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Default', value: 'default' },\n\t\t\t\t\t{ label: 'Filled', value: 'filled' },\n\t\t\t\t\t{ label: 'Dark mode', value: 'dark' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show association tests',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'showAssocTests',\n\t\t\t\ttitle: `Show association tests next to the box plots.`,\n\t\t\t\tgetDisplayStyle: plot => {\n\t\t\t\t\treturn plot?.term2 ? '' : 'none'\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tif (state.termdbConfig?.boxplots?.removeOutliers) {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Remove outliers',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'boxplot',\n\t\t\t\tsettingsKey: 'removeOutliers',\n\t\t\t\ttitle: `Option to remove outliers from the analysis`\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.style('display', 'inline-block'),\n\t\t\tinputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.boxplot', event => {\n\t\t\tthis.download(event)\n\t\t})\n\t\tthis.components.controls.on('helpClick.boxplot', () => {\n\t\t\tthis.interactions!.help()\n\t\t})\n\n\t\tif (state.vocab.dslabel.toLowerCase() == 'gdc') {\n\t\t\t//Remove for now. May add gdc specific user guide\n\t\t\t//in interactions.help later.\n\t\t\tthis.dom.controls.select('div[aria-label=\"Documentation\"]').remove()\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\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: any) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\ttermfilter,\n\t\t\tvocab: appState.vocab,\n\t\t\tconfig: Object.assign({}, config, {\n\t\t\t\tsettings: {\n\t\t\t\t\tboxplot: config.settings.boxplot\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tasync init() {\n\t\tthis.dom.div.style('display', 'inline-block').style('margin-left', '20px')\n\t\tthis.interactions = new BoxPlotInteractions(this.app, this.dom, this.id)\n\t\tawait this.setControls()\n\t}\n\n\tasync main() {\n\t\ttry {\n\t\t\tconst config = structuredClone(this.state.config)\n\t\t\tif (config.childType != this.type && config.chartType != this.type) return\n\n\t\t\tif (!this.interactions) throw new Error('Interactions not initialized [box plot main()]')\n\n\t\t\tconst settings = config.settings.boxplot\n\t\t\tconst model = new Model(this, config)\n\t\t\tconst data = await model.getData()\n\t\t\tconfig.term.q.descrStats = data.descrStats\n\n\t\t\tif (data.error) throw new Error(data.error)\n\t\t\tif (!data.charts || !Object.keys(data.charts).length) {\n\t\t\t\tthis.interactions!.clearDom()\n\t\t\t\tthis.dom.error.style('padding', '20px 20px 20px 60px').text('No visible box plot data to render')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.data = data\n\t\t\tthis.dom.charts.selectAll('*').remove()\n\n\t\t\t/** TODO: Refactor all of the code below into mvvm\n\t\t\t * pattern. This breaks maintainability and separation of concerns. */\n\t\t\tconst labels: any = []\n\t\t\tconst tempsvg = this.dom.charts.append('svg')\n\t\t\tfor (const key of Object.keys(data.charts)) {\n\t\t\t\tconst chart = data.charts[key]\n\t\t\t\tconst chartLabels = chart.plots.filter(p => !p.isHidden).map(p => p.boxplot.label)\n\t\t\t\tlabels.push(...chartLabels)\n\t\t\t}\n\t\t\tconst maxLabelLgth = getMaxLabelWidth(tempsvg.append('g'), labels)\n\t\t\ttempsvg.remove()\n\n\t\t\t// plot charts\n\t\t\tconst legend: any = [] // legend items across charts\n\t\t\tfor (const key of Object.keys(data.charts)) {\n\t\t\t\tconst chart = data.charts[key]\n\t\t\t\tchart.absMin = data.absMin\n\t\t\t\tchart.absMax = data.absMax\n\t\t\t\tchart.uncomputableValues = data.uncomputableValues\n\t\t\t\t// get view model of chart\n\t\t\t\tconst viewModel = new ViewModel(config, chart, settings, maxLabelLgth, this.useDefaultSettings)\n\t\t\t\t// collect legend items\n\t\t\t\tfor (const l of viewModel.viewData.legend) {\n\t\t\t\t\tif (!legend.find(x => x.label == l.label)) legend.push(l)\n\t\t\t\t}\n\t\t\t\tif (\n\t\t\t\t\t(viewModel.rowSpace !== settings.rowSpace || viewModel.rowHeight !== settings.rowHeight) &&\n\t\t\t\t\tthis.useDefaultSettings == true\n\t\t\t\t) {\n\t\t\t\t\t/** Fix this. Move to ViewModel, figure out for all plots once, only call app.save once.*/\n\n\t\t\t\t\t/** If the row height or space changed during data processing,\n\t\t\t\t\t * save the new settings without calling app.dispatch.\n\t\t\t\t\t * Will show updated value in the controls. */\n\t\t\t\t\tsettings.rowSpace = viewModel.rowSpace\n\t\t\t\t\tsettings.rowHeight = viewModel.rowHeight\n\n\t\t\t\t\tthis.app.save({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\tboxplot: {\n\t\t\t\t\t\t\t\t\trowSpace: viewModel.rowSpace,\n\t\t\t\t\t\t\t\t\trowHeight: viewModel.rowHeight\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\t// render view of chart\n\t\t\t\t// setup a dom{} object for the chart\n\t\t\t\tconst chartDiv = this.dom.charts\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sjpp-boxplot-chartDiv')\n\t\t\t\t\t.style('padding', Object.keys(data.charts).length > 1 ? '20px 20px 0px 0px' : '0px')\n\t\t\t\tconst chartSvg = chartDiv.append('svg')\n\t\t\t\tchart.svg = chartSvg // for downloading svg\n\t\t\t\tconst chartTitle = chartDiv\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', config.term0 ? 'block' : 'none')\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', '20px')\n\t\t\t\t//Temp fix\n\t\t\t\tconst assocTableDiv = chartDiv\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sjpp-boxplot-assocTableDiv')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\tconst chartDom = Object.assign({}, this.dom, {\n\t\t\t\t\tsvg: chartSvg,\n\t\t\t\t\tchartTitle,\n\t\t\t\t\tplotTitle: chartSvg.append('text'),\n\t\t\t\t\taxis: chartSvg.append('g'),\n\t\t\t\t\tboxplots: chartSvg.append('g'),\n\t\t\t\t\tassocTableDiv: assocTableDiv\n\t\t\t\t})\n\t\t\t\t// render the view\n\t\t\t\tnew View(viewModel.viewData, settings, chartDom, this.app, this.interactions)\n\t\t\t\t//Temp fix: This should be handled by the view\n\t\t\t\tif (chart.wilcoxon) new AssociationTableRender(chartDom.assocTableDiv, chart.wilcoxon)\n\t\t\t}\n\t\t\t// render legend (applies to all charts)\n\t\t\tthis.dom.legend.selectAll('*').remove()\n\t\t\tconst textColor = settings.displayMode == 'dark' ? 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+  "names": ["event"]
+}

package/dist/chunk-YFZH3WDM.js

@@ -0,0 +1,55 @@
+import {
+  colorinframe
+} from "./chunk-PX7A6LBY.js";
+import {
+  IN_frame,
+  OUT_frame
+} from "./chunk-6VQ4C735.js";
+
+// src/spliceevent.phrase.js
+function spliceevent_phrase_default(evt) {
+  const htmls = [];
+  if (evt.isaltexon || evt.isskipexon) {
+    const exonstart = Math.min(...evt.skippedexon);
+    const exonstop = Math.max(...evt.skippedexon);
+    htmls.push(
+      '<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
+    );
+    if (evt.isaltexon) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
+      );
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
+    }
+    if (evt.junctionB.data) {
+      htmls.push(
+        "<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
+      );
+    }
+    htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
+    if (evt.framenocheck) {
+      if (evt.utr3) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
+      } else if (evt.utr5) {
+        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
+      }
+    } else if (evt.frame == IN_frame) {
+      htmls.push(
+        '<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
+      );
+    } else if (evt.frame == OUT_frame) {
+      htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
+    } else {
+      htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
+    }
+  } else {
+    return "unknown event type!!";
+  }
+  return htmls.join(" ");
+}
+
+export {
+  spliceevent_phrase_default
+};
+//# sourceMappingURL=chunk-YFZH3WDM.js.map