@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/CorrelationVolcano-H6DHMTYZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/corrVolcano/model/Model.ts", "../plots/corrVolcano/viewModel/ViewModel.ts", "../plots/corrVolcano/view/ItemToolTip.ts", "../plots/corrVolcano/view/View.ts", "../plots/corrVolcano/interactions/CorrVolcanoInteractions.ts", "../plots/corrVolcano/CorrelationVolcano.ts"],
+  "sourcesContent": ["import type { TermWrapper } from '#types'\nimport type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { CorrVolcanoPlotConfig, CorrVolcanoSettings } from '../CorrelationVolcanoTypes'\n\nexport class Model {\n\tconfig: CorrVolcanoPlotConfig\n\tstate: MassState\n\tapp: MassAppApi\n\tsettings: CorrVolcanoSettings\n\tvariableTwLst: TermWrapper[]\n\t/** the plot-scoped vocabApi from PlotBase, so that an unrelated app dispatch does not cancel this request */\n\tvocabApi: any\n\tconstructor(\n\t\tconfig: CorrVolcanoPlotConfig,\n\t\tstate: MassState,\n\t\tapp: MassAppApi,\n\t\tsettings: CorrVolcanoSettings,\n\t\tvariableTwLst: TermWrapper[],\n\t\tvocabApi: any\n\t) {\n\t\tthis.config = config\n\t\tthis.state = state\n\t\tthis.app = app\n\t\tthis.settings = settings\n\t\tthis.variableTwLst = variableTwLst\n\t\tthis.vocabApi = vocabApi\n\t}\n\n\tasync getData() {\n\t\tconst opts = await this.setRequestOpts()\n\t\tconst data = await this.vocabApi.getCorrelationVolcanoData(opts)\n\t\treturn data\n\t}\n\n\tasync setRequestOpts() {\n\t\treturn {\n\t\t\tfeatureTw: this.config.featureTw,\n\t\t\tvariableTwLst: this.variableTwLst,\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0: this.state.termfilter.filter0,\n\t\t\tcorrelationMethod: this.settings.method\n\t\t}\n\t}\n}\n", "import type { TermWrapper } from '#types'\nimport { scaleLinear } from 'd3-scale'\nimport { termType2label } from '#shared/terms.js'\nimport type { CorrelationVolcanoResponse } from '#types'\nimport type {\n\tCorrVolcanoDom,\n\tCorrVolcanoPlotConfig,\n\tCorrVolcanoSettings,\n\tCorrVolcanoViewData,\n\tCorrVolcanoPlotDimensions\n} from '../CorrelationVolcanoTypes'\n\nexport class ViewModel {\n\tvariableTwLst: TermWrapper[]\n\tviewData: CorrVolcanoViewData\n\treadonly bottomPad = 60\n\t/** Only one side, left or right */\n\treadonly horizPad = 70\n\treadonly topPad = 40\n\tconstructor(\n\t\tconfig: CorrVolcanoPlotConfig,\n\t\tdata: CorrelationVolcanoResponse,\n\t\tdom: CorrVolcanoDom,\n\t\tsettings: CorrVolcanoSettings,\n\t\tvariableTwLst: TermWrapper[]\n\t) {\n\t\tthis.variableTwLst = variableTwLst\n\t\tconst pValueKey = settings.isAdjustedPValue ? 'adjusted_pvalue' : 'original_pvalue'\n\t\tconst d = this.transformPValues(data, pValueKey) as any\n\t\tconst [absYMax, absYMin] = this.setMinMax(d, `transformed_${pValueKey}`)\n\t\tconst [absXMax, absXMin] = this.setMinMax(d, 'correlation')\n\t\tconst [absSampleMax, absSampleMin] = this.setMinMax(d, 'sampleSize')\n\n\t\tconst plotDim = this.setPlotDimensions(config, settings, absYMax, absYMin, absXMax, absXMin)\n\n\t\tthis.viewData = {\n\t\t\tplotDim,\n\t\t\tvariableItems: this.setVariablesData(absSampleMax, absSampleMin, d, dom, pValueKey, plotDim, settings),\n\t\t\tlegendData: this.setLegendData(absSampleMin, absSampleMax, data.skippedVariables)\n\t\t}\n\t}\n\n\ttransformPValues(data: CorrelationVolcanoResponse, key: string) {\n\t\t//Items rendered in log scale\n\t\t//Remove any items with negative p values\n\t\tdata.variableItems = data.variableItems.filter(v => v[key] > 0)\n\t\t//For each item, transform the p value to -log10\n\t\tfor (const item of data.variableItems) {\n\t\t\tif (item[key] > 0) item[`transformed_${key}`] = -Math.log10(item[key])\n\t\t\telse item[key] = null\n\t\t}\n\t\treturn data\n\t}\n\n\tsetMinMax(data: CorrelationVolcanoResponse, key: string) {\n\t\tconst sortedValues = data.variableItems.map(v => v[key]).sort((a, b) => a - b)\n\t\tconst max = sortedValues[sortedValues.length - 1]\n\t\tconst min = sortedValues[0]\n\t\treturn [max, min]\n\t}\n\n\tsetPlotDimensions(\n\t\tconfig: CorrVolcanoPlotConfig,\n\t\tsettings: CorrVolcanoSettings,\n\t\tabsYMax: number,\n\t\tabsYMin: number,\n\t\tabsXMax: number,\n\t\tabsXMin: number\n\t) {\n\t\t//Ensure the neg and pos side of the plot are equal\n\t\tconst maxXRange = Math.max(Math.abs(absXMin), absXMax)\n\t\tconst xScale = scaleLinear().domain(this.setDomain(-maxXRange, maxXRange, 0.05)).range([0, settings.width])\n\t\tconst yScale = scaleLinear().domain(this.setDomain(absYMin, absYMax)).range([settings.height, 0])\n\t\treturn {\n\t\t\tsvg: {\n\t\t\t\theight: settings.height + this.topPad + this.bottomPad * 2,\n\t\t\t\twidth: settings.width + this.horizPad * 2\n\t\t\t},\n\t\t\ttitle: {\n\t\t\t\ttext: `${config.featureTw.term.name} ${termType2label(config.featureTw.term.type)}`,\n\t\t\t\tx: this.horizPad + settings.width / 2,\n\t\t\t\ty: this.topPad / 2\n\t\t\t},\n\t\t\txAxisLabel: {\n\t\t\t\tx: this.horizPad + settings.width / 2,\n\t\t\t\ty: this.topPad + settings.height + this.bottomPad\n\t\t\t},\n\t\t\tyAxisLabel: {\n\t\t\t\tx: this.horizPad / 3,\n\t\t\t\ty: this.topPad + settings.height / 2\n\t\t\t},\n\t\t\txScale: {\n\t\t\t\tscale: xScale,\n\t\t\t\tx: this.horizPad,\n\t\t\t\ty: settings.height + this.topPad\n\t\t\t},\n\t\t\tyScale: {\n\t\t\t\t//Do not use scaleLog() here. scaleLog is for raw values before the log transformation\n\t\t\t\t//Using it will distort the values.\n\t\t\t\tscale: yScale,\n\t\t\t\tx: this.horizPad,\n\t\t\t\ty: this.topPad\n\t\t\t},\n\t\t\tdivideLine: {\n\t\t\t\tx: xScale(0) + this.horizPad,\n\t\t\t\ty1: settings.height + this.topPad,\n\t\t\t\ty2: this.topPad\n\t\t\t},\n\t\t\tthresholdLine: {\n\t\t\t\ty: yScale(-Math.log10(settings.threshold)) + this.topPad,\n\t\t\t\tx1: this.horizPad,\n\t\t\t\tx2: settings.width + this.horizPad\n\t\t\t}\n\t\t}\n\t}\n\n\t/** Increase the domain slightly so all data points fit within the plot */\n\tsetDomain(min: number, max: number, percent = 0.1) {\n\t\tconst rangeInc = (max - min) * percent\n\t\tconst domain = [min - rangeInc, max + rangeInc]\n\t\treturn domain\n\t}\n\n\tsetVariablesData(\n\t\tabsSampleMax: number,\n\t\tabsSampleMin: number,\n\t\tdata: CorrVolcanoViewData,\n\t\tdom: CorrVolcanoDom,\n\t\tkey: string,\n\t\tplotDim: CorrVolcanoPlotDimensions,\n\t\tsettings: CorrVolcanoSettings\n\t) {\n\t\tconst radiusScale = scaleLinear()\n\t\t\t.domain([absSampleMin, absSampleMax])\n\t\t\t.range([settings.radiusMin, settings.radiusMax])\n\t\tconst renderedCircles = dom.plot\n\t\t\t?.selectAll('circle')\n\t\t\t.nodes()\n\t\t\t.map((d: any) => d.__data__)\n\t\tfor (const item of data.variableItems) {\n\t\t\titem.color = item.correlation > 0 ? settings.corrColor : settings.antiCorrColor\n\t\t\titem.label = this.variableTwLst.find(t => t.$id == item.tw$id)!.term.name\n\t\t\titem.x = plotDim.xScale.scale(item.correlation) + this.horizPad\n\t\t\titem.y = plotDim.yScale.scale(item[`transformed_${key}`]) + this.topPad\n\t\t\titem.radius = radiusScale(item.sampleSize)\n\t\t\tif (renderedCircles?.length > 0) {\n\t\t\t\tconst findRenderdCircle = renderedCircles.find((d: any) => d.tw$id === item.tw$id) as any\n\t\t\t\tif (findRenderdCircle) {\n\t\t\t\t\titem.previousX = findRenderdCircle.x\n\t\t\t\t\titem.previousY = findRenderdCircle.y\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\titem.previousX = item.x\n\t\t\t\titem.previousY = item.y\n\t\t\t}\n\t\t}\n\t\treturn data.variableItems\n\t}\n\n\tsetLegendData(absSampleMin: number, absSampleMax: number, skippedVariables: { tw$id: string }[]) {\n\t\tconst opts = {\n\t\t\tabsMin: absSampleMin,\n\t\t\tabsMax: absSampleMax,\n\t\t\tskippedVariables:\n\t\t\t\tskippedVariables.length == 0\n\t\t\t\t\t? []\n\t\t\t\t\t: skippedVariables.map((t: any) => {\n\t\t\t\t\t\t\treturn { label: this.variableTwLst.find(tw => tw.$id == t.tw$id)!.term.name }\n\t\t\t\t\t  })\n\t\t}\n\n\t\treturn opts\n\t}\n}\n", "import { table2col } from '#dom'\nimport { roundValue } from '#shared/roundValue.js'\nimport type { Menu } from '#dom'\nimport type { SvgCircle } from '../../../types/d3'\nimport type { CorrVolcanoSettings, VariableItem } from '../CorrelationVolcanoTypes'\n\nexport class ItemToolTip {\n\tconstructor(item: VariableItem, circle: SvgCircle, tip: Menu, settings: CorrVolcanoSettings) {\n\t\tcircle.on('mouseover', () => {\n\t\t\ttip.clear().showunder(circle.node())\n\t\t\tconst table = table2col({ holder: tip.d.append('table') })\n\t\t\ttable.addRow('Item', item.label)\n\t\t\ttable.addRow('Correlation (\u03C1)', roundValue(item.correlation, 3))\n\t\t\tconst pValue = settings.isAdjustedPValue ? item.adjusted_pvalue : item.original_pvalue\n\t\t\ttable.addRow(settings.isAdjustedPValue ? 'Adjusted p value' : 'Original p value', roundValue(pValue, 5))\n\t\t\ttable.addRow('Sample size', item.sampleSize)\n\t\t})\n\t\tcircle.on('mouseout', () => {\n\t\t\ttip.hide()\n\t\t})\n\t}\n}\n", "import { axisstyle } from '#src/client'\nimport { axisBottom, axisLeft } from 'd3-axis'\nimport { select } from 'd3-selection'\nimport { LegendCircleReference } from '#dom'\nimport type {\n\tCorrVolcanoDom,\n\tCorrVolcanoSettings,\n\tCorrVolcanoLegendData,\n\tCorrVolcanoPlotDimensions,\n\tCorrVolcanoViewData\n} from '../CorrelationVolcanoTypes'\nimport type { CorrVolcanoInteractions } from '../interactions/CorrVolcanoInteractions'\nimport { ItemToolTip } from './ItemToolTip'\n\n/**\n * TODO - finish typing this file\n *\n * Using the data formated in ViewModel, renders the correlation\n * volcano plot. */\nexport class View {\n\tdom: CorrVolcanoDom\n\treadonly duration = 500\n\tviewData: CorrVolcanoViewData\n\tconstructor(\n\t\tdom: CorrVolcanoDom,\n\t\tviewData: CorrVolcanoViewData,\n\t\tinteractions: CorrVolcanoInteractions,\n\t\tsettings: CorrVolcanoSettings,\n\t\tdefaultMaxRadius: number,\n\t\tdefaultMinRadius: number\n\t) {\n\t\tthis.dom = dom\n\t\tthis.viewData = viewData\n\n\t\tinteractions.clearDom()\n\n\t\tconst plotDim = viewData.plotDim\n\t\tthis.renderDom(plotDim)\n\t\t// Draw all circles for variables\n\t\trenderVariables(this, settings, interactions)\n\t\tthis.renderLegend(viewData.legendData, settings, interactions, defaultMaxRadius, defaultMinRadius)\n\t}\n\n\trenderDom(plotDim: CorrVolcanoPlotDimensions) {\n\t\tthis.dom.svg.attr('width', plotDim.svg.width).attr('height', plotDim.svg.height)\n\n\t\tthis.dom.title\n\t\t\t.attr('class', 'sjpp-corr-volcano-title')\n\t\t\t.style('font-weight', 600)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('x', plotDim.title.x)\n\t\t\t.attr('y', plotDim.title.y)\n\t\t\t.text(plotDim.title.text)\n\n\t\tthis.dom.yAxisLabel\n\t\t\t.attr('class', 'sjpp-corr-volcano-y-axis')\n\t\t\t.style('font-weight', 600)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('transform', `translate(${plotDim.yAxisLabel.x}, ${plotDim.yAxisLabel.y}) rotate(-90)`)\n\t\t\t.text('-log10(p value)')\n\n\t\tthis.dom.xAxisLabel\n\t\t\t.attr('class', 'sjpp-corr-volcano-x-axis')\n\t\t\t.style('font-weight', 600)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('transform', `translate(${plotDim.xAxisLabel.x}, ${plotDim.xAxisLabel.y})`)\n\t\t\t.html('Correlation Coefficient (ρ)') //unicode for rho\n\n\t\t//Y, left scale\n\t\tthis.renderScale(plotDim.yScale, true)\n\t\t//X, bottom scale\n\t\tthis.renderScale(plotDim.xScale)\n\n\t\t// Draw a line demarcating correlation and anticorrelation\n\t\tthis.dom.svg\n\t\t\t.append('line')\n\t\t\t.attr('class', 'sjpp-corr-volcano-divide-line')\n\t\t\t.attr('stroke', 'black')\n\t\t\t.attr('stroke-dasharray', '5 4')\n\t\t\t.attr('stroke-opacity', 0.4)\n\t\t\t.attr('x1', plotDim.divideLine.x)\n\t\t\t.attr('x2', plotDim.divideLine.x)\n\t\t\t.attr('y1', plotDim.divideLine.y1)\n\t\t\t.attr('y2', plotDim.divideLine.y2)\n\n\t\t//Draw threshold indicating statiscally significant values\n\t\tthis.dom.svg\n\t\t\t.append('line')\n\t\t\t.attr('class', 'sjpp-corr-volcano-threshold-line')\n\t\t\t.attr('stroke', 'black')\n\t\t\t.attr('stroke-dasharray', '5 4')\n\t\t\t.attr('stroke-opacity', 0.4)\n\t\t\t.attr('x1', plotDim.thresholdLine.x1)\n\t\t\t.attr('x2', plotDim.thresholdLine.x2)\n\t\t\t.attr('y1', plotDim.thresholdLine.y)\n\t\t\t.attr('y2', plotDim.thresholdLine.y)\n\t}\n\n\trenderScale(scale, isLeft = false) {\n\t\tconst scaleG = this.dom.plot\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${scale.x}, ${scale.y})`)\n\t\t\t.transition()\n\t\t\t.duration(this.duration)\n\t\t\t.call(isLeft ? axisLeft(scale.scale) : axisBottom(scale.scale))\n\n\t\taxisstyle({\n\t\t\taxis: scaleG,\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t}\n\n\trenderLegend(\n\t\tlegendData: CorrVolcanoLegendData,\n\t\tsettings: CorrVolcanoSettings,\n\t\tinteractions: CorrVolcanoInteractions,\n\t\tdefaultMaxRadius: number,\n\t\tdefaultMinRadius: number\n\t) {\n\t\tconst svg = this.dom.legend\n\t\t\t.attr('width', 400)\n\t\t\t//TODO: calculate the height based on the number of skipped terms and max radius\n\t\t\t.attr('height', 400)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('padding-top', '20px')\n\n\t\tconst startXPos = 20\n\t\tconst startYPos = 20\n\n\t\tnew LegendCircleReference({\n\t\t\tg: svg.append('g').attr('transform', `translate(${startXPos}, ${startYPos})`),\n\t\t\tinputMax: defaultMaxRadius,\n\t\t\tinputMin: defaultMinRadius,\n\t\t\tmaxLabel: legendData.absMax,\n\t\t\tmaxRadius: settings.radiusMax,\n\t\t\tminLabel: legendData.absMin,\n\t\t\tminRadius: settings.radiusMin,\n\t\t\ttitle: 'Sample Size',\n\t\t\tmenu: {\n\t\t\t\tminMaxLabel: 'pixels',\n\t\t\t\tcallback: async obj => {\n\t\t\t\t\tawait interactions.changeRadius(obj)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\t/** Show terms with no data to the user */\n\t\tif (legendData.skippedVariables.length > 0) {\n\t\t\tconst newYPos = startYPos + settings.radiusMax + 60\n\t\t\tlet incrY = 30\n\t\t\tconst skippedVariablesG = svg.append('g').attr('transform', `translate(${startXPos}, ${newYPos})`)\n\t\t\t//Styling matches the legend circle reference\n\t\t\tskippedVariablesG\n\t\t\t\t.append('text')\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t.text('Skipped Variables')\n\n\t\t\tfor (const term of legendData.skippedVariables) {\n\t\t\t\tskippedVariablesG\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('transform', `translate(${startXPos}, ${incrY})`)\n\t\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t\t.text(term.label)\n\t\t\t\tincrY += 20\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction renderVariables(self, settings: CorrVolcanoSettings, interactions: CorrVolcanoInteractions) {\n\tself.dom.plot\n\t\t.selectAll('circle')\n\t\t.data(self.viewData.variableItems)\n\t\t.enter()\n\t\t.append('circle')\n\t\t.attr('id', item => `sjpp-corr-volcano-circle-${item.label}`)\n\t\t.attr('stroke', item => item.color)\n\t\t.attr('fill', item => item.color)\n\t\t.attr('fill-opacity', 0.5)\n\t\t.attr('cx', item => item.previousX)\n\t\t.attr('cy', item => item.previousY)\n\t\t//Allows for a subtle transition to new position\n\t\t.attr('r', item => item.radius * 0.9)\n\t\t.transition()\n\t\t.duration(self.duration)\n\t\t.attr('cx', item => item.x)\n\t\t.attr('cy', item => item.y)\n\t\t.attr('r', item => item.radius)\n\t\t.each(function (this, item) {\n\t\t\tconst circle = select(this)\n\t\t\tnew ItemToolTip(item, circle, self.dom.tip, settings)\n\t\t\tcircle.on('click', () => {\n\t\t\t\tinteractions.launchSampleScatter(item)\n\t\t\t})\n\t\t})\n}\n", "import { to_svg } from '#src/client'\nimport { termType2label } from '#shared/terms.js'\nimport { appInit } from '#termdb/app'\nimport type { MassAppApi } from '#mass/types/mass'\nimport type { CorrVolcanoDom } from '../CorrelationVolcanoTypes'\nimport type { TermWrapper } from '#types'\n\nexport class CorrVolcanoInteractions {\n\tapp: MassAppApi\n\tdom: CorrVolcanoDom\n\tid: string\n\tvariableTwLst: TermWrapper[]\n\tconstructor(app: MassAppApi, dom: CorrVolcanoDom, id: string) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.id = id\n\t\tthis.variableTwLst = []\n\t}\n\n\tdownload() {\n\t\tconst svg = this.dom.svg.node() as Node\n\t\tto_svg(svg, `correlationVolcano`, { apply_dom_styles: true })\n\t}\n\n\t//If no featureTw is set, show the tree to select a feature\n\tasync showTree() {\n\t\tthis.dom.div.selectAll('*').remove()\n\t\tawait appInit({\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tholder: this.dom.div,\n\t\t\tstate: this.app.getState(),\n\t\t\ttree: {\n\t\t\t\tclick_term: _term => {\n\t\t\t\t\tconst term = _term.term || _term\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\t\t\t\tfeatureTw: _term.term ? _term : { term }\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\t\tid: this.id\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\t//When clicking on dot, launch the sample scatter by gene and drug\n\tlaunchSampleScatter(item: any) {\n\t\tconst config = this.app.getState()\n\t\tconst plot = config.plots.find(p => p.id === this.id)\n\t\tconst term2 = this.variableTwLst?.find((t: any) => t.$id === item.tw$id)?.term\n\t\tif (!term2) throw `No term found for ${item.tw$id}`\n\t\tconst scatterConfig = {\n\t\t\tchartType: 'sampleScatter',\n\t\t\tname: `${plot.featureTw.term.name} ${termType2label(plot.featureTw.term.type)} v ${term2.name}`,\n\t\t\tterm: { term: plot.featureTw.term },\n\t\t\tterm2: { id: term2.id },\n\t\t\tfilter: config.termfilter.filter\n\t\t}\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: scatterConfig\n\t\t})\n\t}\n\n\t//Obj is returned from LegendCircleReference callback\n\tasync changeRadius(obj: { min: number; max: number }) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tcorrelationVolcano: {\n\t\t\t\t\t\tradiusMax: obj.max,\n\t\t\t\t\t\tradiusMin: obj.min\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tclearDom() {\n\t\tthis.dom.error.style('padding', '').text('')\n\t\tthis.dom.plot.selectAll('*').remove()\n\t\tthis.dom.legend.selectAll('*').remove()\n\t\tthis.dom.svg.selectAll('line').remove()\n\t\tthis.dom.title.text('')\n\t\tthis.dom.yAxisLabel.text('')\n\t\tthis.dom.xAxisLabel.text('')\n\t}\n}\n", "import { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { PlotBase } from '../PlotBase'\nimport { fillTermWrapper, fillTwLst } from '#termsetting'\nimport type { BasePlotConfig, MassAppApi, MassState } from '#mass/types/mass'\nimport { controlsInit } from '../controls'\nimport type { CorrVolcanoDom, CorrVolcanoOpts, CorrVolcanoSettings } from './CorrelationVolcanoTypes'\nimport { Menu } from '#dom'\nimport { Model } from './model/Model'\nimport { ViewModel } from './viewModel/ViewModel'\nimport { View } from './view/View'\nimport { CorrVolcanoInteractions } from './interactions/CorrVolcanoInteractions'\n\n/** TODO:\n *  - Clean up noted tech debt\n *  - Add tests\n */\n\nclass CorrelationVolcano extends PlotBase implements RxComponent {\n\tstatic type = 'correlationVolcano'\n\treadonly type = 'correlationVolcano'\n\tcomponents: { controls: any }\n\t/** Max radius user may enter in control or legend menu */\n\treadonly defaultInputMaxRadius = 35\n\t/** Min radius user may enter in control or legend menu */\n\treadonly defaultInputMinRadius = 1\n\tdom: CorrVolcanoDom\n\tvariableTwLst: any\n\tinteractions?: CorrVolcanoInteractions\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.opts = opts\n\t\tthis.components = {\n\t\t\tcontrols: {}\n\t\t}\n\t\tconst holder = opts.holder.classed('sjpp-corrVolcano-main', true)\n\t\tconst controls = opts.controls ? holder : holder.append('div')\n\t\tconst div = holder.append('div').style('padding', '5px').style('display', 'inline-block')\n\t\tconst errorDiv = div.append('div').attr('id', 'sjpp-corrVolcano-error').style('opacity', 0.75)\n\t\tconst svg = div.append('svg').style('display', 'inline-block').attr('id', 'sjpp-corrVolcano-svg')\n\t\tthis.dom = {\n\t\t\tcontrols: controls.style('display', 'block'),\n\t\t\tdiv,\n\t\t\terror: errorDiv,\n\t\t\tsvg,\n\t\t\tplot: svg.append('g'),\n\t\t\ttitle: svg.append('text'),\n\t\t\tyAxisLabel: svg.append('text'),\n\t\t\txAxisLabel: svg.append('text'),\n\t\t\tlegend: div.append('svg'),\n\t\t\ttip: new Menu({ padding: '' })\n\t\t}\n\t\tif (opts.header)\n\t\t\tthis.dom.header = opts.header.text('CORRELATION VOLCANO').style('font-size', '0.7em').style('opacity', 0.6)\n\t\tthis.variableTwLst = []\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tcorrelationVolcano: appState.termdbConfig.correlationVolcano,\n\t\t\tconfig: Object.assign({}, config, {\n\t\t\t\tsettings: {\n\t\t\t\t\tcorrelationVolcano: config.settings.correlationVolcano\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tasync setControls() {\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'featureTw',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tusecase: { target: 'correlationVolcano', detail: 'numeric' },\n\t\t\t\tlabel: 'Feature',\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['continuous'],\n\t\t\t\tmenuOptions: 'replace'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Correlation method',\n\t\t\t\ttitle: 'Change the correlation method',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'method',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Pearson', value: 'pearson' },\n\t\t\t\t\t{ label: 'Spearman', value: 'spearman' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P value',\n\t\t\t\ttitle: 'Change the p value',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'isAdjustedPValue',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Adjusted', value: true },\n\t\t\t\t\t{ label: 'Original', value: false }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Significant p value',\n\t\t\t\ttitle: 'Set the significant p value threshold',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'threshold',\n\t\t\t\tdebounceInterval: 0.05\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Maximum radius size',\n\t\t\t\ttitle: 'Set maximum radius size in pixels',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'radiusMax',\n\t\t\t\tmin: this.defaultInputMinRadius,\n\t\t\t\tmax: this.defaultInputMaxRadius,\n\t\t\t\tdebounceInterval: 500\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Minimum radius size',\n\t\t\t\ttitle: 'Set minimum radius size in pixels',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'radiusMin',\n\t\t\t\tmin: this.defaultInputMinRadius,\n\t\t\t\tmax: this.defaultInputMaxRadius,\n\t\t\t\tdebounceInterval: 500\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Height',\n\t\t\t\ttitle: 'Set the height of the plot',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'height',\n\t\t\t\tdebounceInterval: 500\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Width',\n\t\t\t\ttitle: 'Set the width of the plot',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'width',\n\t\t\t\tdebounceInterval: 500\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Correlation color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'corrColor',\n\t\t\t\ttitle: 'Color of correlated values'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Anticorrelation color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'correlationVolcano',\n\t\t\t\tsettingsKey: 'antiCorrColor',\n\t\t\t\ttitle: 'Color of anticorrelated values'\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.correlationVolcano', () => {\n\t\t\tthis.interactions!.download()\n\t\t})\n\t\tthis.components.controls.on('helpClick.correlationVolcano', () => {\n\t\t\twindow.open('https://github.com/stjude/proteinpaint/wiki/Correlation-volcano', '_blank')\n\t\t})\n\t}\n\n\tasync init(appState: MassState) {\n\t\tthis.interactions = new CorrVolcanoInteractions(this.app, this.dom, this.id)\n\t\tconst state = this.getState(appState)\n\t\tif (state.config['featureTw']) await this.setControls()\n\t\t//Hack because obj not returning in getState(). Will fix later.\n\t\tconst dsCorrVolcano = state.termdbConfig.correlationVolcano\n\n\t\t//Fill the term wrapper for the drug list from the ds\n\t\tthis.variableTwLst = dsCorrVolcano.variables.termIds.map((id: string) => {\n\t\t\treturn { id }\n\t\t})\n\t\tthis.interactions.variableTwLst = this.variableTwLst\n\n\t\tawait fillTwLst(this.variableTwLst, this.app.vocabApi)\n\t}\n\n\tasync main() {\n\t\tconst config = structuredClone(this.state.config)\n\t\tif (config.childType != this.type && config.chartType != this.type) return\n\n\t\tif (!this.interactions) throw 'Interactions not initialized [correlationVolcano main()]'\n\n\t\tif (config.featureTw == null) {\n\t\t\tthis.interactions.showTree()\n\t\t\treturn\n\t\t}\n\n\t\tconst settings = config.settings.correlationVolcano\n\t\t/** Request data from the server*/\n\t\tconst model = new Model(config, this.state, this.app, settings, this.variableTwLst, this.vocabApi)\n\t\tconst data = await model.getData()\n\t\tif (!data || data.error || !data.variableItems.length) {\n\t\t\tthis.interactions.clearDom()\n\t\t\tthis.dom.error.style('padding', '20px 20px 20px 60px').text(data.error || 'No correlation data to render.')\n\t\t\treturn\n\t\t}\n\n\t\t/** Format returned data for rendering */\n\t\tconst viewModel = new ViewModel(config, data, this.dom, settings, this.variableTwLst)\n\n\t\t/** Render correlation volcano plot */\n\t\tnew View(\n\t\t\tthis.dom,\n\t\t\tviewModel.viewData,\n\t\t\tthis.interactions,\n\t\t\tsettings,\n\t\t\tthis.defaultInputMaxRadius,\n\t\t\tthis.defaultInputMinRadius\n\t\t)\n\t}\n}\n\nexport const corrVolcanoInit = getCompInit(CorrelationVolcano)\nexport const componentInit = corrVolcanoInit\n\nexport function getDefaultCorrVolcanoSettings(overrides = {}) {\n\tconst defaults: CorrVolcanoSettings = {\n\t\tantiCorrColor: '#ff0000', //red\n\t\tcorrColor: '#0000ff', //blue\n\t\tisAdjustedPValue: false,\n\t\tmethod: 'pearson',\n\t\tthreshold: 0.05,\n\t\theight: 500,\n\t\twidth: 500,\n\t\tradiusMax: 20,\n\t\tradiusMin: 5\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n\nexport async function getPlotConfig(opts: CorrVolcanoOpts, app: MassAppApi) {\n\t//Opts.numeric returned from tree search when clicking on charts button\n\t//See logic in shared/utils/src/termdb.usecase.js for how tree is limited\n\t//May change this later\n\tif (opts.numeric && !opts.featureTw) opts.featureTw = { term: opts.numeric.term } as any\n\t/** If featureTw is passed, the plot will load per usual\n\t * else a UI will appear allowing the uses to select the feature */\n\tif (opts.featureTw) {\n\t\ttry {\n\t\t\tawait fillTermWrapper(opts.featureTw, app.vocabApi)\n\t\t} catch (e) {\n\t\t\tconsole.error(new Error(`${e} [correlationVolcano getPlotConfig()]`))\n\t\t\tthrow `correlationVolcano getPlotConfig() failed`\n\t\t}\n\t}\n\n\tconst config = {\n\t\tchartType: 'correlationVolcano',\n\t\tfeatureTw: opts.featureTw ?? null,\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null,\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\tcorrelationVolcano: getDefaultCorrVolcanoSettings(opts.overrides || {})\n\t\t}\n\t}\n\treturn copyMerge(config, opts)\n}\n"],
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+  "names": []
+}

package/dist/DE-AABMOSEE.js

@@ -0,0 +1,95 @@
+import {
+  appInit
+} from "./chunk-HR7XPTAV.js";
+import "./chunk-2TWVFQD2.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-BIDQ4OZH.js";
+import "./chunk-OMIUJ7JT.js";
+import "./chunk-OCC5HEPR.js";
+import "./chunk-RL3IRMOA.js";
+import "./chunk-WJTRQ3ZC.js";
+import "./chunk-UILBQKQ6.js";
+import "./chunk-FCOX5Q4Q.js";
+import "./chunk-RVRRHEUG.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/DE.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  const genome = genomes[useGenome];
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome,
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: "hidden" },
+      plots: [{ chartType: "DEinput" }]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=DE-AABMOSEE.js.map

package/dist/DEinput-3HVHJE2I.js

@@ -0,0 +1,409 @@
+import {
+  PlotBase,
+  Tabs,
+  excludeFilterByTag,
+  filterInit,
+  filterJoin,
+  filterPromptInit,
+  getNormalRoot,
+  make_radios,
+  negateFilter,
+  renderPreAnalysisData,
+  renderTable
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import {
+  dofetch3
+} from "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import {
+  termType2label
+} from "./chunk-X6VTVZY7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import {
+  TermTypeGroups,
+  getColors
+} from "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/DEinput.ts
+var colorScale = getColors(5);
+var DEinputPlot = class _DEinputPlot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.components = {};
+    this.type = _DEinputPlot.type;
+    this.opts = opts;
+    this.dom = this.getDom();
+    this.groups = [];
+  }
+  static {
+    this.type = "DEinput";
+  }
+  getDom() {
+    const header = this.opts?.header?.html("Differential Gene Expression") || void 0;
+    const holder = this.opts.holder.append("div").style("margin", "10px");
+    const expressionSource = holder.append("div").style("margin-bottom", "15px");
+    const table = holder.append("div");
+    const btns = holder.append("div").style("margin-top", "5px");
+    const addGroup = btns.append("div").style("display", "inline-block");
+    const submit = btns.append("div").style("display", "none").style("margin-left", "15px").attr("class", "sja_new_filter_btn sja_menuoption");
+    const loading = holder.append("div").style("display", "none").style("margin", "20px 10px").text("Loading...");
+    const preAnalysis = holder.append("div").style("display", "none").style("margin-top", "20px").style("margin-left", "5px");
+    const dom = { header, expressionSource, table, addGroup, submit, loading, preAnalysis };
+    return dom;
+  }
+  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)?`;
+    }
+    return {
+      termfilter: appState.termfilter,
+      config,
+      // quick fix to skip history tracking as needed
+      _scope_: appState._scope_
+    };
+  }
+  async init() {
+    await this.renderExpressionSourceUI();
+  }
+  // TODO: handle errors
+  async main() {
+    this.dom.preAnalysis.selectAll("*").remove();
+    if (!this.expressionSource || this.expressionSource === "pseudobulk" && !this.pseudobulk) {
+      this.dom.table.style("display", "none");
+      this.dom.addGroup.style("display", "none");
+      this.dom.submit.style("display", "none");
+      return;
+    }
+    this.dom.addGroup.style("display", "inline-block");
+    this.makeGroupsUI();
+    this.hasCohort0 = this.groups.some((g) => g.filter.lst.some((item) => item.tvs?.term.type == "cohort"));
+    this.mayRenderSubmit();
+  }
+  async renderExpressionSourceUI() {
+    const config = this.app.vocabApi.termdbConfig;
+    const hasBulk = !!config.queries?.rnaseqGeneCount;
+    const terms = config.termType2terms?.[TermTypeGroups.PSEUDOBULK] || [];
+    const hasPseudobulk = terms.length > 0;
+    if (!hasBulk && !hasPseudobulk)
+      throw new Error("No gene expression count data configured for differential analysis");
+    if (hasBulk && !hasPseudobulk) {
+      this.expressionSource = "bulk";
+      return;
+    }
+    if (!hasBulk) {
+      this.expressionSource = "pseudobulk";
+      this.renderPseudobulkSelection(this.dom.expressionSource, terms);
+      return;
+    }
+    const tabs = [
+      {
+        label: "Bulk RNA-seq",
+        active: true,
+        callback: async () => {
+          this.expressionSource = "bulk";
+          await this.main();
+        }
+      },
+      {
+        label: "Single-cell pseudobulk",
+        callback: async (_event, tab) => {
+          this.expressionSource = "pseudobulk";
+          tab.contentHolder.selectAll("*").remove();
+          this.renderPseudobulkSelection(tab.contentHolder, terms);
+          await this.main();
+        }
+      }
+    ];
+    await new Tabs({ holder: this.dom.expressionSource, tabs }).main();
+  }
+  renderPseudobulkSelection(holder, terms) {
+    const assayMap = /* @__PURE__ */ new Map();
+    for (const term of terms) {
+      if (!assayMap.has(term.assay)) assayMap.set(term.assay, /* @__PURE__ */ new Map());
+      const memberMap = assayMap.get(term.assay);
+      if (!memberMap.has(term.memberId)) memberMap.set(term.memberId, []);
+      memberMap.get(term.memberId).push(term);
+    }
+    const renderAssay = (assayHolder, assay, memberMap) => {
+      assayHolder.selectAll("*").remove();
+      const renderMember = (memberHolder, memberId, memberTerms) => {
+        memberHolder.selectAll("*").remove();
+        memberHolder.append("div").style("opacity", 0.7).text(`Select from ${memberId}:`);
+        make_radios({
+          holder: memberHolder,
+          inputName: `sjpp-de-pseudobulk-${this.id}-${assay}-${memberId}`,
+          options: memberTerms.map((term) => ({
+            label: term.name,
+            value: term.id,
+            checked: this.pseudobulk?.assay === assay && this.pseudobulk?.memberId === memberId && this.pseudobulk?.category === (term.category || term.id),
+            testid: `sjpp-de-pseudobulk-category-${term.id}`
+          })),
+          styles: { display: "block", padding: "3px 5px" },
+          callback: async (value) => {
+            const term = memberTerms.find((term2) => term2.id == value);
+            this.pseudobulk = { assay, memberId, category: term.category || term.id };
+            await this.main();
+          }
+        });
+      };
+      if (memberMap.size === 1) {
+        const [memberId, memberTerms] = memberMap.entries().next().value;
+        renderMember(assayHolder, memberId, memberTerms);
+      } else {
+        const memberTabs = Array.from(memberMap, ([memberId, memberTerms]) => ({
+          label: memberId,
+          callback: (_event, tab) => renderMember(tab.contentHolder, memberId, memberTerms)
+        }));
+        new Tabs({ holder: assayHolder, tabs: memberTabs }).main();
+      }
+    };
+    if (assayMap.size === 1) {
+      const [assay, memberMap] = Array.from(assayMap)[0];
+      holder.append("div").text("Single-cell pseudobulk " + termType2label(assay));
+      renderAssay(holder.append("div"), assay, memberMap);
+    } else {
+      const assayTabs = Array.from(assayMap, ([assay, memberMap]) => ({
+        label: termType2label(assay),
+        callback: (_event, tab) => renderAssay(tab.contentHolder, assay, memberMap)
+      }));
+      new Tabs({ holder, tabs: assayTabs, linePosition: "right", tabsPosition: "vertical" }).main();
+    }
+  }
+  async makeGroupsUI() {
+    if (!this.filterPrompt) {
+      this.filterPrompt = await filterPromptInit({
+        holder: this.dom.addGroup,
+        vocabApi: this.app.vocabApi,
+        emptyLabel: "Add group",
+        header_mode: this.opts?.header_mode,
+        callback: async (f) => {
+          const filter2 = getNormalRoot(f);
+          this.addNewGroup(filter2, this.groups);
+          await this.main();
+        },
+        debug: this.opts.debug
+      });
+    }
+    const filter = structuredClone(this.state?.termfilter?.filter);
+    this.filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
+    if (!this.groups.length) {
+      this.dom.table.style("display", "none");
+      return;
+    }
+    this.dom.table.style("display", "block").selectAll("*").remove();
+    const tableArg = {
+      div: this.dom.table,
+      columns: [
+        {},
+        // blank column to add delete buttons
+        {
+          label: "NAME",
+          editCallback: async (i, cell) => {
+            const newName = cell.value;
+            const index = this.groups.findIndex((group) => group.name == newName);
+            if (index != -1) {
+              alert(`Group named ${newName} already exists`);
+              await this.main();
+            } else {
+              this.groups[i].name = newName;
+              await this.main();
+            }
+          }
+        },
+        {
+          label: "COLOR",
+          editCallback: async (i, cell) => {
+            this.groups[i].color = cell.color;
+            this.main();
+          }
+        },
+        // dataset may rename what a row counts (GDC: cases, not samples)
+        { label: `#${(this.app.vocabApi.termdbConfig?.uiLabels?.Sample || "Sample").toUpperCase()}` },
+        { label: "FILTER" }
+      ],
+      rows: [],
+      striped: false,
+      // no alternating row bg color so delete button appears more visible
+      showLines: false
+    };
+    for (const g of this.groups) {
+      tableArg.rows.push([
+        {},
+        // blank cell to add delete button
+        { value: g.name },
+        // to allow click to show <input>
+        { color: g.color },
+        { value: "" },
+        // filled in asynchronously below, so one slow count does not hold up the table
+        {}
+        // blank cell to show filter ui
+      ]);
+    }
+    renderTable(tableArg);
+    for (const [i, row] of tableArg.rows.entries()) {
+      row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
+        this.groups.splice(i, 1);
+        this.main();
+      });
+      this.app.vocabApi.getFilteredSampleCount(this.groups[i].filter, this.hasCohort0 ? null : this.state.termfilter.filter0).then((n) => row[3].__td.text(n)).catch((e) => row[3].__td.text("n/a").attr("title", e?.message || e));
+      const group = this.groups[i];
+      filterInit({
+        holder: row[4].__td,
+        vocabApi: this.app.vocabApi,
+        header_mode: "hide_search",
+        callback: (f) => {
+          if (!f || f.lst.length == 0) {
+            const i2 = this.groups.findIndex((g) => g.name == group.name);
+            this.groups.splice(i2, 1);
+          } else {
+            group.filter = f;
+          }
+          this.main();
+        }
+      }).main(group.filter);
+    }
+    this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "auto").style("opacity", 1);
+  }
+  addNewGroup(filter, groups, name) {
+    if (!groups) throw "groups is missing";
+    if (!name) {
+      const base = "New group";
+      name = base;
+      for (let i = 0; ; i++) {
+        name = base + (i === 0 ? "" : " " + i);
+        if (!groups.find((g) => g.name === name)) break;
+      }
+    }
+    const newGroup = {
+      name,
+      filter,
+      color: rgb(colorScale(groups.length)).formatHex()
+    };
+    groups.push(newGroup);
+  }
+  mayRenderSubmit() {
+    if (!this.groups.length || this.groups.length == 1 && this.hasCohort0) {
+      this.dom.submit.style("display", "none");
+      return;
+    }
+    this.dom.submit.style("display", "inline-block");
+    if (this.groups.length == 1) {
+      this.dom.submit.text(`Submit (${this.groups[0].name} vs others)`);
+      this.dom.submit.on("click", async () => {
+        const groups = [this.groups[0]];
+        const otherGroup = {
+          name: "Not in " + groups[0].name,
+          color: "#ccc",
+          filter: negateFilter(groups[0].filter)
+        };
+        groups.push(otherGroup);
+        await this.clickSubmit(groups);
+      });
+    } else if (this.groups.length == 2) {
+      this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "none").style("opacity", 0.5);
+      this.dom.submit.text(`Submit (${this.groups[0].name} vs ${this.groups[1].name})`);
+      this.dom.submit.on("click", async () => {
+        await this.clickSubmit(this.groups);
+      });
+    } else {
+      throw new Error("cannot exceed 2 groups");
+    }
+  }
+  async clickSubmit(groups) {
+    this.dom.loading.style("display", "block");
+    const samplelstTW = {
+      q: { groups: [] },
+      term: {
+        name: groups.map((g) => g.name).join(" vs "),
+        type: "samplelst",
+        values: {}
+      }
+    };
+    if (this.expressionSource === "pseudobulk") samplelstTW.pseudobulk = this.pseudobulk;
+    const filter0 = this.hasCohort0 ? null : this.state.termfilter.filter0;
+    for (const g of groups) {
+      const samples = await this.vocabApi.getFilteredSampleList(
+        filterJoin([g.filter, this.state.termfilter.filter]),
+        filter0
+      );
+      const sampleIds = samples.map((s) => {
+        return { sampleId: s.id };
+      });
+      samplelstTW.q.groups.push({
+        name: g.name,
+        in: true,
+        values: sampleIds
+      });
+      samplelstTW.term.values[g.name] = {
+        color: g.color,
+        key: g.name,
+        label: g.name
+      };
+    }
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: { groups: samplelstTW.q.groups },
+      filter: this.state.termfilter.filter,
+      filter0,
+      preAnalysis: true
+    };
+    if (this.expressionSource === "pseudobulk") body.pseudobulk = this.pseudobulk;
+    const preAnalysisData = await dofetch3("termdb/DE", { body });
+    this.dom.loading.style("display", "none");
+    this.dom.preAnalysis.style("display", "block").selectAll("*").remove();
+    renderPreAnalysisData({
+      preAnalysisData,
+      samplelstTW,
+      groups: samplelstTW.q.groups,
+      holder: this.dom.preAnalysis,
+      self: this
+    });
+  }
+};
+var DEinputInit = getCompInit(DEinputPlot);
+var componentInit = DEinputInit;
+async function getPlotConfig(opts) {
+  const config = {
+    chartType: "DEinput",
+    settings: {}
+  };
+  return copyMerge(config, opts);
+}
+export {
+  DEinputInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DEinput-3HVHJE2I.js.map