@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/CorrelationVolcano-XIMXCSHG.js.map

@@ -1,7 +0,0 @@
-{
-  "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, type ComponentApi } 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, formatHeaderText } 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\n\ttype: string\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\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = CorrelationVolcano.type\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) formatHeaderText({\n\t\t\theader: opts.header,\n\t\t\tchartType: 'CORRELATION VOLCANO'\n\t\t})\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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