@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-YL7VT4QT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/survival/survival.ts"],
+  "sourcesContent": ["import { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.ts'\nimport { controlsInit, term0_term2_defaultQ } from '#plots/controls.js'\nimport { select } from 'd3-selection'\nimport { scaleLinear, scaleOrdinal } from 'd3-scale'\nimport { schemeCategory10 } from 'd3-scale-chromatic'\nimport { schemeCategory20 } from '#common/legacy-d3-polyfill'\nimport { axisLeft, axisBottom } from 'd3-axis'\nimport { line, area, curveStepAfter } from 'd3-shape'\nimport { rgb } from 'd3-color'\nimport htmlLegend from '#dom/html.legend'\nimport Partjson from 'partjson'\nimport { rgb2hex } from '#src/client'\nimport { fillTermWrapper } from '#termsetting'\nimport { Menu } from '#dom/menu'\nimport { getSeriesTip } from '#dom/svgSeriesTips'\nimport { renderAtRiskG } from '#dom/renderAtRisk'\nimport { renderPvalues } from '#dom/renderPvalueTable'\nimport { downloadChart } from '#common/svg.download'\nimport { getCombinedTermFilter } from '#filter'\nimport { DownloadMenu } from '#dom/downloadMenu'\nimport { isNumericTerm } from '#shared/terms.js'\n\nexport const t0_t2_defaultQ = structuredClone(term0_term2_defaultQ)\nObject.assign(t0_t2_defaultQ, {\n\tnumeric: {\n\t\tmode: 'discrete',\n\t\ttype: 'custom-bin',\n\t\tpreferredBins: 'median'\n\t},\n\tgeneExpression: {\n\t\tmode: 'discrete',\n\t\ttype: 'custom-bin',\n\t\tpreferredBins: 'median'\n\t}\n})\n\nclass TdbSurvival extends PlotBase implements RxComponent {\n\tstatic type = 'survival'\n\n\t// expected RxComponent props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: { [name: string]: ComponentApi } = {}\n\n\t// expected class-specific props\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\tsettings: any\n\tlineFxn: any\n\tpj: any\n\tactiveMenu = false\n\tlegendRenderer: any\n\thiddenRenderer: any\n\tlegendClick = (_, __, ___) => {}\n\tdownload: () => void = () => {}\n\tgetChartImages = () => this.getChartImages()\n\tloadingWait = 0\n\n\tcolorScale: any\n\n\trefs: any\n\tsymbol: any\n\tserverData?: any\n\tcurrData?: any\n\tlegendData?: any\n\tlegendOrder: any[] = []\n\thiddenData?: any\n\ttests?: { [name: string]: any }\n\tterm2toColor: { [name: string]: { orig: string; rgb: any; adjusted: string; hex: string } } = {}\n\n\tuniqueSeriesIds: Set<any> = new Set()\n\n\t// TODO: migrate to this.view method\n\trender = () => {}\n\tgetSymbol = (_: number) => {\n\t\treturn ''\n\t}\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = TdbSurvival.type\n\t\tthis.settings = Object.assign({}, opts.settings)\n\t\tthis.dom = this.getDom()\n\t\tthis.pj = getPj(this)\n\n\t\tthis.lineFxn = line()\n\t\t\t.curve(curveStepAfter)\n\t\t\t.x(c => (c as any).scaledX)\n\t\t\t.y(c => (c as any).scaledY)\n\n\t\tthis.legendRenderer = htmlLegend(this.dom.legendDiv, {\n\t\t\tsettings: {\n\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t},\n\t\t\thandlers: {\n\t\t\t\tlegend: {\n\t\t\t\t\tclick: e => this.legendClick(e.target.__data__, e.clientX, e.clientY)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tthis.hiddenRenderer = htmlLegend(this.dom.hiddenDiv, {\n\t\t\tsettings: {\n\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t},\n\t\t\thandlers: {\n\t\t\t\tlegend: {\n\t\t\t\t\tclick: e => this.legendClick(e.target.__data__, e.clientX, e.clientY)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tgetDom() {\n\t\tconst opts = this.opts\n\t\tconst controls = this.opts.controls ? null : opts.holder.append('div')\n\t\tconst holder = opts.controls ? opts.holder : opts.holder.append('div')\n\t\tconst loadingDiv = holder\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('display', 'none')\n\t\t\t.style('padding', '20px')\n\t\t\t.html('Loading ...')\n\t\tconst chartsDiv = holder\n\t\t\t.append('div')\n\t\t\t.style('margin', '10px')\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\tconst dom = {\n\t\t\tloadingDiv,\n\t\t\theader: opts.header,\n\t\t\tcontrols,\n\t\t\tholder,\n\t\t\tchartsDiv,\n\t\t\tlegendDiv: holder.append('div').style('margin', '5px 5px 15px 5px'),\n\t\t\thiddenDiv: holder.append('div').style('margin', '5px 5px 15px 5px'),\n\t\t\ttip: new Menu({ padding: '5px' }),\n\t\t\tlegendTip: new Menu({ padding: '5px' })\n\t\t}\n\n\t\tdom.tip.onHide = () => {\n\t\t\tthis.activeMenu = false\n\t\t}\n\n\t\tif (dom.header) dom.header.html('Survival Plot')\n\t\treturn dom\n\t}\n\n\tasync init() {\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\t\tawait this.setControls()\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 'controls labels not found'\n\t\tif (this.opts.controls) {\n\t\t\tthis.opts.controls.on('downloadClick.survival', this.download)\n\t\t} else {\n\t\t\tthis.dom.holder.attr('class', 'pp-termdb-plot-viz').style('display', 'inline-block').style('min-width', '300px')\n\n\t\t\tthis.components = {\n\t\t\t\tcontrols: await controlsInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tholder: this.dom.controls.style('display', 'inline-block'),\n\t\t\t\t\tinputs: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\t\tconfigKey: 'term2',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tusecase: { target: 'survival', detail: 'term2' },\n\t\t\t\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\t\t\t\tdefaultQ4fillTW: t0_t2_defaultQ\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\t\tconfigKey: 'term0',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tusecase: { target: 'survival', detail: 'term0' },\n\t\t\t\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t\t\t\t\tdefaultQ4fillTW: t0_t2_defaultQ\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Chart width',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\t\t\t\ttitle: 'The internal width of the chart plot'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Chart height',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'svgh',\n\t\t\t\t\t\t\ttitle: 'The internal height of the chart plot'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: '95% Confidence Interval',\n\t\t\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'ciVisible',\n\t\t\t\t\t\t\ttitle: 'Display the 95% confidence interval'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Censored Symbol',\n\t\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'symbol',\n\t\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t\t{ label: 'Tick', value: 'vtick' },\n\t\t\t\t\t\t\t\t{ label: 'X', value: 'x' }\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\ttitle: 'Symbol for displaying censored samples'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Survival Time Visualized',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'maxTimeToEvent',\n\t\t\t\t\t\t\ttitle:\n\t\t\t\t\t\t\t\t'The maximum time-to-event to be displayed in the survival plot, affects only the visual representation and does not impact other analyses. All available data is still used to compute p-values. If this value is left empty or set to 0, no cutoff will be applied.'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Time Unit',\n\t\t\t\t\t\t\ttype: 'radio',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'timeUnit',\n\t\t\t\t\t\t\toptions: [\n\t\t\t\t\t\t\t\t{ label: 'years', value: 'years' },\n\t\t\t\t\t\t\t\t{ label: 'months', value: 'months' },\n\t\t\t\t\t\t\t\t{ label: 'weeks', value: 'weeks' },\n\t\t\t\t\t\t\t\t{ label: 'days', value: 'days' }\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\ttitle: `The unit to display in the x-axis title, like 'years'`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'X-axis ticks',\n\t\t\t\t\t\t\ttype: 'text',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'xTickValues',\n\t\t\t\t\t\t\ttitle: `Option to customize the x-axis tick values, enter as comma-separated values. Will be ignored if empty`,\n\t\t\t\t\t\t\tprocessInput: value => (value ? value.split(',').map(Number) : [])\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'At-risk counts',\n\t\t\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'atRiskVisible',\n\t\t\t\t\t\t\ttitle: 'Display the at-risk counts'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t//{label: 'At-risk label offset', type: 'numeric', chartType: 'survival', settingsKey: 'atRiskLabelOffset'},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Default color',\n\t\t\t\t\t\t\ttype: 'color',\n\t\t\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\t\t\tsettingsKey: 'defaultColor',\n\t\t\t\t\t\t\ttitle: 'Default plot color'\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t\tthis.components.controls.on('downloadClick.survival', this.download)\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\n\t\treturn {\n\t\t\tisVisible: config.term.term.type == 'survival' || config.term2?.term.type == 'survival',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\ttermfilter,\n\n\t\t\tconfig: {\n\t\t\t\t// NOTE: will create mutable copies of tw terms in async main() below\n\t\t\t\tterm: config.term,\n\t\t\t\tterm0: config.term0 || null,\n\t\t\t\tterm2: config.term2 || null,\n\t\t\t\tcontrolLabels: config.controlLabels,\n\t\t\t\tsettings: config.settings.survival\n\t\t\t},\n\t\t\ttermdbConfig: appState.termdbConfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tif (!this.state.isVisible) {\n\t\t\tthis.dom.holder.style('display', 'none')\n\t\t\treturn\n\t\t}\n\n\t\tthis.state.config = await this.getMutableConfig()\n\t\tthis.maySetSandboxHeader()\n\t\tthis.toggleLoadingDiv()\n\n\t\tObject.assign(this.settings, this.state.config.settings)\n\t\tthis.settings.defaultHidden = this.getDefaultHidden()\n\t\tthis.settings.hidden = this.settings.customHidden || this.settings.defaultHidden\n\t\tthis.settings.xTitleLabel = this.getXtitleLabel()\n\t\tconst reqOpts = this.getDataRequestOpts()\n\t\tlet data\n\t\ttry {\n\t\t\t// do not directly set this.serverData to response, since it could be an error\n\t\t\tdata = await this.app.vocabApi.getNestedChartSeriesData(reqOpts, this.api?.getAbortSignal())\n\t\t} catch (e) {\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthrow e\n\t\t}\n\t\tthis.serverData = data\n\t\tthis.toggleLoadingDiv('none')\n\t\tthis.app.vocabApi.syncTermData(this.state.config, data)\n\t\tthis.currData = this.processData(data)\n\t\tthis.refs = data.refs\n\t\tthis.pj.refresh({ data: this.currData })\n\t\tthis.setTerm2Color(this.pj.tree.charts)\n\t\tthis.symbol = this.getSymbol(7) // hardcode the symbol size for now\n\t\tthis.render()\n\t}\n\n\tmaySetSandboxHeader() {\n\t\tif (!this.dom.header) return\n\t\tconst { term, term2 } = this.state.config\n\t\tconst mainTerm = term.term.name\n\t\tif (term2?.type) {\n\t\t\tthis.dom.header.html(`${term2.getTitleText?.() || term2.term.name}  vs ${mainTerm}`)\n\t\t} else {\n\t\t\tthis.dom.header.html(`${mainTerm} plot`)\n\t\t}\n\t}\n\n\t// creates an opts object for the vocabApi.getNestedChartsData()\n\tgetDataRequestOpts() {\n\t\tconst c = this.state.config\n\t\tconst opts: any = {\n\t\t\tchartType: 'survival',\n\t\t\tterm: c.term,\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0: this.state.termfilter.filter0\n\t\t}\n\t\tif (c.term2) {\n\t\t\topts.term2 = c.term2\n\t\t}\n\t\tif (c.term0) opts.term0 = c.term0\n\t\treturn opts\n\t}\n\n\tgetDefaultHidden() {\n\t\tconst hidden: any[] = []\n\t\tconst term2 = this.state.config.term2\n\t\tif (!term2) return hidden\n\t\tconst hiddenValues = term2.q.hiddenValues\n\t\tif (hiddenValues && Object.keys(hiddenValues).length) {\n\t\t\t// term2 has default hidden values\n\t\t\tfor (const k in hiddenValues) {\n\t\t\t\thidden.push(term2.term.values[k].label)\n\t\t\t}\n\t\t}\n\t\treturn hidden\n\t}\n\n\tgetXtitleLabel() {\n\t\tconst termNum = this.state.config.term.term.type == 'survival' ? 'term' : 'term2'\n\t\tconst xUnit = this.settings.timeUnit ? this.settings.timeUnit : this.state.config[termNum].term.unit\n\t\tconst xTitleLabel = `Time to Event (${xUnit})`\n\t\treturn xTitleLabel\n\t}\n\n\tprocessData(data) {\n\t\tthis.uniqueSeriesIds = new Set()\n\t\tconst rows: any[] = []\n\t\tconst estKeys = ['survival', 'lower', 'upper']\n\t\tfor (const d of data.case) {\n\t\t\tconst obj: { [name: string]: any } = {}\n\t\t\tdata.keys.forEach((k, i) => {\n\t\t\t\tobj[k] = estKeys.includes(k) ? Number(d[i]) : d[i]\n\t\t\t})\n\t\t\tobj.time = obj.time * this.getTimeFactor()\n\t\t\trows.push(obj)\n\t\t\tthis.uniqueSeriesIds.add(obj.seriesId)\n\t\t}\n\n\t\t// process statistical tests\n\t\tthis.tests = {}\n\t\tif (data.tests) {\n\t\t\tfor (const chartId in data.tests) {\n\t\t\t\tconst chartTests = data.tests[chartId]\n\t\t\t\tthis.tests[chartId] = []\n\t\t\t\tfor (const test of chartTests) {\n\t\t\t\t\tif (this.settings.hidden.includes(test.series1) || this.settings.hidden.includes(test.series2)) continue // hide tests that contain hidden series\n\t\t\t\t\tthis.tests[chartId].push({\n\t\t\t\t\t\tpvalue: { id: 'pvalue', text: test.pvalue },\n\t\t\t\t\t\tseries1: { id: test.series1 },\n\t\t\t\t\t\tseries2: { id: test.series2 }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tif (!this.tests[chartId].length) delete this.tests[chartId]\n\t\t\t}\n\t\t}\n\n\t\treturn rows\n\t}\n\n\t// time factor that converts survival data from default time unit to the current time unit.\n\tgetTimeFactor() {\n\t\tconst numUnitInOneYear = this.settings.numUnitInOneYear || 1\n\t\tconst timeUnit = this.settings.timeUnit || 'years'\n\t\tswitch (timeUnit) {\n\t\t\tcase 'years':\n\t\t\t\treturn (1 / numUnitInOneYear) * 1\n\t\t\tcase 'months':\n\t\t\t\treturn (1 / numUnitInOneYear) * 12\n\t\t\tcase 'weeks':\n\t\t\t\treturn (1 / numUnitInOneYear) * 52\n\t\t\tcase 'days':\n\t\t\t\treturn (1 / numUnitInOneYear) * 365.25\n\t\t\tdefault:\n\t\t\t\tthrow 'unknown time Unit for survival data'\n\t\t}\n\t}\n\n\tsetTerm2Color(charts) {\n\t\tif (!charts) return\n\t\tconst config = this.state.config\n\t\t// color override via legend clicks is saved in term2.values, not by directly editing term2.term.values\n\t\tconst t2values = copyMerge({}, config.term2?.term?.values || {}, config.term2?.values || {})\n\t\tconst values = (this.refs.bins[2] && [this.refs.bins[2]]) || Object.values(t2values)\n\t\tlet t2groups\n\t\tif (config.term2?.q.type == 'predefined-groupset' || config.term2?.q.type == 'custom-groupset') {\n\t\t\tconst groupset =\n\t\t\t\tconfig.term2.q.type == 'predefined-groupset'\n\t\t\t\t\t? config.term2.term.groupsetting.lst[config.term2.q.predefined_groupset_idx]\n\t\t\t\t\t: config.term2.q.customset\n\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\tt2groups = groupset.groups\n\t\t}\n\t\tthis.term2toColor = {}\n\t\tthis.colorScale = this.uniqueSeriesIds.size < 11 ? scaleOrdinal(schemeCategory10) : scaleOrdinal(schemeCategory20)\n\t\tconst legendItems: any[] = []\n\t\tfor (const chart of charts) {\n\t\t\tfor (const series of chart.serieses) {\n\t\t\t\tlet color\n\t\t\t\t// color override via legend clicks is saved in t2values, does not edit term.values or group.color directly\n\t\t\t\tconst v = values.find(\n\t\t\t\t\tv =>\n\t\t\t\t\t\tv.seriesId === series.seriesId ||\n\t\t\t\t\t\tv.key === series.seriesId ||\n\t\t\t\t\t\tv.name === series.seriesId ||\n\t\t\t\t\t\tv.label === series.seriesId\n\t\t\t\t)\n\t\t\t\tcolor = v?.color\n\t\t\t\tif (!color && t2groups?.length) {\n\t\t\t\t\tconst group = t2groups.find(g => g.name == series.seriesId)\n\t\t\t\t\tcolor = group?.color\n\t\t\t\t\t// quick fix to make WT gray darker to pass Section 508 contrast requirement;\n\t\t\t\t\t// doing this in common.js makes this gray in all tools darker and conflicts\n\t\t\t\t\t// with other mclass colors like in-frame insertion, also visually overwhelming\n\t\t\t\t\t// in GDC oncomatrix\n\t\t\t\t\tif (color === '#D3D3D3' && group?.filter?.lst?.find(f => f?.type === 'tvs' && f.tvs.genotype == 'wt'))\n\t\t\t\t\t\tcolor = 'rgb(105,105,105)'\n\t\t\t\t}\n\t\t\t\tconst orig = color || (series.seriesId == '' ? this.settings.defaultColor : this.colorScale(series.seriesId))\n\t\t\t\tconst _rgb = rgb(orig)\n\t\t\t\tconst adjusted = _rgb.toString()\n\t\t\t\tconst c = { orig, rgb: _rgb, adjusted, hex: rgb2hex(adjusted) }\n\t\t\t\tthis.term2toColor[series.seriesId] = c\n\n\t\t\t\tif (!legendItems.find(d => d.seriesId == series.seriesId)) {\n\t\t\t\t\tlegendItems.push({\n\t\t\t\t\t\tkey: series.seriesId,\n\t\t\t\t\t\tseriesId: series.seriesId,\n\t\t\t\t\t\ttext: series.seriesLabel,\n\t\t\t\t\t\tcolor: this.term2toColor[series.seriesId].adjusted,\n\t\t\t\t\t\tisHidden: this.settings.hidden.includes(series.seriesId)\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (this.refs.orderedKeys) {\n\t\t\tconst s = this.refs.orderedKeys.series\n\t\t\tlegendItems.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId))\n\t\t}\n\n\t\tif (!this.legendOrder.length) {\n\t\t\tthis.legendOrder = legendItems.map(item => item.seriesId)\n\t\t} else {\n\t\t\tlegendItems.sort((a, b) => this.legendOrder.indexOf(a.seriesId) - this.legendOrder.indexOf(b.seriesId))\n\t\t}\n\n\t\tif ((config.term.term.type == 'survival' || config.term2) && legendItems.length) {\n\t\t\tconst termNum = config.term.term.type == 'survival' && config.term2 ? 'term2' : 'term'\n\t\t\tthis.legendData = [\n\t\t\t\t{\n\t\t\t\t\tname: config[termNum].term.name,\n\t\t\t\t\titems: legendItems.filter(s => !s.isHidden)\n\t\t\t\t}\n\t\t\t]\n\n\t\t\tthis.hiddenData = [\n\t\t\t\t{\n\t\t\t\t\tname: `<span style='color:#aaa; font-weight:400'><span>Hidden categories</span><span style='font-size:0.8rem'> CLICK TO SHOW</span></span>`,\n\t\t\t\t\titems: legendItems.filter(s => s.isHidden).map(item => Object.assign({}, item, { isHidden: false }))\n\t\t\t\t}\n\t\t\t]\n\t\t} else {\n\t\t\tthis.legendData = []\n\t\t}\n\t\tfor (const chartId in this.tests) {\n\t\t\tconst chartTests = this.tests[chartId]\n\t\t\tfor (const test of chartTests) {\n\t\t\t\tfor (const key in test) {\n\t\t\t\t\tif (key == 'pvalue') {\n\t\t\t\t\t\t// p-value of test\n\t\t\t\t\t\ttest[key].color = '#000'\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// series of test\n\t\t\t\t\t\tconst item = legendItems.find(item => item.seriesId == test[key].id)\n\t\t\t\t\t\ttest[key].color = item.color\n\t\t\t\t\t\ttest[key].text = item.text\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// helper so that 'Loading...' does not flash when not needed\n\ttoggleLoadingDiv(display = '') {\n\t\tif (display != 'none') {\n\t\t\tthis.dom.loadingDiv\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.style('display', display)\n\t\t\t\t.transition()\n\t\t\t\t.duration('loadingWait' in this ? this.loadingWait : 0)\n\t\t\t\t.style('opacity', 1)\n\t\t} else {\n\t\t\tthis.dom.loadingDiv.style('display', display)\n\t\t}\n\t\t// do not transition on initial chart load\n\t\tthis.loadingWait = 1000\n\t}\n}\n\nexport const survivalInit = getCompInit(TdbSurvival)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = survivalInit\n\nfunction setRenderers(self) {\n\tself.render = function () {\n\t\tconst data = self.pj.tree.charts || [{ chartId: 'No survival data' }]\n\t\tconst chartDivs = self.dom.chartsDiv.selectAll('.pp-survival-chart').data(data, d => d.chartId)\n\t\tchartDivs.exit().remove()\n\t\tchartDivs.each(self.updateCharts)\n\t\tchartDivs.enter().each(self.addCharts)\n\n\t\tself.dom.holder.style('display', 'inline-block')\n\t\tself.dom.chartsDiv.on('mouseover', self.mouseover).on('mouseout', self.mouseout)\n\n\t\tself.legendRenderer(self.settings.atRiskVisible ? [] : self.legendData)\n\t\tif (!self.hiddenData?.[0]?.items.length) self.dom.hiddenDiv.style('display', 'none')\n\t\telse {\n\t\t\tself.dom.hiddenDiv.style('display', '')\n\t\t\tself.hiddenRenderer(self.hiddenData)\n\t\t}\n\t}\n\n\tconst updateHiddenPvalues = hiddenPvalues => {\n\t\tself.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tsurvival: {\n\t\t\t\t\t\thiddenPvalues\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tconst setActiveMenu = bool => (self.activeMenu = bool)\n\n\tself.addCharts = function (chart) {\n\t\tconst s = self.settings\n\t\tsetVisibleSerieses(chart, s)\n\n\t\tconst div = select(this)\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-survival-chart')\n\t\t\t.style('opacity', chart.serieses ? 0 : 1) // if the data can be plotted, slowly reveal plot\n\t\t\t.style('width', 'fit-content')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin', s.chartMargin + 'px')\n\t\t\t.style('padding', '10px')\n\t\t\t.style('top', 0)\n\t\t\t.style('left', 0)\n\t\t\t.style('text-align', 'left')\n\t\t\t.style('vertical-align', 'top')\n\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('width', s.svgw + 50 + 'px')\n\t\t\t.style('height', s.chartTitleDivHt + 'px')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('font-weight', '600')\n\t\t\t.style('margin', '5px')\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-survival-title')\n\t\t\t.attr('data-testid', 'sjpp-survival-plotTitle')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('width', 'fit-content')\n\t\t\t.datum(chart)\n\t\t\t.html(chart => chart.chartId)\n\n\t\tif (chart.serieses) {\n\t\t\tconst svg = div.append('svg').attr('class', 'pp-survival-svg')\n\t\t\trenderSVG(svg, chart, s, 0)\n\n\t\t\tdiv.transition().duration(s.duration).style('opacity', 1)\n\n\t\t\t// div for chart-specific legends\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'pp-survival-chartLegends')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('margin', '10px 10px 10px 10px')\n\t\t\t\t.style('display', 'none')\n\n\t\t\t// p-values legend\n\t\t\tif (self.tests && chart.rawChartId in self.tests) {\n\t\t\t\tconst holder = div.select('.pp-survival-chartLegends').style('display', 'inline-block').append('div')\n\t\t\t\trenderPvalues({\n\t\t\t\t\ttitle: 'Group comparisons (log-rank test)',\n\t\t\t\t\tholder,\n\t\t\t\t\tplot: 'survival',\n\t\t\t\t\ttests: self.tests[chart.rawChartId],\n\t\t\t\t\ts,\n\t\t\t\t\tbins: self.refs.bins,\n\t\t\t\t\ttip: self.app.tip,\n\t\t\t\t\tsetActiveMenu,\n\t\t\t\t\tupdateHiddenPvalues\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\tfunction setVisibleSerieses(chart, s) {\n\t\tchart.visibleSerieses = chart.serieses?.filter(series => !s.hidden.includes(series.seriesId)) || []\n\t\tconst maxSeriesLabelLen = chart.visibleSerieses.reduce(\n\t\t\t(maxlen, a) => (a.seriesLabel && a.seriesLabel.length > maxlen ? a.seriesLabel.length : maxlen),\n\t\t\t0\n\t\t)\n\t\tchart.atRiskLabelWidth = s.atRiskVisible\n\t\t\t? maxSeriesLabelLen * (s.axisTitleFontSize - 2) * 0.4 + s.atRiskLabelOffset\n\t\t\t: 0\n\t}\n\n\tself.updateCharts = function (chart) {\n\t\tif (!chart.serieses) return\n\t\tconst s = self.settings\n\t\tsetVisibleSerieses(chart, s)\n\n\t\tconst div = select(this)\n\t\tdiv.transition().duration(s.duration).style('width', 'fit-content')\n\n\t\tdiv\n\t\t\t.select('.sjpp-survival-title')\n\t\t\t.style('width', s.svgw + 50)\n\t\t\t.style('height', s.chartTitleDivHt + 'px')\n\t\t\t.datum(chart.chartId)\n\t\t\t.html(chart.chartId)\n\n\t\tdiv.selectAll('.sjpp-lock-icon').style('display', s.scale == 'byChart' ? 'block' : 'none')\n\n\t\tdiv.selectAll('.sjpp-unlock-icon').style('display', s.scale == 'byChart' ? 'none' : 'block')\n\n\t\trenderSVG(div.select('svg'), chart, s, s.duration)\n\n\t\t// div for chart-specific legends\n\t\tdiv.select('.pp-survival-chartLegends').selectAll('*').remove()\n\n\t\t// p-values legend\n\t\tif (self.tests && chart.rawChartId in self.tests) {\n\t\t\tconst holder = div.select('.pp-survival-chartLegends').style('display', 'inline-block').append('div')\n\t\t\trenderPvalues({\n\t\t\t\ttitle: 'Group comparisons (log-rank test)',\n\t\t\t\tholder,\n\t\t\t\tplot: 'survival',\n\t\t\t\ttests: self.tests[chart.rawChartId],\n\t\t\t\ts,\n\t\t\t\tbins: self.refs.bins,\n\t\t\t\ttip: self.app.tip,\n\t\t\t\tsetActiveMenu,\n\t\t\t\tupdateHiddenPvalues\n\t\t\t})\n\t\t}\n\t}\n\n\tfunction renderSVG(svg, chart, s, duration) {\n\t\tchart.svg = svg\n\t\tconst extraHeight = s.atRiskVisible\n\t\t\t? s.axisTitleFontSize + 4 + chart.visibleSerieses.length * 2 * (s.axisTitleFontSize + 4)\n\t\t\t: 0\n\n\t\tsvg\n\t\t\t.transition()\n\t\t\t.duration(duration)\n\t\t\t.attr('width', s.svgw + chart.atRiskLabelWidth)\n\t\t\t.attr('height', s.svgh + extraHeight)\n\t\t\t.style('overflow', 'visible')\n\t\t\t.style('padding-left', '5px')\n\n\t\t/* eslint-disable */\n\t\tconst [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect] = getSvgSubElems(svg)\n\t\t/* eslint-enable */\n\t\tconst xOffset = chart.atRiskLabelWidth + s.svgPadding.left + 10 //adding 10 avoids clipping of the svg when downloading\n\t\tmainG.attr('transform', 'translate(' + xOffset + ',' + s.svgPadding.top + ')')\n\n\t\tconst serieses = seriesesG\n\t\t\t.selectAll('.sjpp-survival-series')\n\t\t\t.data(chart.visibleSerieses, d => (d && d[0] ? d[0].seriesId : ''))\n\n\t\tserieses.exit().remove()\n\t\tserieses.each(function (this: HTMLElement, series, i) {\n\t\t\trenderSeries(select(this), chart, series, i, s)\n\t\t})\n\t\tserieses\n\t\t\t.enter()\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-survival-series')\n\t\t\t.each(function (this: HTMLElement, series, i) {\n\t\t\t\trenderSeries(select(this), chart, series, i, s)\n\t\t\t})\n\n\t\trenderAxes(xAxis, xTitle, yAxis, yTitle, s, chart)\n\t\trenderAtRiskG({\n\t\t\tg: atRiskG,\n\t\t\ts,\n\t\t\tchart,\n\t\t\torder: self.legendOrder,\n\t\t\tterm2toColor: self.term2toColor,\n\t\t\tonSerieClick: self.legendClick\n\t\t})\n\n\t\tplotRect\n\t\t\t.attr('x', 0) //s.svgPadding.left) //s.svgh - s.svgPadding.top - s.svgPadding.bottom + 5)\n\t\t\t.attr('width', s.svgw - s.svgPadding.left - s.svgPadding.right)\n\t\t\t.attr('y', 0) //s.svgPadding.top) // - s.svgPadding.bottom + 5)\n\t\t\t.attr('height', s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset)\n\n\t\tsvg.seriesTip.update({\n\t\t\txScale: chart.xScale,\n\t\t\txTitleLabel: s.xTitleLabel,\n\t\t\tdecimals: s.seriesTipDecimals,\n\t\t\tserieses: chart.visibleSerieses.map(s => {\n\t\t\t\tconst seriesLabel = `${s.seriesLabel || 'Probability'}:`\n\t\t\t\tconst color = self.term2toColor[s.seriesId].adjusted || '#000'\n\t\t\t\treturn {\n\t\t\t\t\tdata: s.data.map(d => {\n\t\t\t\t\t\treturn {\n\t\t\t\t\t\t\tx: d.x,\n\t\t\t\t\t\t\thtml:\n\t\t\t\t\t\t\t\t`<span style='color: ${color}'>` +\n\t\t\t\t\t\t\t\t`${seriesLabel} ${(100 * d.y).toFixed(2)}% (${(100 * d.lower).toFixed(2)} - ${(100 * d.upper).toFixed(\n\t\t\t\t\t\t\t\t\t2\n\t\t\t\t\t\t\t\t)})` +\n\t\t\t\t\t\t\t\t`</span>`\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\t}\n\n\tfunction getSvgSubElems(svg) {\n\t\tlet mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, line\n\t\tif (!svg.select('.sjpp-survival-mainG').size()) {\n\t\t\tmainG = svg.append('g').attr('class', 'sjpp-survival-mainG')\n\t\t\tseriesesG = mainG.append('g').attr('class', 'sjpcb-survival-seriesesG')\n\t\t\taxisG = mainG.append('g').attr('class', 'sjpp-survival-axis')\n\t\t\txAxis = axisG.append('g').attr('class', 'sjpp-survival-x-axis')\n\t\t\tyAxis = axisG.append('g').attr('class', 'sjpp-survival-y-axis')\n\t\t\txTitle = axisG.append('g').attr('class', 'sjpp-survival-x-title')\n\t\t\tyTitle = axisG.append('g').attr('class', 'sjpp-survival-y-title')\n\t\t\tatRiskG = mainG.append('g').attr('class', 'sjpp-survival-atrisk')\n\t\t\tline = mainG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', 'sjpcb-plot-tip-line')\n\t\t\t\t.attr('stroke', '#000')\n\t\t\t\t.attr('stroke-width', '1px')\n\t\t\tplotRect = mainG.append('rect').attr('class', 'sjpcb-plot-tip-rect').style('fill', 'transparent')\n\t\t} else {\n\t\t\tmainG = svg.select('.sjpp-survival-mainG')\n\t\t\tseriesesG = mainG.select('.sjpcb-survival-seriesesG')\n\t\t\taxisG = mainG.select('.sjpp-survival-axis')\n\t\t\txAxis = axisG.select('.sjpp-survival-x-axis')\n\t\t\tyAxis = axisG.select('.sjpp-survival-y-axis')\n\t\t\txTitle = axisG.select('.sjpp-survival-x-title')\n\t\t\tyTitle = axisG.select('.sjpp-survival-y-title')\n\t\t\tatRiskG = mainG.select('.sjpp-survival-atrisk')\n\t\t\tplotRect = mainG.select('.sjpcb-plot-tip-rect')\n\t\t\tline = mainG.select('.sjpcb-plot-tip-line')\n\t\t}\n\n\t\tif (!svg.seriesTip) {\n\t\t\tsvg.seriesTip = getSeriesTip(line, plotRect, self.dom.tip)\n\t\t}\n\n\t\treturn [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect]\n\t}\n\n\tfunction renderSeries(g, chart, series, i, s) {\n\t\t// do not show samples with time to event larger than maxTimeToEvent\n\t\tlet processedData = series.data\n\t\tif (s.maxTimeToEvent) {\n\t\t\tprocessedData = series.data.filter(d => d.x <= s.maxTimeToEvent)\n\t\t}\n\t\t// todo: allow update of exiting path instead of replacing\n\t\tg.selectAll('path').remove()\n\t\tg.append('path')\n\t\t\t.attr(\n\t\t\t\t'd',\n\t\t\t\tarea()\n\t\t\t\t\t.curve(curveStepAfter)\n\t\t\t\t\t.x(c => (c as any).scaledX)\n\t\t\t\t\t.y0(c => (c as any).scaledY[1])\n\t\t\t\t\t.y1(c => (c as any).scaledY[2])(processedData)\n\t\t\t)\n\t\t\t.style('display', s.ciVisible ? '' : 'none')\n\t\t\t.style('fill', self.term2toColor[series.seriesId].adjusted)\n\t\t\t.style('opacity', '0.15')\n\t\t\t.style('stroke', 'none')\n\n\t\trenderSubseries(\n\t\t\ts,\n\t\t\tg,\n\t\t\tprocessedData.map(d => {\n\t\t\t\treturn {\n\t\t\t\t\tseriesId: d.seriesId,\n\t\t\t\t\tx: d.x,\n\t\t\t\t\ty: d.y,\n\t\t\t\t\tscaledX: d.scaledX,\n\t\t\t\t\tscaledY: d.scaledY[0],\n\t\t\t\t\tseriesName: 'survival',\n\t\t\t\t\tseriesLabel: series.seriesLabel,\n\t\t\t\t\tnevent: d.nevent,\n\t\t\t\t\tncensor: d.ncensor,\n\t\t\t\t\tnrisk: d.nrisk\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\n\t\trenderSubseries(\n\t\t\ts,\n\t\t\tg.append('g'),\n\t\t\tprocessedData.map(d => {\n\t\t\t\treturn {\n\t\t\t\t\tseriesId: d.seriesId,\n\t\t\t\t\tx: d.x,\n\t\t\t\t\ty: d.lower,\n\t\t\t\t\tscaledX: d.scaledX,\n\t\t\t\t\tscaledY: d.scaledY[1],\n\t\t\t\t\tseriesName: 'lower',\n\t\t\t\t\tseriesLabel: series.seriesLabel,\n\t\t\t\t\tnevent: d.nevent,\n\t\t\t\t\tncensor: 0, // no censor marks for lower CI\n\t\t\t\t\tnrisk: d.nrisk\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\n\t\trenderSubseries(\n\t\t\ts,\n\t\t\tg.append('g'),\n\t\t\tprocessedData.map(d => {\n\t\t\t\treturn {\n\t\t\t\t\tseriesId: d.seriesId,\n\t\t\t\t\tx: d.x,\n\t\t\t\t\ty: d.upper,\n\t\t\t\t\tscaledX: d.scaledX,\n\t\t\t\t\tscaledY: d.scaledY[2],\n\t\t\t\t\tseriesName: 'upper', // no censor marks for upper CI\n\t\t\t\t\tseriesLabel: series.seriesLabel,\n\t\t\t\t\tnevent: d.nevent,\n\t\t\t\t\tncensor: 0,\n\t\t\t\t\tnrisk: d.nrisk\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\t}\n\n\tfunction renderSubseries(s, g, data) {\n\t\t// todo: allow update of exiting g's instead of replacing\n\t\tg.selectAll('g').remove()\n\n\t\tconst lineData = data.filter((d, i) => i === 0 || d.nevent || i === data.length - 1)\n\t\tconst censoredData = data.filter(d => d.ncensor)\n\n\t\tconst seriesName = data[0].seriesName\n\t\tconst color = self.term2toColor[data[0].seriesId].adjusted\n\t\tif (seriesName == 'survival') {\n\t\t\tg.append('path')\n\t\t\t\t.attr('d', self.lineFxn(lineData))\n\t\t\t\t.style('fill', 'none')\n\t\t\t\t.style('stroke', color)\n\t\t\t\t.style('opacity', 1)\n\t\t\t\t.style('stroke-opacity', 1)\n\t\t}\n\n\t\tconst subg1 = g.append('g').attr('class', 'sjpp-survival-censored')\n\t\tconst censored = subg1.selectAll('.sjpp-survival-censored-x').data(censoredData, d => d.x)\n\n\t\tcensored.exit().remove()\n\n\t\tcensored\n\t\t\t.attr('transform', c => `translate(${c.scaledX},${c.scaledY})`)\n\t\t\t.style('stroke', color)\n\t\t\t.style('display', '')\n\n\t\tcensored\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('class', 'sjpp-survival-censored-x')\n\t\t\t.attr('transform', c => `translate(${c.scaledX},${c.scaledY})`)\n\t\t\t.attr('d', self.symbol)\n\t\t\t.style('fill', 'transparent')\n\t\t\t.style('fill-opacity', s.fillOpacity)\n\t\t\t.style('stroke', color)\n\t\t\t.style('display', '')\n\t}\n\n\tfunction renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart) {\n\t\tlet xTicks\n\t\tif (s.xTickValues?.length) {\n\t\t\t// xTicksValues should not be larger than maxTimeToEvent\n\t\t\tchart.xTickValues = s.xTickValues.filter(\n\t\t\t\tv => v === 0 || (v >= chart.xMin && v <= Math.min(s.maxTimeToEvent || chart.xMax, chart.xMax))\n\t\t\t)\n\t\t\txTicks = axisBottom(chart.xScale).tickValues(chart.xTickValues)\n\t\t} else {\n\t\t\tchart.xTickValues = []\n\t\t\txTicks = axisBottom(chart.xScale)\n\t\t\t\t.ticks(4)\n\t\t\t\t.tickFormat((xval: any) => {\n\t\t\t\t\tchart.xTickValues.push(xval)\n\t\t\t\t\treturn xval\n\t\t\t\t})\n\t\t}\n\n\t\t// without this pixel offset, the axes and data are slightly misaligned\n\t\t// this could be because the axes have a 0.5 offset in their path,\n\t\t// for example: <path class=\"domain\" stroke=\"#000\" d=\"M0.5,6V0.5H325.5V6\"></path>\n\t\tconst pixelOffset = -0.5\n\n\t\txAxis\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t`translate(${pixelOffset}, ${s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset + pixelOffset})`\n\t\t\t)\n\t\t\t.call(xTicks)\n\n\t\tyAxis\n\t\t\t.attr('transform', `translate(${s.yAxisOffset + pixelOffset}, ${pixelOffset})`)\n\t\t\t.call(axisLeft(scaleLinear().domain(chart.yScale.domain()).range(chart.yScale.range())).ticks(5))\n\n\t\txTitle.select('text, title').remove()\n\t\txTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.axisTitleFontSize - 4) +\n\t\t\t\t\t')'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(s.xTitleLabel)\n\n\t\tconst yTitleLabel = 'Probability of Survival'\n\t\tyTitle.select('text, title').remove()\n\t\tyTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(-s.svgPadding.left / 2 - s.axisTitleFontSize) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 +\n\t\t\t\t\t')rotate(-90)'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(yTitleLabel)\n\t}\n\n\tself.getSymbol = function (size) {\n\t\tconst s = size,\n\t\t\th = s / 2\n\n\t\tswitch (self.settings.symbol) {\n\t\t\tcase 'x':\n\t\t\t\treturn `M -${h},-${h} l ${s},${s} M ${h},-${h} l -${s},${s}`\n\n\t\t\tcase 'vtick':\n\t\t\t\treturn `M 0,-${h} L 0,${h}`\n\n\t\t\tdefault:\n\t\t\t\tthrow `Unrecognized survival plot symbol='${self.settings.symbol}'`\n\t\t}\n\t}\n}\n\nfunction setInteractivity(self) {\n\tself.download = function (event) {\n\t\tconst charts = self.getChartImages()\n\t\tconst menu = new DownloadMenu(charts, self.state.config.term.term.name)\n\t\tmenu.show(event.clientX, event.clientY, event.target)\n\t}\n\n\tself.getChartImages = function () {\n\t\tconst charts: any[] = []\n\t\tif (!self.pj.tree.charts) return charts // no charts to download\n\t\tfor (const chart of self.pj.tree.charts) {\n\t\t\tcharts.push({ name: chart.chartId, svg: chart.svg })\n\t\t}\n\t\treturn charts\n\t}\n\n\t// The logic is replaced by the downloadMenu SVG option\n\t// self.download = function () {\n\t// \tif (!self.state) return\n\t// \tdownloadChart(\n\t// \t\tself.dom.chartsDiv.selectAll('.sjpp-survival-mainG'),\n\t// \t\t'Survival_Plot',\n\t// \t\tself.dom.chartsDiv.select('.pp-survival-chart').node()\n\t// \t)\n\t// }\n\n\tself.mouseover = function () {}\n\n\tself.mouseout = function () {\n\t\tif (self.activeMenu) return\n\t\tself.app.tip.hide()\n\t}\n\n\tself.legendClick = function (d, x, y) {\n\t\tif (d === undefined) return\n\t\tconst hidden = self.settings.hidden.slice()\n\t\tconst i = hidden.indexOf(d.seriesId)\n\t\tif (i == -1) {\n\t\t\thidden.push(d.seriesId)\n\t\t\tself.showLegendItemMenu(d, hidden, x, y)\n\t\t} else {\n\t\t\thidden.splice(i, 1)\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tsurvival: {\n\t\t\t\t\t\t\tcustomHidden: hidden\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tself.showLegendItemMenu = function (d, hidden, x, y) {\n\t\tconst term2 = self.state.config.term2?.term || null\n\t\tconst seriesLabel = term2?.values?.[d.seriesId]?.label || d.seriesId\n\n\t\tconst header = `<div style='padding-bottom:8px'><b>${seriesLabel}</b></div>`\n\t\tconst data = d.seriesId || d.seriesId === 0 ? d : { seriesId: d.id, dataId: d.dataId }\n\t\tif (!data.seriesId && !data.dataId) {\n\t\t\tif (!term2) {\n\t\t\t\tconst label = self.dom.legendTip.clear().d.append('div').html('Edit color: ')\n\t\t\t\tconst input = label\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.attr('value', self.settings.defaultColor)\n\t\t\t\t\t.on('change', () => self.adjustColor(input.property('value'), d))\n\t\t\t\tself.dom.legendTip.show(x, y)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\tconst options: any[] = []\n\t\toptions.push({\n\t\t\tlabel: 'Hide',\n\t\t\tcallback: () => {\n\t\t\t\tmenu.hide()\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tsurvival: {\n\t\t\t\t\t\t\t\tcustomHidden: hidden\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}\n\t\t})\n\n\t\tif (self.legendData[0]?.items.length > 1) {\n\t\t\toptions.push({\n\t\t\t\tlabel: 'Move&nbsp;',\n\t\t\t\tsetInput: holder => {\n\t\t\t\t\tconst legendIndex = self.legendOrder.indexOf(d.seriesId)\n\t\t\t\t\tif (legendIndex != 0)\n\t\t\t\t\t\tholder\n\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t.html('up')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t\t\tself.adjustLegendOrder(d, -1)\n\t\t\t\t\t\t\t})\n\t\t\t\t\tif (legendIndex < self.legendData[0]?.items.length - 1)\n\t\t\t\t\t\tholder\n\t\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t\t.html('down')\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t\t\t\tself.adjustLegendOrder(d, 1)\n\t\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\toptions.push({\n\t\t\t//label: 'Color',\n\t\t\t//callback: d => {}\n\t\t\tsetInput: holder => {\n\t\t\t\tconst label = holder.append('div')\n\t\t\t\tlabel.html('Edit color: ')\n\t\t\t\tconst input = label\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'color')\n\t\t\t\t\t.attr('value', self.term2toColor[d.seriesId].hex)\n\t\t\t\t\t.on('change', () => self.adjustColor(input.property('value'), d))\n\t\t\t}\n\t\t})\n\n\t\tif (!options.length) return\n\t\tconst menu = self.dom.legendTip.clear()\n\t\tmenu.d.append('div').html(header)\n\t\tmenu.d\n\t\t\t.append('div')\n\t\t\t.selectAll('div')\n\t\t\t.data(options)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', d => (d.label == 'Hide' ? 'sja_menuoption' : 'sja_menuoption_not_interactive'))\n\t\t\t.on('click', (event, c) => {\n\t\t\t\tif (c.setInput) return\n\t\t\t\tself.app.tip.hide()\n\t\t\t\tc.callback(d)\n\t\t\t})\n\n\t\t\t.each(function (this: HTMLElement, d) {\n\t\t\t\tconst div = select(this)\n\t\t\t\tif (d.label) div.append('div').style('display', 'inline-block').html(d.label)\n\t\t\t\tif (d.setInput)\n\t\t\t\t\td.setInput(\n\t\t\t\t\t\tdiv.append('div').style('display', 'inline-block')\n\t\t\t\t\t\t//.style('margin-left', '10px')\n\t\t\t\t\t)\n\t\t\t})\n\n\t\tmenu.show(x, y)\n\t}\n\n\tself.adjustLegendOrder = (d, increment) => {\n\t\tconst oldIndex = self.legendOrder.indexOf(d.seriesId)\n\t\tif (oldIndex == -1) return\n\t\tlet newIndex = oldIndex + increment\n\t\t// clamp to array bounds\n\t\tnewIndex = Math.max(0, Math.min(self.legendOrder.length - 1, newIndex))\n\t\t// remove item\n\t\tself.legendOrder.splice(oldIndex, 1)\n\t\t// insert at new index\n\t\tself.legendOrder.splice(newIndex, 0, d.seriesId)\n\t\tself.app.dispatch({\n\t\t\ttype: 'app_refresh'\n\t\t})\n\t\tself.app.tip.hide()\n\t}\n\n\tself.adjustColor = (value, d) => {\n\t\tconst color = rgb(value).formatHex()\n\t\tconst t2 = self.state.config.term2\n\t\tif (!t2) {\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: { settings: { survival: { defaultColor: color } } }\n\t\t\t})\n\t\t} else {\n\t\t\t// this is the overlay termwrapper\n\t\t\tconst term2 = structuredClone(t2)\n\t\t\t// do not replace term2.term.values directly, will set term2.values to use as overrides\n\t\t\tif (!term2.values) term2.values = {}\n\t\t\tconst values = term2.values\n\t\t\tif (!values[d.seriesId]) values[d.seriesId] = {}\n\t\t\tif (!('key' in values[d.seriesId])) values[d.seriesId].key = d.seriesId\n\t\t\tvalues[d.seriesId].color = color\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: self.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tterm2\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tself.app.tip.hide()\n\t}\n\n\t// disabled as a click handler for now, need to review\n\t// before completely removing this code\n\tself.showMenuForSelectedChart = function () {\n\t\tself.dom.tip.clear()\n\t\tself.activeMenu = true\n\t\tself.dom.tip\n\t\t\t.showunder(this)\n\t\t\t.d.append('button')\n\t\t\t.html('Download SVG')\n\t\t\t.on('click', () => {\n\t\t\t\tif (!self.state) return\n\t\t\t\tconst chartDiv = select(this.closest('.pp-survival-chart'))\n\t\t\t\tdownloadChart(\n\t\t\t\t\tchartDiv.select('.sjpp-survival-mainG'),\n\t\t\t\t\t'Survival_Plot',\n\t\t\t\t\tchartDiv.node() // use to get computed styles\n\t\t\t\t)\n\t\t\t})\n\t}\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'survival getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\t// supply t0_t2_defaultQ if opts.term0/2.bins/q is undefined\n\t\t// so that t0_t2_defaultQ does not override bins or q from user\n\t\tif (opts.term2)\n\t\t\tawait fillTermWrapper(opts.term2, app.vocabApi, opts.term2.bins || opts.term2.q ? undefined : t0_t2_defaultQ)\n\t\tif (opts.term0)\n\t\t\tawait fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? undefined : t0_t2_defaultQ)\n\t} catch (e) {\n\t\tthrow `${e} [survival getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\tsurvival: {\n\t\t\t\tradius: 5,\n\t\t\t\tciVisible: true,\n\t\t\t\tfill: '#fff',\n\t\t\t\tstroke: '#000',\n\t\t\t\tsymbol: 'vtick', // 'x', 'vtick'\n\t\t\t\tfillOpacity: 0,\n\t\t\t\tchartMargin: 10,\n\t\t\t\tsvgw: 400,\n\t\t\t\tsvgh: 300,\n\t\t\t\tnumUnitInOneYear: 1,\n\t\t\t\ttimeUnit: 'years',\n\t\t\t\tatRiskVisible: true,\n\t\t\t\tatRiskLabelOffset: -20,\n\t\t\t\txTickValues: [], // if undefined or empty, will be ignored\n\t\t\t\tseriesTipDecimals: 1,\n\t\t\t\tsvgPadding: {\n\t\t\t\t\ttop: 20,\n\t\t\t\t\tleft: 55,\n\t\t\t\t\tright: 20,\n\t\t\t\t\tbottom: 50\n\t\t\t\t},\n\t\t\t\taxisTitleFontSize: 16,\n\t\t\t\txAxisOffset: 5,\n\t\t\t\tyAxisOffset: -5,\n\t\t\t\thiddenPvalues: [],\n\t\t\t\tdefaultColor: '#2077b4'\n\t\t\t}\n\t\t}\n\t}\n\n\t// default survival settings will be overwritten by the survival settings defined in dataset\n\tconst overrides = app.vocabApi.termdbConfig.survival || {}\n\tcopyMerge(config.settings.survival, overrides.settings)\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\nfunction getPj(self) {\n\tconst pj = new Partjson({\n\t\ttemplate: {\n\t\t\tyMin: '>=yMin()',\n\t\t\tyMax: '<=yMax()',\n\t\t\tcharts: [\n\t\t\t\t{\n\t\t\t\t\tchartId: '@key',\n\t\t\t\t\trawChartId: '$chartId',\n\t\t\t\t\txMin: '>$time',\n\t\t\t\t\txMax: '<$time',\n\t\t\t\t\t'__:xScale': '=xScale()',\n\t\t\t\t\t'__:yScale': '=yScale()',\n\t\t\t\t\tyMin: '>=yMin()',\n\t\t\t\t\tyMax: '<=yMax()',\n\t\t\t\t\tserieses: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tchartId: '@parent.@parent.@key',\n\t\t\t\t\t\t\tseriesId: '@key',\n\t\t\t\t\t\t\t'__:seriesLabel': '=seriesLabel()',\n\t\t\t\t\t\t\tdata: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t'__:seriesId': '@parent.@parent.seriesId',\n\t\t\t\t\t\t\t\t\t//color: \"$color\",\n\t\t\t\t\t\t\t\t\tx: '$time',\n\t\t\t\t\t\t\t\t\ty: '$survival',\n\t\t\t\t\t\t\t\t\tlower: '$lower',\n\t\t\t\t\t\t\t\t\tupper: '$upper',\n\t\t\t\t\t\t\t\t\t'_1:scaledX': '=scaledX()',\n\t\t\t\t\t\t\t\t\t'_1:scaledY': '=scaledY()',\n\t\t\t\t\t\t\t\t\tnevent: '$nevent',\n\t\t\t\t\t\t\t\t\tncensor: '$ncensor',\n\t\t\t\t\t\t\t\t\tnrisk: '$nrisk'\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t'=timeCensored()'\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t},\n\t\t\t\t\t\t'$seriesId'\n\t\t\t\t\t],\n\t\t\t\t\t'@done()': '=sortSerieses()'\n\t\t\t\t},\n\t\t\t\t'=chartTitle()'\n\t\t\t],\n\t\t\t'@done()': '=sortCharts()'\n\t\t},\n\t\t'=': {\n\t\t\tchartTitle(row) {\n\t\t\t\tif (!row.chartId || row.chartId == '-') {\n\t\t\t\t\tconst termNum = self.state.config.term.term.type == 'survival' ? 'term' : 'term2'\n\t\t\t\t\treturn self.state.config[termNum].term.name\n\t\t\t\t}\n\t\t\t\tconst t0 = self.state.config.term0\n\t\t\t\tif (!t0 || !t0.term.values) return row.chartId\n\t\t\t\tif (t0.q?.type == 'predefined-groupset' || t0.q?.type == 'custom-groupset') return row.chartId\n\t\t\t\tconst value = self.state.config.term0.term.values[row.chartId]\n\t\t\t\treturn value && value.label ? value.label : row.chartId\n\t\t\t},\n\t\t\tseriesLabel(row, context) {\n\t\t\t\tconst t2 = self.state.config.term2\n\t\t\t\tif (!t2) return\n\t\t\t\tconst seriesId = context.self.seriesId\n\t\t\t\tif (t2?.q?.type == 'predefined-groupset' || t2?.q?.type == 'custom-groupset') return seriesId\n\t\t\t\tif (t2 && t2.term.values && seriesId in t2.term.values) return t2.term.values[seriesId].label\n\t\t\t\tif (isNumericTerm(t2.term)) {\n\t\t\t\t\t// numeric term\n\t\t\t\t\t// seriesId on its own (e.g. \"<5\") will be vague,\n\t\t\t\t\t// so include term name in series label\n\t\t\t\t\treturn t2.term.name + ' ' + seriesId\n\t\t\t\t}\n\t\t\t\treturn seriesId\n\t\t\t},\n\t\t\ttimeCensored(row) {\n\t\t\t\treturn row.time + '-' + row.ncensor\n\t\t\t},\n\t\t\ty(row, context) {\n\t\t\t\tconst seriesId = context.context.parent.seriesId\n\t\t\t\treturn seriesId == 'CI' ? [row.lower, row.upper] : row[seriesId]\n\t\t\t},\n\t\t\tyMin(row) {\n\t\t\t\treturn row.lower\n\t\t\t},\n\t\t\tyMax(row) {\n\t\t\t\treturn row.upper\n\t\t\t},\n\t\t\txScale(_, context) {\n\t\t\t\tconst s = self.settings\n\t\t\t\treturn (\n\t\t\t\t\tscaleLinear()\n\t\t\t\t\t\t// force x to start at 0 because first data point will always\n\t\t\t\t\t\t// be at x=0 (see survival.R)\n\t\t\t\t\t\t.domain([0, Math.min(s.maxTimeToEvent || context.self.xMax, context.self.xMax)])\n\t\t\t\t\t\t.range([0, s.svgw - s.svgPadding.left - s.svgPadding.right])\n\t\t\t\t)\n\t\t\t},\n\t\t\tscaledX(_, context) {\n\t\t\t\treturn context.context.context.context.parent.xScale(context.self.x)\n\t\t\t},\n\t\t\tscaledY(_, context) {\n\t\t\t\tconst yScale = context.context.context.context.parent.yScale\n\t\t\t\tconst s = context.self\n\t\t\t\treturn [yScale(s.y), yScale(s.lower), yScale(s.upper)]\n\t\t\t},\n\t\t\tyScale() {\n\t\t\t\tconst s = self.settings\n\t\t\t\tconst domain = [1.05, 0]\n\t\t\t\treturn scaleLinear()\n\t\t\t\t\t.domain(domain)\n\t\t\t\t\t.range([0, s.svgh - s.svgPadding.top - s.svgPadding.bottom])\n\t\t\t},\n\t\t\tsortSerieses(result) {\n\t\t\t\tfor (const series of result.serieses) {\n\t\t\t\t\tseries.data.sort((a, b) => (a.x < b.x ? -1 : 1))\n\t\t\t\t}\n\t\t\t\tif (self.refs.orderedKeys) {\n\t\t\t\t\tconst s = self.refs.orderedKeys.series\n\t\t\t\t\tresult.serieses.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId))\n\t\t\t\t}\n\t\t\t\tif (self.refs.bins) {\n\t\t\t\t\tconst labelOrder = self.refs.bins.map(b => b.label)\n\t\t\t\t\tresult.serieses.sort((a, b) => labelOrder.indexOf(a.seriesId) - labelOrder.indexOf(b.seriesId))\n\t\t\t\t}\n\t\t\t},\n\t\t\tsortCharts(result) {\n\t\t\t\tif (!self.refs.orderedKeys) return\n\t\t\t\tconst c = self.refs.orderedKeys.chart\n\t\t\t\tresult.charts.sort(\n\t\t\t\t\t(a, b) =>\n\t\t\t\t\t\t(c.indexOf(a.chartId) == -1 ? c.indexOf(a.rawChartId) : c.indexOf(a.chartId)) -\n\t\t\t\t\t\t(c.indexOf(b.chartId) == -1 ? c.indexOf(b.rawChartId) : c.indexOf(b.chartId))\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t})\n\n\treturn pj\n}\n"],
+  "mappings": 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+  "names": ["v", "item", "chart", "s", "d", "Partjson"]
+}

package/dist/chunk-YWBUK4B7.js

@@ -0,0 +1,291 @@
+import {
+  getSortOptions
+} from "./chunk-IABWKPRK.js";
+import {
+  defaultUiLabels,
+  fillTermWrapper
+} from "./chunk-2YC6ZVE4.js";
+import {
+  copyMerge
+} from "./chunk-MVTCBVSX.js";
+import {
+  isDictionaryType
+} from "./chunk-EGWVYY7K.js";
+import {
+  CNVClasses,
+  dtcnv,
+  mclass,
+  mutationClasses,
+  proteinChangingMutations,
+  synonymousMutations,
+  truncatingMutations
+} from "./chunk-AMYSEKPF.js";
+
+// plots/matrix/matrix.config.js
+async function getPlotConfig(opts = {}, app) {
+  const controlLabels = structuredClone(defaultUiLabels);
+  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
+  const config = {
+    // data configuration
+    termgroups: [],
+    samplegroups: [],
+    divideBy: null,
+    legendValueFilter: {
+      isAtomic: true,
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: []
+    },
+    legendGrpFilter: {
+      isAtomic: true,
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: []
+    },
+    filter: {
+      isAtomic: true,
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: []
+    },
+    // cnvCutoffs: {},
+    // rendering options
+    settings: {
+      matrix: {
+        svgCanvasSwitch: 1e3,
+        // the number of samples to trigger switching between svg and canvas
+        useMinPixelWidth: true,
+        // canvas may be hazy if false, but more accurately reflects column density
+        cellEncoding: "",
+        // can be "oncoprint" | "stacked" | "single"
+        margin: {
+          top: 10,
+          right: 5,
+          bottom: 20,
+          left: 50
+        },
+        // set any dataset-defined sample limits and sort priority, otherwise undefined
+        // put in settings, so that later may be overridden by a user
+        maxGenes: opts.settings?.maxGenes || 50,
+        maxSample: opts.settings?.maxSample || 1e3,
+        sampleNameFilter: "",
+        sortSamplesBy: "a",
+        sortPriority: void 0,
+        // will be filled-in
+        // sortByMutation: 'consequence', computed
+        // sortByCNV: true, computed
+        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
+        sortSampleGrpsBy: "name",
+        // 'hits' | 'name' | 'sampleCount'
+        sortSamplesTieBreakers: [{
+          $id: "sample",
+          sortSamples: {}
+          /*split: {char: '', index: 0}*/
+        }],
+        sortTermsBy: "sampleCount",
+        // or 'as listed'
+        // do not show number of samples at hiercluster gene row labels
+        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
+        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
+        geneVariantCountSamplesSkipMclass: [],
+        cellbg: "#ececec",
+        showGrid: "",
+        // false | 'pattern' | 'rect'
+        // whether to show these controls buttons
+        addMutationCNVButtons: false,
+        truncatingMutations,
+        proteinChangingMutations,
+        synonymousMutations,
+        mutationClasses,
+        CNVClasses,
+        gridStroke: "#fff",
+        outlineStroke: "#ccc",
+        beamStroke: "#f00",
+        colw: 0,
+        colwMin: 0.1 / devicePixelRatio,
+        colwMax: 16,
+        colspace: 1,
+        colgspace: 8,
+        colglabelpos: true,
+        collabelpos: "bottom",
+        collabelvisible: true,
+        collabelgap: 5,
+        collabelpad: 1,
+        collabelmaxchars: 32,
+        rowh: 18,
+        //use 0 to auto-compute row height, previous default=18,
+        rowhMin: 1,
+        rowhMax: 20,
+        rowspace: 1,
+        rowgspace: 8,
+        rowlabelpos: "left",
+        // | 'right'
+        rowlabelgap: 5,
+        rowlabelvisible: true,
+        rowlabelpad: 1,
+        rowlabelmaxchars: 32,
+        legendGrpLabelMaxChars: 26,
+        grpLabelFontSize: 12,
+        minLabelFontSize: 6,
+        maxLabelFontSize: 14,
+        transpose: false,
+        sampleLabelsToggle: opts.chartType === "hierCluster" ? "hide" : "auto",
+        // 'auto' | 'hide'
+        sampleLabelOffset: 120,
+        sampleGrpLabelOffset: 120,
+        sampleGrpLabelMaxChars: 32,
+        termLabelOffset: 80,
+        termGrpLabelOffset: 80,
+        termGrpLabelMaxChars: 32,
+        duration: 0,
+        zoomLevel: 1,
+        zoomCenterPct: 0,
+        zoomIndex: 0,
+        zoomGrpIndex: 0,
+        zoomMin: 0.5,
+        zoomIncrement: 0.1,
+        zoomStep: 1,
+        // renderedWMax should not be exposed as a user-input
+        // 60000 pixels is based on laptop and external monitor tests,
+        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
+        imgWMax: 6e4 / devicePixelRatio,
+        scrollHeight: 12,
+        controlLabels,
+        cnvUnit: "log2ratio",
+        ignoreCnvValues: false,
+        //will ignore numeric CNV values if true
+        barh: 32,
+        // default bar height for continuous terms,
+        // possible string entries:
+        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
+        // - may add other optional hints later
+        showHints: [],
+        genesetEditUiVersion: "",
+        // '' | 'withTabs'
+        // settings for a specific tw
+        twSpecificSettings: {},
+        oncoPrintSNVindelCellBorder: false,
+        // whether to show white cell border for SNVindel in oncoPrint mode
+        cnvValues: {
+          //Properties match the args for the ColorScales
+          //numericInput arg
+          cutoffMode: "percentile",
+          defaultPercentile: 99,
+          min: null,
+          max: null,
+          percentile: 99
+        }
+      }
+    }
+  };
+  const s = config.settings;
+  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
+  s.legend = {
+    ontop: false,
+    lineh: 25,
+    padx: 5,
+    padleft: 0,
+    //150,
+    padright: 20,
+    padbtm: 30,
+    fontsize,
+    iconh: fontsize - 2,
+    iconw: fontsize - 2,
+    hangleft: 1,
+    linesep: false
+  };
+  const overrides = app.vocabApi.termdbConfig.matrix || {};
+  copyMerge(config.settings.matrix, overrides.settings);
+  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
+  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
+  if (overrides.filter) config.filter = overrides.filter;
+  if (opts.name) {
+    const data = await app.vocabApi.getMatrixByName(opts.name);
+    if (!data) throw "error from getMatrixByName()";
+    if (data.error) throw data.error;
+    copyMerge(config, data);
+  }
+  const os = opts?.settings?.matrix;
+  if (os) {
+    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
+      os.sortSamplesBy = "a";
+    }
+    if (os.sortOptions) {
+      delete os.sortOptions.custom;
+      delete os.sortOptions.asListed;
+    }
+  }
+  copyMerge(config, opts);
+  const m = config.settings.matrix;
+  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
+  m.duration = 0;
+  m.colw = 0;
+  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
+  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
+  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
+  if (window.location.hostname == "localhost") {
+    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
+  }
+  for (const grp of config.termgroups) {
+    const promises = [];
+    for (const tw of grp.lst) {
+      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
+        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
+          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
+          tw.id = tw.term.id;
+        }
+        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
+      }
+      promises.push(fillTermWrapper(tw, app.vocabApi));
+    }
+    grp.lst = await Promise.all(promises);
+  }
+  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
+  return config;
+}
+function setComputedConfig(config) {
+  const s = config.settings.matrix;
+  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
+  s.filterByClass = { isAtomic: true };
+  for (const f of config.legendGrpFilter.lst) {
+    if (!f.dt) continue;
+    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
+      s.filterByClass[key2] = "value";
+    });
+  }
+  for (const f of config.legendValueFilter.lst) {
+    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
+    if (f.tvs.values?.[0].mclasslst)
+      f.tvs.values[0].mclasslst.forEach((key2) => {
+        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
+      });
+    else if (f.tvs.values)
+      f.tvs.values.forEach((v) => {
+        s.filterByClass[key] = "value";
+      });
+    else throw `unhandled tvs from legendValueFilter`;
+  }
+  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
+  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
+  s.hiddenCNVs = [...hiddenCNVs];
+  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
+  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
+  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
+  s.hiddenMutations = [...hiddenMutations];
+  const PCset = new Set(s.proteinChangingMutations);
+  const TMset = new Set(s.truncatingMutations);
+  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
+  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
+  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
+  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
+  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
+}
+
+export {
+  getPlotConfig,
+  setComputedConfig
+};
+//# sourceMappingURL=chunk-YWBUK4B7.js.map

package/dist/chunk-YWBUK4B7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.config.js"],
+  "sourcesContent": ["import { copyMerge } from '#rx'\nimport { getSortOptions } from './matrix.sort'\nimport { fillTermWrapper } from '#termsetting'\nimport {\n\tmclass,\n\tdtcnv,\n\tproteinChangingMutations,\n\ttruncatingMutations,\n\tsynonymousMutations,\n\tmutationClasses,\n\tCNVClasses\n} from '#shared/common.js'\nimport { isDictionaryType } from '#shared/terms.js'\nimport { defaultUiLabels } from '#plots/PlotBase.js'\n\nexport async function getPlotConfig(opts = {}, app) {\n\tconst controlLabels = structuredClone(defaultUiLabels)\n\tconst devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio\n\tconst config = {\n\t\t// data configuration\n\t\ttermgroups: [],\n\t\tsamplegroups: [],\n\t\tdivideBy: null,\n\t\tlegendValueFilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tlegendGrpFilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tfilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\t// cnvCutoffs: {},\n\n\t\t// rendering options\n\t\tsettings: {\n\t\t\tmatrix: {\n\t\t\t\tsvgCanvasSwitch: 1000, // the number of samples to trigger switching between svg and canvas\n\t\t\t\tuseMinPixelWidth: true, // canvas may be hazy if false, but more accurately reflects column density\n\t\t\t\tcellEncoding: '', // can be \"oncoprint\" | \"stacked\" | \"single\"\n\t\t\t\tmargin: {\n\t\t\t\t\ttop: 10,\n\t\t\t\t\tright: 5,\n\t\t\t\t\tbottom: 20,\n\t\t\t\t\tleft: 50\n\t\t\t\t},\n\t\t\t\t// set any dataset-defined sample limits and sort priority, otherwise undefined\n\t\t\t\t// put in settings, so that later may be overridden by a user\n\t\t\t\tmaxGenes: opts.settings?.maxGenes || 50,\n\t\t\t\tmaxSample: opts.settings?.maxSample || 1000,\n\n\t\t\t\tsampleNameFilter: '',\n\t\t\t\tsortSamplesBy: 'a',\n\t\t\t\tsortPriority: undefined, // will be filled-in\n\t\t\t\t// sortByMutation: 'consequence', computed\n\t\t\t\t// sortByCNV: true, computed\n\t\t\t\t//sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),\n\t\t\t\tsortSampleGrpsBy: 'name', // 'hits' | 'name' | 'sampleCount'\n\t\t\t\tsortSamplesTieBreakers: [{ $id: 'sample', sortSamples: {} /*split: {char: '', index: 0}*/ }],\n\t\t\t\tsortTermsBy: 'sampleCount', // or 'as listed'\n\t\t\t\t// do not show number of samples at hiercluster gene row labels\n\t\t\t\tsamplecount4gene: opts.chartType == 'hierCluster' ? '' : 'abs', //true, // 'abs' (default, previously true), 'pct', ''  (previously false)\n\t\t\t\tgeneVariantCountSamplesSkipMclass: [],\n\t\t\t\tcellbg: '#ececec',\n\t\t\t\tshowGrid: '', // false | 'pattern' | 'rect'\n\t\t\t\t// whether to show these controls buttons\n\t\t\t\taddMutationCNVButtons: false,\n\t\t\t\ttruncatingMutations,\n\t\t\t\tproteinChangingMutations,\n\t\t\t\tsynonymousMutations,\n\t\t\t\tmutationClasses,\n\t\t\t\tCNVClasses,\n\t\t\t\tgridStroke: '#fff',\n\t\t\t\toutlineStroke: '#ccc',\n\t\t\t\tbeamStroke: '#f00',\n\t\t\t\tcolw: 0,\n\t\t\t\tcolwMin: 0.1 / devicePixelRatio,\n\t\t\t\tcolwMax: 16,\n\t\t\t\tcolspace: 1,\n\t\t\t\tcolgspace: 8,\n\t\t\t\tcolglabelpos: true,\n\t\t\t\tcollabelpos: 'bottom',\n\t\t\t\tcollabelvisible: true,\n\t\t\t\tcollabelgap: 5,\n\t\t\t\tcollabelpad: 1,\n\t\t\t\tcollabelmaxchars: 32,\n\t\t\t\trowh: 18, //use 0 to auto-compute row height, previous default=18,\n\t\t\t\trowhMin: 1,\n\t\t\t\trowhMax: 20,\n\t\t\t\trowspace: 1,\n\t\t\t\trowgspace: 8,\n\t\t\t\trowlabelpos: 'left', // | 'right'\n\t\t\t\trowlabelgap: 5,\n\t\t\t\trowlabelvisible: true,\n\t\t\t\trowlabelpad: 1,\n\t\t\t\trowlabelmaxchars: 32,\n\t\t\t\tlegendGrpLabelMaxChars: 26,\n\t\t\t\tgrpLabelFontSize: 12,\n\t\t\t\tminLabelFontSize: 6,\n\t\t\t\tmaxLabelFontSize: 14,\n\t\t\t\ttranspose: false,\n\t\t\t\tsampleLabelsToggle: opts.chartType === 'hierCluster' ? 'hide' : 'auto', // 'auto' | 'hide'\n\t\t\t\tsampleLabelOffset: 120,\n\t\t\t\tsampleGrpLabelOffset: 120,\n\t\t\t\tsampleGrpLabelMaxChars: 32,\n\t\t\t\ttermLabelOffset: 80,\n\t\t\t\ttermGrpLabelOffset: 80,\n\t\t\t\ttermGrpLabelMaxChars: 32,\n\t\t\t\tduration: 0,\n\t\t\t\tzoomLevel: 1,\n\t\t\t\tzoomCenterPct: 0,\n\t\t\t\tzoomIndex: 0,\n\t\t\t\tzoomGrpIndex: 0,\n\t\t\t\tzoomMin: 0.5,\n\t\t\t\tzoomIncrement: 0.1,\n\t\t\t\tzoomStep: 1,\n\t\t\t\t// renderedWMax should not be exposed as a user-input\n\t\t\t\t// 60000 pixels is based on laptop and external monitor tests,\n\t\t\t\t// when a canvas dataURL image in a zoomed-in matrix svg stops rendering\n\t\t\t\timgWMax: 60000 / devicePixelRatio,\n\t\t\t\tscrollHeight: 12,\n\t\t\t\tcontrolLabels,\n\t\t\t\tcnvUnit: 'log2ratio',\n\t\t\t\tignoreCnvValues: false, //will ignore numeric CNV values if true\n\n\t\t\t\tbarh: 32, // default bar height for continuous terms,\n\n\t\t\t\t// possible string entries:\n\t\t\t\t// - \"genesetEdit\", for gene-centric embedders only like GDC OncoMatrix\n\t\t\t\t// - may add other optional hints later\n\t\t\t\tshowHints: [],\n\t\t\t\tgenesetEditUiVersion: '', // '' | 'withTabs'\n\t\t\t\t// settings for a specific tw\n\t\t\t\ttwSpecificSettings: {},\n\t\t\t\toncoPrintSNVindelCellBorder: false, // whether to show white cell border for SNVindel in oncoPrint mode\n\t\t\t\tcnvValues: {\n\t\t\t\t\t//Properties match the args for the ColorScales\n\t\t\t\t\t//numericInput arg\n\t\t\t\t\tcutoffMode: 'percentile',\n\t\t\t\t\tdefaultPercentile: 99,\n\t\t\t\t\tmin: null,\n\t\t\t\t\tmax: null,\n\t\t\t\t\tpercentile: 99\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst s = config.settings\n\tconst fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12)\n\n\ts.legend = {\n\t\tontop: false,\n\t\tlineh: 25,\n\t\tpadx: 5,\n\t\tpadleft: 0, //150,\n\t\tpadright: 20,\n\t\tpadbtm: 30,\n\t\tfontsize,\n\t\ticonh: fontsize - 2,\n\t\ticonw: fontsize - 2,\n\t\thangleft: 1,\n\t\tlinesep: false\n\t}\n\n\tconst overrides = app.vocabApi.termdbConfig.matrix || {}\n\tcopyMerge(config.settings.matrix, overrides.settings)\n\tif (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter\n\tif (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter\n\tif (overrides.filter) config.filter = overrides.filter\n\n\tif (opts.name) {\n\t\t// name should be identifier of a premade plot from the datase; load data of the premade plot and override into config{}\n\t\tconst data = await app.vocabApi.getMatrixByName(opts.name)\n\t\tif (!data) throw 'error from getMatrixByName()'\n\t\tif (data.error) throw data.error\n\t\tcopyMerge(config, data)\n\t}\n\n\tconst os = opts?.settings?.matrix\n\tif (os) {\n\t\tif (\n\t\t\t(os.sortSamplesBy == 'custom' || os.sortSamplesBy == 'asListed') &&\n\t\t\tos.sortOptions?.custom.label == 'against alteration type'\n\t\t) {\n\t\t\tos.sortSamplesBy = 'a'\n\t\t}\n\t\tif (os.sortOptions) {\n\t\t\tdelete os.sortOptions.custom\n\t\t\tdelete os.sortOptions.asListed\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\tcopyMerge(config, opts)\n\tconst m = config.settings.matrix\n\tm.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m)\n\t// harcode these overrides for now\n\tm.duration = 0\n\t// force auto-dimensions for colw\n\tm.colw = 0\n\t// support deprecated sortSamplesBy value from a saved session\n\tif (m.sortSamplesBy != 'asListed' && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = 'a'\n\telse if (['selectedTerms', 'class', 'dt', 'hits'].includes(m.sortSamplesBy)) m.sortSamplesBy = 'a'\n\tif (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = 'abs'\n\t// support overrides in localhost\n\tif (window.location.hostname == 'localhost') {\n\t\tif (window.location.hash == '#canvas') m.svgCanvasSwitch = 0\n\t}\n\n\tfor (const grp of config.termgroups) {\n\t\tconst promises = []\n\t\t//grp.lst = JSON.parse(JSON.stringify(grp.lst))\n\t\tfor (const tw of grp.lst) {\n\t\t\t// may force the saved session to request the most up-to-data dictionary term data from server\n\t\t\t// TODO: should skip samplelst term here\n\t\t\tif (!tw.term?.type || isDictionaryType(tw.term.type)) {\n\t\t\t\tif (!tw.id && tw.term.type != 'samplelst' && tw.term.type != 'termCollection') {\n\t\t\t\t\tif (!tw.term.id) throw `missing tw.id and tw.term.id`\n\t\t\t\t\ttw.id = tw.term.id // tw.id will be used to rehydrate tw with new term data from server. tw.id will be deleted following rehydration.\n\t\t\t\t}\n\t\t\t\tif (tw.term?.type != 'samplelst' && tw.term?.type != 'termCollection') delete tw.term\n\t\t\t}\n\t\t\t/** If tw fails at this step, consider using structuredClone(tw) in\n\t\t\t * the config for app.dispatch() to make the tw mutable. Should\n\t\t\t * not fail from runpp(), only app.dispatch(). */\n\t\t\tpromises.push(fillTermWrapper(tw, app.vocabApi))\n\t\t}\n\t\tgrp.lst = await Promise.all(promises)\n\t}\n\tif (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi)\n\treturn config\n}\n\n// config: a hydrated matrix config object\nexport function setComputedConfig(config) {\n\tconst s = config.settings.matrix\n\tconst allClasses = [...s.mutationClasses, ...s.CNVClasses]\n\n\ts.filterByClass = { isAtomic: true }\n\tfor (const f of config.legendGrpFilter.lst) {\n\t\tif (!f.dt) continue\n\t\tallClasses\n\t\t\t.filter(m => f.dt.includes(mclass[m].dt))\n\t\t\t.forEach(key => {\n\t\t\t\ts.filterByClass[key] = 'value'\n\t\t\t})\n\t}\n\tfor (const f of config.legendValueFilter.lst) {\n\t\tif (!f.legendGrpName || f.tvs?.term?.type !== 'geneVariant') continue\n\t\tif (f.tvs.values?.[0].mclasslst)\n\t\t\tf.tvs.values[0].mclasslst.forEach(key => {\n\t\t\t\ts.filterByClass[key] = f.legendFilterType?.endsWith('_hard') ? 'case' : 'value'\n\t\t\t})\n\t\telse if (f.tvs.values)\n\t\t\tf.tvs.values.forEach(v => {\n\t\t\t\t//hiddenVariants.add(v.key)\n\t\t\t\ts.filterByClass[key] = 'value'\n\t\t\t})\n\t\telse throw `unhandled tvs from legendValueFilter`\n\t}\n\ts.hiddenVariants = Object.keys(s.filterByClass).filter(c => c !== 'isAtomic')\n\n\tconst hiddenCNVs = new Set(s.hiddenVariants.filter(key => mclass[key]?.dt === dtcnv))\n\ts.hiddenCNVs = [...hiddenCNVs]\n\n\ts.showMatrixCNV = !hiddenCNVs.size ? 'all' : hiddenCNVs.size == s.CNVClasses.length ? 'none' : 'bySelection'\n\ts.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length\n\n\tconst hiddenMutations = new Set(s.hiddenVariants.filter(key => s.mutationClasses.find(k => k === key)))\n\ts.hiddenMutations = [...hiddenMutations]\n\tconst PCset = new Set(s.proteinChangingMutations)\n\tconst TMset = new Set(s.truncatingMutations)\n\n\ts.showMatrixMutation = !hiddenMutations.size\n\t\t? 'all'\n\t\t: hiddenMutations.size == s.mutationClasses.length\n\t\t? 'none'\n\t\t: hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every(m => !PCset.has(m))\n\t\t? 'onlyPC'\n\t\t: hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every(m => !TMset.has(m))\n\t\t? 'onlyTruncating'\n\t\t: 'bySelection'\n\ts.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length\n\n\tconst tiebreakers =\n\t\ts.sortOptions.a?.sortPriority.find(sp => sp.types.length == 1 && sp.types[0] == 'geneVariant')?.tiebreakers || []\n\n\t//Backwards compatibility fix for old saved sessions missing .isOrdered and/or .disabled\n\ts.sortByMutation = tiebreakers.find(tb => tb.filter?.values[0]?.dt === 1)?.isOrdered ? 'consequence' : 'presence'\n\n\ts.sortByCNV = tiebreakers.find(tb => tb.filter?.values[0]?.dt === 4)?.disabled !== true\n}\n"],
+  "mappings": 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+  "names": ["key"]
+}

package/dist/chunk-YZHGLSKQ.js

@@ -0,0 +1,50 @@
+import {
+  addGeneSearchbox,
+  getSCGEunit
+} from "./chunk-2YC6ZVE4.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-EGWVYY7K.js";
+
+// termdb/handlers/singleCellGeneExpression.ts
+var SearchHandler = class {
+  init(opts) {
+    this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => this.selectGene(geneSearch.geneSymbol, opts.usecase?.specialCase?.config?.sample)
+    });
+  }
+  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
+   * with sample info not included.*/
+  async selectGene(gene, sample) {
+    if (!gene) throw new Error("No gene selected");
+    const unit = getSCGEunit(this.app.vocabApi);
+    const name = `${gene} ${unit}`;
+    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
+  }
+  validateOpts(opts) {
+    if (opts.callback == null) throw new Error("callback is required");
+    if (opts.app == null) throw new Error("app is required");
+    if (opts.holder == null) throw new Error("holder is required");
+    if (opts.genomeObj == null) throw new Error("genomeObj is required");
+    if (opts.usecase == null) throw new Error("usecase is required");
+    if (!opts.usecase?.specialCase?.config?.sample) {
+      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
+    }
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-YZHGLSKQ.js.map