@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/cuminc-WQB6FHVS.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/cuminc.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge } from '../rx'\nimport { controlsInit, renderTerm1Label } from './controls'\nimport { getT0T2defaultQ } from './summaryQ.ts'\nimport { fillTermWrapper } from '#termsetting'\nimport { select } from 'd3-selection'\nimport { sayerror } from '#dom'\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 { getSeriesTip } from '#dom/svgSeriesTips'\nimport { renderAtRiskG } from '#dom/renderAtRisk'\nimport { renderPvalues } from '#dom/renderPvalueTable'\nimport { Menu } from '#dom/menu'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\n\n/*\nclass Cuminc\n- for cox regression cumulative incidence test\n- simpler workflow relative to class MassCumInc:\n\t- input data is for a single chart\n\t- no hidden series\n\t- no skipped series\n\t- no skipped charts\n*/\nexport class Cuminc extends PlotBase {\n\tstatic type = 'cuminc'\n\n\tconstructor(opts) {\n\t\tthis.type = Cuminc.type\n\t\tthis.pj = getPj(this)\n\t\tthis.state = {\n\t\t\tconfig: copyMerge(\n\t\t\t\t{\n\t\t\t\t\tsettings: JSON.parse(defaultSettings)\n\t\t\t\t},\n\t\t\t\topts.config\n\t\t\t)\n\t\t}\n\n\t\tconst holder = opts.holder\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tchartsDiv: holder.append('div').style('margin', '10px'),\n\t\t\tlegendDiv: holder.append('div').style('margin', '5px'),\n\t\t\thiddenDiv: holder.append('div').style('margin', '5px 5px 15px 5px')\n\t\t}\n\t\tthis.tip = new Menu({ padding: '5px' })\n\t\tthis.lineFxn = line()\n\t\t\t.curve(curveStepAfter)\n\t\t\t.x(c => c.scaledX)\n\t\t\t.y(c => c.scaledY)\n\n\t\tthis.hidePlotTitle = true\n\n\t\tsetRenderers(this)\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\t}\n\n\tmain(results) {\n\t\tthis.config = structuredClone(this.state.config)\n\t\tif (this.config.term.term.type != 'condition') throw 'cuminc term is not a condition term'\n\t\tthis.settings = this.config.settings.cuminc\n\t\tthis.settings.xTitleLabel = 'Years since entry into the cohort' // TODO: do not harcode time unit (see survival.js)\n\t\tthis.settings.atRiskVisible = false\n\n\t\tthis.processResults(results)\n\t\tthis.pj.refresh({ data: this.currData })\n\t\tthis.setTerm2Color(this.pj.tree.charts)\n\t\tthis.render()\n\t}\n\n\tprocessResults(results) {\n\t\tconst chartIds = Object.keys(results)\n\t\tif (chartIds.length != 1) throw 'must be a single chart'\n\t\tconst chartId = chartIds[0]\n\t\tconst chart = results[chartId]\n\t\tthis.currData = []\n\t\tthis.uniqueSeriesIds = new Set()\n\t\t// process cumulative incidence estimates\n\t\tfor (const seriesId in chart.estimates) {\n\t\t\tconst series = chart.estimates[seriesId]\n\t\t\tfor (const timepoint of series) {\n\t\t\t\tconst { time, est, low, up, nrisk, nevent, ncensor } = timepoint\n\t\t\t\tconst d = {\n\t\t\t\t\tchartId,\n\t\t\t\t\tseriesId,\n\t\t\t\t\ttime,\n\t\t\t\t\tcuminc: est * 100, // convert to percentage\n\t\t\t\t\tlow: low * 100,\n\t\t\t\t\thigh: up * 100,\n\t\t\t\t\tnrisk,\n\t\t\t\t\tnevent,\n\t\t\t\t\tncensor\n\t\t\t\t}\n\t\t\t\tthis.currData.push(d)\n\t\t\t\tthis.uniqueSeriesIds.add(d.seriesId)\n\t\t\t}\n\t\t}\n\t\t// process results of Grey's tests\n\t\tthis.tests = {}\n\t\tif (chart.tests?.length != 1) throw 'must have a single test'\n\t\tconst test = chart.tests[0]\n\t\tthis.tests[chartId] = [\n\t\t\t{\n\t\t\t\tpvalue: { id: 'pvalue', text: test.permutation ? test.pvalue + '*' : test.pvalue },\n\t\t\t\tseries1: { id: test.series1 },\n\t\t\t\tseries2: { id: test.series2 },\n\t\t\t\tpermutation: test.permutation\n\t\t\t}\n\t\t]\n\n\t\tthis.refs = {}\n\t}\n\n\tsetTerm2Color(charts) {\n\t\tif (!charts) return\n\t\tif (charts.length != 1) throw 'should be a single chart'\n\t\tconst chart = charts[0]\n\t\tthis.term2toColor = {}\n\t\tthis.colorScale = this.uniqueSeriesIds.size < 11 ? scaleOrdinal(schemeCategory10) : scaleOrdinal(schemeCategory20)\n\t\tconst legendItems = []\n\t\tfor (const series of chart.serieses) {\n\t\t\tconst color = this.config.term2?.term.values?.[series.seriesId]?.color\n\t\t\tconst c = {\n\t\t\t\torig: color || (series.seriesId == '' ? this.settings.defaultColor : this.colorScale(series.seriesId))\n\t\t\t}\n\t\t\tc.rgb = rgb(c.orig)\n\t\t\tc.adjusted = c.rgb.toString()\n\t\t\tthis.term2toColor[series.seriesId] = c\n\n\t\t\tif (!legendItems.find(d => d.seriesId == series.seriesId)) {\n\t\t\t\tlegendItems.push({\n\t\t\t\t\tseriesId: series.seriesId,\n\t\t\t\t\ttext: series.seriesLabel,\n\t\t\t\t\tcolor: this.term2toColor[series.seriesId].adjusted\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (this.config.term2 && legendItems.length) {\n\t\t\tthis.legendData = [\n\t\t\t\t{\n\t\t\t\t\tname: this.config.term2.term.name,\n\t\t\t\t\titems: legendItems\n\t\t\t\t}\n\t\t\t]\n\t\t} else {\n\t\t\tthis.legendData = []\n\t\t}\n\t\tconst chartTests = this.tests[chart.chartId]\n\t\tif (chartTests.length != 1) throw 'should have one test'\n\t\tconst test = chartTests[0]\n\t\tfor (const key in test) {\n\t\t\tif (key == 'pvalue') {\n\t\t\t\t// p-value of test\n\t\t\t\ttest[key].color = '#000'\n\t\t\t} else if (key.startsWith('series')) {\n\t\t\t\t// series of test\n\t\t\t\tconst item = legendItems.find(item => item.seriesId == test[key].id)\n\t\t\t\ttest[key].color = item.color\n\t\t\t\ttest[key].text = item.text\n\t\t\t} else {\n\t\t\t\t// permutation flag\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t}\n}\n\n/*\nclass MassCumInc\n- for general cumulative incidence analysis\n- input data is for one or more charts\n*/\nclass MassCumInc {\n\tstatic type = 'cuminc'\n\n\tconstructor(opts) {\n\t\tthis.type = MassCumInc.type\n\t\tthis.chartIncrement = 0\n\t}\n\n\tasync init(appState) {\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\tthis.dom = {\n\t\t\terrorDiv: holder.append('div'),\n\t\t\tloadingDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.html('Loading ...'),\n\t\t\theader: opts.header,\n\t\t\tcontrols,\n\t\t\tholder,\n\t\t\tchartsDiv: holder.append('div').style('margin', '10px'),\n\t\t\tlegendDiv: holder.append('div').style('margin', '5px'),\n\t\t\thiddenDiv: holder.append('div').style('margin', '5px 5px 15px 5px')\n\t\t}\n\t\tthis.tip = new Menu({ padding: '5px' })\n\n\t\tif (this.dom.header) this.dom.header.html('Cumulative Incidence Plot')\n\t\t// hardcode for now, but may be set as option later\n\t\tthis.settings = Object.assign({}, this.opts.settings)\n\t\tthis.pj = getPj(this)\n\t\tthis.lineFxn = line()\n\t\t\t.curve(curveStepAfter)\n\t\t\t.x(c => c.scaledX)\n\t\t\t.y(c => c.scaledY)\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\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\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.hideLegendItem(e.target.__data__)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\tawait this.setControls(appState)\n\t}\n\n\tasync setControls(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tconst controlLabels = 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.cuminc', this.download)\n\t\t} else {\n\t\t\tthis.dom.holder\n\t\t\t\t.attr('class', 'pp-termdb-plot-viz')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('min-width', '300px')\n\t\t\t\t.style('margin-left', '50px')\n\n\t\t\tconst options = []\n\t\t\tfor (const grade in config.term.term.values) {\n\t\t\t\t//Fix for dropdown not displaying options\n\t\t\t\tconst v = config.term.term.values[grade]\n\t\t\t\tif (v.uncomputable) continue\n\t\t\t\toptions.push({\n\t\t\t\t\tlabel: v.label,\n\t\t\t\t\tvalue: grade\n\t\t\t\t})\n\t\t\t}\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\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: 'term',\n\t\t\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\t\t\tusecase: { target: 'cuminc', detail: 'term' },\n\t\t\t\t\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\t\tmenuOptions: 'edit'\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: 'term2',\n\t\t\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\t\t\tusecase: { target: 'cuminc', 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: getT0T2defaultQ(true)\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: 'cuminc',\n\t\t\t\t\t\t\tusecase: { target: 'cuminc', 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: getT0T2defaultQ(true)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Minimum sample size of series',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\t\t\tsettingsKey: 'minSampleSize'\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Minimum at-risk count of event',\n\t\t\t\t\t\t\ttype: 'number',\n\t\t\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\t\t\tsettingsKey: 'minAtRisk'\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: 'cuminc',\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: 'cuminc',\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: 'X-axis ticks',\n\t\t\t\t\t\t\ttype: 'text',\n\t\t\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\t\t\tsettingsKey: 'xTickValues',\n\t\t\t\t\t\t\tplaceholder: 'tick,tick,...',\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: 'Y-axis ticks',\n\t\t\t\t\t\t\ttype: 'text',\n\t\t\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\t\t\tsettingsKey: 'yTickValues',\n\t\t\t\t\t\t\tplaceholder: 'tick,tick,...',\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: 'cuminc',\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{\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: 'cuminc',\n\t\t\t\t\t\t\tsettingsKey: 'ciVisible'\n\t\t\t\t\t\t},\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: 'cuminc',\n\t\t\t\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tthis.components.controls.on('downloadClick.cuminc', 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 = this.parentId && 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\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\t\t\tconfig: {\n\t\t\t\tterm: JSON.parse(JSON.stringify(config.term)),\n\t\t\t\tterm0: config.term0 ? JSON.parse(JSON.stringify(config.term0)) : null,\n\t\t\t\tterm2: config.term2 ? JSON.parse(JSON.stringify(config.term2)) : null,\n\t\t\t\tsettings: config.settings.cuminc\n\t\t\t}\n\t\t}\n\t}\n\n\tasync main() {\n\t\ttry {\n\t\t\tthis.config = structuredClone(this.state.config)\n\t\t\tthis.dom.errorDiv.html('')\n\t\t\tif (this.dom.header)\n\t\t\t\tthis.dom.header.html(\n\t\t\t\t\tthis.state.config.term.term.name +\n\t\t\t\t\t\t' <span style=\"opacity:.6;font-size:.7em;margin-left:10px;\">CUMULATIVE INCIDENCE</span>'\n\t\t\t\t)\n\n\t\t\tif (this.config.term.term.type != 'condition') throw 'cuminc term is not a condition term'\n\t\t\tthis.toggleLoadingDiv()\n\t\t\tObject.assign(this.settings, this.config.settings)\n\t\t\tthis.settings.defaultHidden = this.getDefaultHidden()\n\t\t\tthis.settings.hidden = this.settings.customHidden || this.settings.defaultHidden\n\t\t\tthis.settings.xTitleLabel = 'Years since diagnosis' // TODO: do not harcode time unit (see survival.js)\n\t\t\tconst reqOpts = this.getDataRequestOpts()\n\t\t\tconst results = await this.app.vocabApi.getNestedChartSeriesData(reqOpts)\n\t\t\tif (results.error) throw results.error\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthis.app.vocabApi.syncTermData(this.config, results)\n\t\t\tthis.processResults(results)\n\t\t\tthis.pj.refresh({ data: this.currData })\n\t\t\tthis.sortSerieses(this.pj.tree.charts)\n\t\t\tthis.setTerm2Color(this.pj.tree.charts)\n\t\t\tthis.render()\n\t\t} catch (e) {\n\t\t\tconsole.error(e)\n\t\t}\n\t}\n\n\t// creates an opts object for the vocabApi.getNestedChartsData()\n\tgetDataRequestOpts() {\n\t\tconst c = this.config\n\t\tconst opts = {\n\t\t\tchartType: 'cuminc',\n\t\t\tterm: c.term,\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tminSampleSize: c.settings.minSampleSize\n\t\t}\n\t\tif (c.term2) opts.term2 = c.term2\n\t\tif (c.term0) opts.term0 = c.term0\n\t\treturn opts\n\t}\n\n\tgetDefaultHidden() {\n\t\tconst hidden = []\n\t\tconst term2 = this.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\tprocessResults(results) {\n\t\tconst s = this.settings\n\t\tconst c = this.config\n\t\tconst estimates = {}\n\t\tconst tests = {}\n\t\tthis.currData = []\n\t\tthis.tests = {}\n\t\tthis.noData = []\n\n\t\tif (Object.keys(results.data).length === 0) {\n\t\t\tsayerror(this.dom.errorDiv, 'No data available')\n\t\t}\n\t\tthis.uniqueSeriesIds = new Set()\n\t\tconst lowSampleSize = results.lowSampleSize\n\t\tconst noEvents = results.noEvents\n\t\tthis.refs = results.refs\n\n\t\t// filter the data\n\t\tfor (const chartId in results.data) {\n\t\t\tconst chart = results.data[chartId]\n\t\t\t// filter the estimates\n\t\t\tif (chart.estimates) {\n\t\t\t\tfor (const seriesId in chart.estimates) {\n\t\t\t\t\tconst series = chart.estimates[seriesId]\n\t\t\t\t\tif (!series.filter(timepoint => timepoint.nrisk >= s.minAtRisk && timepoint.est > 0).length) {\n\t\t\t\t\t\t// discard series with no events after applying\n\t\t\t\t\t\t// the at-risk count filter\n\t\t\t\t\t\tchartId in noEvents ? noEvents[chartId].push(seriesId) : (noEvents[chartId] = [seriesId])\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tchartId in estimates ? (estimates[chartId][seriesId] = series) : (estimates[chartId] = { [seriesId]: series })\n\t\t\t\t}\n\t\t\t\tif (!(chartId in estimates)) this.noData.push(chartId)\n\t\t\t} else {\n\t\t\t\t// chart does not have any data\n\t\t\t\tthis.noData.push(chartId)\n\t\t\t}\n\t\t\t// filter the tests\n\t\t\tif (chart.tests && Object.keys(estimates).length > 0) {\n\t\t\t\t// discard tests that have series that are either\n\t\t\t\t// discarded or hidden\n\t\t\t\ttests[chartId] = chart.tests.filter(\n\t\t\t\t\ttest =>\n\t\t\t\t\t\ttest.series1 in estimates[chartId] &&\n\t\t\t\t\t\ttest.series2 in estimates[chartId] &&\n\t\t\t\t\t\t!s.hidden.includes(test.series1) &&\n\t\t\t\t\t\t!s.hidden.includes(test.series2)\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\n\t\t// process the filtered data\n\t\t// process estimates\n\t\tfor (const chartId in estimates) {\n\t\t\tconst chart = estimates[chartId]\n\t\t\tfor (const seriesId in chart) {\n\t\t\t\tconst series = chart[seriesId]\n\t\t\t\tfor (const timepoint of series) {\n\t\t\t\t\tconst { time, est, low, up, nrisk, nevent, ncensor } = timepoint\n\t\t\t\t\tconst d = {\n\t\t\t\t\t\tchartId,\n\t\t\t\t\t\tseriesId,\n\t\t\t\t\t\ttime,\n\t\t\t\t\t\tcuminc: est * 100, // convert to percentage\n\t\t\t\t\t\tlow: low * 100,\n\t\t\t\t\t\thigh: up * 100,\n\t\t\t\t\t\tnrisk,\n\t\t\t\t\t\tnevent,\n\t\t\t\t\t\tncensor\n\t\t\t\t\t}\n\t\t\t\t\tif (d.nrisk < s.minAtRisk) {\n\t\t\t\t\t\t// keep the first timepoint with a low at-risk count and\n\t\t\t\t\t\t// drop the remaining timepoints\n\t\t\t\t\t\t// this will allow the curve to extend horizontally up to\n\t\t\t\t\t\t// this timepoint\n\t\t\t\t\t\tthis.currData.push(d)\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t\tthis.currData.push(d)\n\t\t\t\t\tthis.uniqueSeriesIds.add(d.seriesId)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t// process tests\n\t\tfor (const chartId in tests) {\n\t\t\tfor (const test of tests[chartId]) {\n\t\t\t\tconst d = {\n\t\t\t\t\tpvalue: { id: 'pvalue', text: test.permutation ? test.pvalue + '*' : test.pvalue },\n\t\t\t\t\tseries1: { id: test.series1 },\n\t\t\t\t\tseries2: { id: test.series2 },\n\t\t\t\t\tpermutation: test.permutation\n\t\t\t\t}\n\t\t\t\tchartId in this.tests ? this.tests[chartId].push(d) : (this.tests[chartId] = [d])\n\t\t\t}\n\t\t}\n\n\t\t// convert series ids to labels if necessary\n\t\tthis.lowSampleSize = {}\n\t\tfor (const chartId in lowSampleSize) {\n\t\t\tthis.lowSampleSize[chartId] = lowSampleSize[chartId].map(\n\t\t\t\tseriesId => c.term2?.term.values?.[seriesId]?.label || seriesId\n\t\t\t)\n\t\t}\n\t\tthis.noEvents = {}\n\t\tfor (const chartId in noEvents) {\n\t\t\tthis.noEvents[chartId] = noEvents[chartId].map(seriesId => c.term2?.term.values?.[seriesId]?.label || seriesId)\n\t\t}\n\t}\n\n\tsortSerieses(charts) {\n\t\tif (!charts) return\n\t\tfor (const chart of charts) {\n\t\t\t// sort series of chart by sorting series that are not hidden by\n\t\t\t// default ahead of series that are hidden by default\n\t\t\t// this will ensure that the default visible series are\n\t\t\t// assigned the first colors of the color scheme, which\n\t\t\t// tend to be colors with the best contrasts\n\t\t\t// NOTE: do not sort by this.settings.hidden because the color\n\t\t\t// assignments will change when a series changes to hidden/visible\n\t\t\tconst seriesIDs = chart.serieses.map(series => series.seriesId)\n\t\t\tconst seriesOrder = [\n\t\t\t\t...seriesIDs.filter(seriesId => !this.settings.defaultHidden.includes(seriesId)),\n\t\t\t\t...seriesIDs.filter(seriesId => this.settings.defaultHidden.includes(seriesId))\n\t\t\t]\n\t\t\tchart.serieses.sort((a, b) => seriesOrder.indexOf(a.seriesId) - seriesOrder.indexOf(b.seriesId))\n\t\t}\n\t}\n\n\tsetTerm2Color(charts) {\n\t\tif (!charts) {\n\t\t\tthis.legendData = []\n\t\t\treturn\n\t\t}\n\t\tthis.term2toColor = {}\n\t\tthis.colorScale = this.uniqueSeriesIds.size < 11 ? scaleOrdinal(schemeCategory10) : scaleOrdinal(schemeCategory20)\n\t\tconst legendItems = []\n\t\tfor (const chart of charts) {\n\t\t\tfor (const series of chart.serieses) {\n\t\t\t\tconst color = this.config.term2?.term.values?.[series.seriesId]?.color\n\t\t\t\tconst c = {\n\t\t\t\t\torig: color || (series.seriesId == '' ? this.settings.defaultColor : this.colorScale(series.seriesId))\n\t\t\t\t}\n\t\t\t\tc.rgb = rgb(c.orig)\n\t\t\t\tc.adjusted = c.rgb.toString()\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\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.config.term2 && legendItems.length) {\n\t\t\tthis.legendData = [\n\t\t\t\t{\n\t\t\t\t\tname: this.config.term2.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 if (key.startsWith('series')) {\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} else {\n\t\t\t\t\t\t// permutation flag\n\t\t\t\t\t\tcontinue\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 cumincInit = getCompInit(MassCumInc)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = cumincInit\n\nfunction setRenderers(self) {\n\tself.render = function () {\n\t\tconst data = self.pj.tree.charts || []\n\t\tif (self.noData?.length) {\n\t\t\t// add in charts with no data\n\t\t\tdata.push(\n\t\t\t\t...self.noData.map(chartId => {\n\t\t\t\t\tlet chartTitle = chartId\n\t\t\t\t\tconst t0 = self.config.term0\n\t\t\t\t\tif (t0) {\n\t\t\t\t\t\tif (t0.q?.type == 'predefined-groupset' || t0.q?.type == 'custom-groupset') return { chartId, chartTitle }\n\t\t\t\t\t\tif (t0.term.values) {\n\t\t\t\t\t\t\tconst value = t0.term.values[chartId]\n\t\t\t\t\t\t\tif (value && value.label) chartTitle = value.label\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\treturn { chartId, chartTitle }\n\t\t\t\t})\n\t\t\t)\n\t\t}\n\t\tconst chartDivs = self.dom.chartsDiv.selectAll('.pp-cuminc-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\n\t\tif (!self.hiddenData?.[0]?.items.length || !self.config.term2) 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\tself.addCharts = function (chart) {\n\t\tconst s = self.settings\n\n\t\tconst div = select(this)\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-cuminc-chart')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-plotDiv')\n\t\t\t.style('opacity', chart.serieses ? 0 : 1) // if the data can be plotted, slowly reveal plot\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', 'center')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('background', 1 || s.orderChartsBy == 'organ-system' ? chart.color : '')\n\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpcb-cuminc-title')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-plotTitle')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('width', `${s.svgw + 50}px`)\n\t\t\t.style('height', s.chartTitleDivHt + 'px')\n\t\t\t.style('font-weight', '600')\n\t\t\t.style('margin', '5px')\n\t\t\t.datum(chart.chartId)\n\t\t\t.html(chart.chartTitle)\n\n\t\tif (self.hidePlotTitle) div.select('.sjpcb-cuminc-title').style('display', 'none')\n\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-cuminc-chart-noData')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-noData')\n\t\t\t.style('display', 'none')\n\t\t\t.style('width', `${s.svgw + 50}px`)\n\t\t\t.style('margin', '40px 5px')\n\t\t\t.text('No cumulative incidence data')\n\n\t\tif (chart.serieses) {\n\t\t\t// series in chart\n\t\t\tsetVisibleSerieses(chart, s)\n\n\t\t\tconst svg = div.append('svg').attr('class', 'pp-cuminc-svg')\n\t\t\trenderSVG(svg, chart, s)\n\n\t\t\tdiv.style('opacity', 1)\n\t\t} else {\n\t\t\t// no series in chart\n\t\t\tdiv.select('.pp-cuminc-chart-noData').style('display', 'block')\n\t\t}\n\n\t\t// div for chart-specific legends\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-cuminc-chartLegends')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('text-align', chart.serieses ? 'left' : 'center')\n\t\t\t.style('margin', chart.serieses ? '10px 30px 0px 20px' : '0px')\n\t\t\t.style('display', 'none')\n\n\t\tif (self.tests && chart.chartId in self.tests) {\n\t\t\t// p-values legend\n\t\t\tconst holder = div\n\t\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\trenderPvalues({\n\t\t\t\ttitle: \"Group comparisons (Gray's test)\",\n\t\t\t\tholder,\n\t\t\t\tplot: 'cuminc',\n\t\t\t\ttests: self.tests[chart.chartId],\n\t\t\t\ts,\n\t\t\t\tbins: self.refs.bins\n\t\t\t})\n\t\t}\n\n\t\tif (self.noEvents && chart.chartId in self.noEvents) {\n\t\t\t// legend for series with no events\n\t\t\tconst skipdiv = div\n\t\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\tconst title = 'Skipped series (no events)'\n\t\t\trenderSkippedSeries(skipdiv, title, self.noEvents[chart.chartId], s)\n\t\t}\n\n\t\tif (self.lowSampleSize && chart.chartId in self.lowSampleSize) {\n\t\t\t// legend for series with low sample size\n\t\t\tconst skipdiv = div\n\t\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\tconst title = 'Skipped series (low sample size)'\n\t\t\trenderSkippedSeries(skipdiv, title, self.lowSampleSize[chart.chartId], s)\n\t\t}\n\t}\n\n\tfunction setVisibleSerieses(chart, s) {\n\t\tchart.visibleSerieses = s.hidden\n\t\t\t? chart.serieses.filter(series => !s.hidden.includes(series.seriesId))\n\t\t\t: chart.serieses\n\t}\n\n\tself.updateCharts = function (chart) {\n\t\tconst s = self.settings\n\n\t\tconst div = select(this)\n\n\t\tdiv.style('background', 1 || s.orderChartsBy == 'organ-system' ? chart.color : '')\n\n\t\tdiv\n\t\t\t.select('.sjpcb-cuminc-title')\n\t\t\t.style('width', `${s.svgw + 50}px`)\n\t\t\t.style('height', s.chartTitleDivHt + 'px')\n\t\t\t.datum(chart.chartId)\n\t\t\t.html(chart.chartTitle)\n\n\t\tif (self.hidePlotTitle) div.select('.sjpcb-cuminc-title').style('display', 'none')\n\n\t\tdiv.selectAll('.sjpcb-lock-icon').style('display', s.scale == 'byChart' ? 'block' : 'none')\n\n\t\tdiv.selectAll('.sjpcb-unlock-icon').style('display', s.scale == 'byChart' ? 'none' : 'block')\n\n\t\tif (chart.serieses) {\n\t\t\tdiv.select('.pp-cuminc-chart-noData').style('display', 'none')\n\n\t\t\tsetVisibleSerieses(chart, s)\n\n\t\t\trenderSVG(div.select('svg'), chart, s)\n\t\t} else {\n\t\t\tdiv\n\t\t\t\t.select('.pp-cuminc-chart-noData')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('width', `${s.svgw + 50}px`)\n\t\t\tdiv.select('svg').remove()\n\t\t\tdiv.select('.pp-cuminc-chartLegends').style('text-align', 'center').style('margin', '0px')\n\t\t}\n\n\t\t// div for chart-specific legends\n\t\tdiv.select('.pp-cuminc-chartLegends').selectAll('*').remove()\n\n\t\tif (self.tests && chart.chartId in self.tests) {\n\t\t\t// p-values legend\n\t\t\tconst holder = div\n\t\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\trenderPvalues({\n\t\t\t\ttitle: \"Group comparisons (Gray's test)\",\n\t\t\t\tholder,\n\t\t\t\tplot: 'cuminc',\n\t\t\t\ttests: self.tests[chart.chartId],\n\t\t\t\ts,\n\t\t\t\tbins: self.refs.bins\n\t\t\t})\n\t\t}\n\n\t\tif (self.noEvents && chart.chartId in self.noEvents) {\n\t\t\t// legend for series with no events\n\t\t\tconst skipdiv = div\n\t\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\tconst title = 'Skipped series (no events)'\n\t\t\trenderSkippedSeries(skipdiv, title, self.noEvents[chart.chartId], s)\n\t\t}\n\n\t\tif (self.lowSampleSize && chart.chartId in self.lowSampleSize) {\n\t\t\t// legend for series with low sample size\n\t\t\tconst skipdiv = div\n\t\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin-bottom', '30px')\n\t\t\tconst title = 'Skipped series (low sample size)'\n\t\t\trenderSkippedSeries(skipdiv, title, self.lowSampleSize[chart.chartId], s)\n\t\t}\n\t}\n\n\tfunction renderSVG(svg, chart, s) {\n\t\tconst extraHeight = s.atRiskVisible\n\t\t\t? s.axisTitleFontSize + 4 + chart.visibleSerieses.length * 2 * s.axisTitleFontSize\n\t\t\t: 0\n\n\t\tsvg\n\t\t\t.attr('width', s.svgw)\n\t\t\t.attr('height', s.svgh + extraHeight)\n\t\t\t.style('overflow', 'visible')\n\t\t\t.style('padding-left', '20px')\n\n\t\tconst [clipRect, clipG, mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect] = getSvgSubElems(\n\t\t\tsvg,\n\t\t\tchart\n\t\t)\n\n\t\t// set dimensions of clipRect\n\t\t// will be same as those of plotRect\n\t\tclipRect\n\t\t\t.attr('x', 0)\n\t\t\t.attr('width', s.svgw - s.svgPadding.left - s.svgPadding.right)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('height', s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset)\n\n\t\tconst xOffset = s.svgPadding.left\n\t\tmainG.attr('transform', 'translate(' + xOffset + ',' + s.svgPadding.top + ')')\n\t\tconst serieses = seriesesG\n\t\t\t.selectAll('.sjpcb-cuminc-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 (series, i) {\n\t\t\tselect(this).attr('data-testid', `sjpp-cuminc-series-${series.seriesId || ''}`)\n\t\t\trenderSeries(select(this), series, s)\n\t\t})\n\t\tserieses\n\t\t\t.enter()\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpcb-cuminc-series')\n\t\t\t.attr('data-testid', d => `sjpp-cuminc-series-${d.seriesId || ''}`)\n\t\t\t.each(function (series, i) {\n\t\t\t\trenderSeries(select(this), series, s)\n\t\t\t})\n\n\t\trenderAxes(xAxis, xTitle, yAxis, yTitle, s, chart)\n\t\trenderAtRiskG({\n\t\t\tg: atRiskG,\n\t\t\ts,\n\t\t\tchart,\n\t\t\tterm2toColor: self.term2toColor,\n\t\t\tonSerieClick: self.legendClick\n\t\t})\n\n\t\tplotRect\n\t\t\t.attr('x', 0)\n\t\t\t.attr('width', s.svgw - s.svgPadding.left - s.svgPadding.right)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('height', s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset)\n\n\t\tsvg.seriesTip.update({\n\t\t\txScale: chart.xScale,\n\t\t\txTitleLabel: s.xTitleLabel,\n\t\t\tdecimals: s.seriesTipDecimals,\n\t\t\tserieses: chart.visibleSerieses.map(s => {\n\t\t\t\tconst seriesLabel = s.seriesLabel ? `${s.seriesLabel}:` : 'Cumulative Incidence:'\n\t\t\t\tconst color = self.term2toColor[s.seriesId].adjusted\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} ${d.y.toFixed(2)} (${d.low.toFixed(2)} - ${d.high.toFixed(2)})` +\n\t\t\t\t\t\t\t\t`</span>`\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\t}\n\n\tfunction renderSkippedSeries(div, title, serieses, s) {\n\t\tconst fontSize = s.axisTitleFontSize - 2\n\n\t\tdiv.selectAll('*').remove()\n\n\t\tif (!serieses.some(v => v)) {\n\t\t\t// no series defined, so do not render legend\n\t\t\treturn\n\t\t}\n\n\t\t// title div\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('padding-bottom', '5px')\n\t\t\t.style('font-size', fontSize + 'px')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text(title)\n\n\t\t// serieses div\n\t\tconst seriesesDiv = div\n\t\t\t.append('div')\n\t\t\t.style('padding-bottom', '5px')\n\t\t\t.style('font-size', fontSize + 'px')\n\n\t\tseriesesDiv\n\t\t\t.selectAll('div')\n\t\t\t.data(serieses)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'pp-cuminc-chartLegends-skipped')\n\t\t\t.text(d => d)\n\t}\n\n\tfunction getSvgSubElems(svg, chart) {\n\t\tlet clipRect, clipG, mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, line\n\t\tif (!svg.select('.sjpcb-cuminc-mainG').size()) {\n\t\t\tconst clipId = `${self.id}-${self.chartIncrement++}`\n\t\t\tclipRect = svg.append('defs').append('clipPath').attr('id', clipId).append('rect')\n\t\t\tclipG = svg.append('g').attr('class', 'sjpcb-cuminc-clipG')\n\t\t\tmainG = svg.append('g').attr('class', 'sjpcb-cuminc-mainG').attr('data-testid', 'sjpp-cuminc-main-g')\n\t\t\tseriesesG = mainG.append('g').attr('class', 'sjpcb-cuminc-seriesesG').attr('clip-path', `url(#${clipId})`)\n\t\t\taxisG = mainG.append('g').attr('class', 'sjpcb-cuminc-axis')\n\t\t\txAxis = axisG.append('g').attr('class', 'sjpcb-cuminc-x-axis')\n\t\t\tyAxis = axisG.append('g').attr('class', 'sjpcb-cuminc-y-axis')\n\t\t\txTitle = axisG.append('g').attr('class', 'sjpcb-cuminc-x-title').attr('data-testid', 'sjpp-cuminc-x-title')\n\t\t\tyTitle = axisG.append('g').attr('class', 'sjpcb-cuminc-y-title').attr('data-testid', 'sjpp-cuminc-y-title')\n\t\t\tatRiskG = mainG.append('g').attr('class', 'sjpp-cuminc-atrisk')\n\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', '2px')\n\t\t\tplotRect = mainG.append('rect').attr('class', 'sjpcb-plot-tip-rect').style('fill', 'transparent')\n\t\t} else {\n\t\t\tclipRect = svg.select('defs clipPath rect')\n\t\t\tclipG = svg.select('.sjpcb-cuminc-clipG')\n\t\t\tmainG = svg.select('.sjpcb-cuminc-mainG')\n\t\t\tseriesesG = mainG.select('.sjpcb-cuminc-seriesesG')\n\t\t\taxisG = mainG.select('.sjpcb-cuminc-axis')\n\t\t\txAxis = axisG.select('.sjpcb-cuminc-x-axis')\n\t\t\tyAxis = axisG.select('.sjpcb-cuminc-y-axis')\n\t\t\txTitle = axisG.select('.sjpcb-cuminc-x-title')\n\t\t\tyTitle = axisG.select('.sjpcb-cuminc-y-title')\n\t\t\tatRiskG = mainG.select('.sjpp-cuminc-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.app?.tip)\n\t\t}\n\n\t\treturn [clipRect, clipG, mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect]\n\t}\n\n\tfunction renderSeries(g, series, s) {\n\t\tg.selectAll('path').remove()\n\n\t\t// cumulative incidence line\n\t\tg.append('path')\n\t\t\t.attr('data-testid', `sjpp-cuminc-curve-${series.seriesId || ''}`)\n\t\t\t.attr('d', self.lineFxn(series.data.map(d => ({ scaledX: d.scaledX, scaledY: d.scaledY[0] }))))\n\t\t\t.style('fill', 'none')\n\t\t\t.style('stroke', self.term2toColor[series.seriesId].adjusted)\n\t\t\t.style('stroke-width', 2)\n\t\t\t.style('stroke-linecap', 'square')\n\t\t\t.style('opacity', 1)\n\t\t\t.style('stroke-opacity', 1)\n\n\t\t// confidence intervals\n\t\tg.append('path')\n\t\t\t.attr('data-testid', `sjpp-cuminc-ci-${series.seriesId || ''}`)\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.scaledX)\n\t\t\t\t\t.y0(c => c.scaledY[1])\n\t\t\t\t\t.y1(c => c.scaledY[2])(series.data)\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\t}\n\n\tfunction renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart) {\n\t\tconst xTicks = axisBottom(chart.xScale).tickValues(chart.xTickValues)\n\t\tconst yTicks = axisLeft(chart.yScale).tickValues(chart.yTickValues)\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}, ${s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset + pixelOffset})`\n\t\t\t)\n\t\t\t.call(xTicks)\n\n\t\tyAxis.attr('transform', `translate(${s.yAxisOffset + pixelOffset}, ${pixelOffset})`).call(yTicks)\n\n\t\txTitle.select('text, title').remove()\n\t\tconst xText = xTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.axisTitleFontSize - 4) +\n\t\t\t\t\t')'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-x-title-text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(s.xTitleLabel)\n\n\t\tconst yTitleLabel = 'Cumulative Incidence (%)'\n\t\tyTitle.select('text, title').remove()\n\t\tconst yText = yTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(-s.svgPadding.left / 2 - s.axisTitleFontSize) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 +\n\t\t\t\t\t')rotate(-90)'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-y-title-text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(yTitleLabel)\n\t}\n}\n\nfunction setInteractivity(self) {\n\tconst labels = {\n\t\tcuminc: 'Cumulative incidence',\n\t\tlow: 'Lower 95% CI',\n\t\thigh: 'Upper 95% CI'\n\t}\n\n\tself.mouseover = function (event) {\n\t\tconst d = event.target.__data__\n\t\t/*if (event.target.tagName == 'circle') {\n\t\t\tconst label = labels[d.seriesName]\n\t\t\tconst x = d.x.toFixed(1)\n\t\t\tconst y = d.y.toPrecision(2)\n\t\t\tconst rows = [\n\t\t\t\t`<tr><td colspan=2 style='text-align: center'>${\n\t\t\t\t\td.seriesLabel ? d.seriesLabel : self.config.term.term.name\n\t\t\t\t}</td></tr>`,\n\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>Time to event:</td><td style='padding:3px; text-align:center'>${x} years</td></tr>`,\n\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>${label}:</td><td style='padding:3px; text-align:center'>${y}%</td></tr>`\n\t\t\t]\n\t\t\t// may also indicate the confidence interval (low%-high%) in a new row\n\t\t\tself.app.tip\n\t\t\t\t.show(event.clientX, event.clientY)\n\t\t\t\t.d.html(`<table class='sja_simpletable'>${rows.join('\\n')}</table>`)\n\t\t} else if (event.target.tagName == 'path' && d && d.seriesId) {\n\t\t\tself.app.tip.show(event.clientX, event.clientY).d.html(d.seriesLabel ? d.seriesLabel : d.seriesId)\n\t\t} else {\n\t\t\tself.app.tip.hide()\n\t\t}*/\n\t}\n\n\tself.mouseout = function () {\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 menu = self.tip.clear()\n\t\tif (self.config.term2 == null) {\n\t\t\tconst color = rgb(self.settings.defaultColor).formatHex()\n\t\t\tconst colorDiv = menu.d\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t.text('Edit color:')\n\t\t\tconst input = colorDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', color)\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tconst color = input.node().value\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig: { settings: { cuminc: { defaultColor: color } } }\n\t\t\t\t\t})\n\t\t\t\t\tmenu.hide()\n\t\t\t\t})\n\t\t\tmenu.show(x, y)\n\t\t\treturn\n\t\t}\n\t\tif (!d.seriesId) return\n\n\t\tmenu.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(`Hide`)\n\t\t\t.on('click', async e => {\n\t\t\t\tmenu.hide()\n\t\t\t\tself.hideLegendItem(d)\n\t\t\t})\n\t\tlet color = self.term2toColor[d.seriesId]?.adjusted\n\t\tif (color) {\n\t\t\tcolor = rgb(color).formatHex()\n\t\t\tconst colorDiv = menu.d\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t.text('Edit color:')\n\t\t\tconst input = colorDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', color)\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tconst t2 = self.config.term2\n\t\t\t\t\tconst term2 = structuredClone(t2)\n\t\t\t\t\tif (!term2.term.values) term2.term.values = { [d.seriesId]: {} }\n\t\t\t\t\telse if (!term2.term.values[d.seriesId]) term2.term.values[d.seriesId] = {}\n\t\t\t\t\tterm2.term.values[d.seriesId].color = input.node().value\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: self.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tterm2\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\tmenu.hide()\n\t\t\t\t})\n\t\t}\n\t\tmenu.show(event.clientX, event.clientY)\n\t}\n\n\tself.hideLegendItem = function (d) {\n\t\tconst hidden = self.settings.hidden.slice()\n\t\tconst i = hidden.indexOf(d.seriesId)\n\t\ti == -1 ? hidden.push(d.seriesId) : hidden.splice(i, 1)\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\tcuminc: {\n\t\t\t\t\t\tcustomHidden: hidden\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n}\n\nconst defaultSettings = JSON.stringify({\n\tcontrols: {\n\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\tterm0: null\n\t},\n\tcuminc: {\n\t\tminSampleSize: 10, // sent to server-side\n\t\tminAtRisk: 10,\n\t\tatRiskVisible: true,\n\t\tatRiskLabelOffset: -10,\n\t\tseriesTipDecimals: 0,\n\t\tciVisible: true,\n\t\tradius: 5,\n\t\tfill: '#fff',\n\t\tstroke: '#000',\n\t\tfillOpacity: 0,\n\t\tchartMargin: 10,\n\t\tsvgw: 400,\n\t\tsvgh: 300,\n\t\tsvgPadding: {\n\t\t\ttop: 20,\n\t\t\tleft: 55,\n\t\t\tright: 20,\n\t\t\tbottom: 50\n\t\t},\n\t\taxisTitleFontSize: 16,\n\t\txAxisOffset: 5,\n\t\tyAxisOffset: -5,\n\t\tdefaultColor: '#2077b4'\n\t}\n})\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'cuminc: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi, {\n\t\t\tcondition: { mode: 'cuminc' }\n\t\t})\n\t\t// supply the default q if opts.term0/2.bins/q is undefined\n\t\t// so that the default q 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 ? null : getT0T2defaultQ(true))\n\t\tif (opts.term0)\n\t\t\tawait fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? null : getT0T2defaultQ(true))\n\t} catch (e) {\n\t\tthrow `${e} [cuminc getPlotConfig()]`\n\t}\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: JSON.parse(defaultSettings)\n\t}\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\nfunction getPj(self) {\n\tconst pj = new Partjson({\n\t\ttemplate: {\n\t\t\txMin: '>=x()',\n\t\t\txMax: '<=x()',\n\t\t\tyMin: '>=yMin()',\n\t\t\tyMax: '<=yMax()',\n\t\t\tcharts: [\n\t\t\t\t{\n\t\t\t\t\tchartId: '@key',\n\t\t\t\t\tchartTitle: '=chartTitle()',\n\t\t\t\t\txMin: '>=x()',\n\t\t\t\t\txMax: '<=x()',\n\t\t\t\t\t'__:xTickValues': '=xTickValues()',\n\t\t\t\t\t'__:yTickValues': '=yTickValues()',\n\t\t\t\t\t'__:xScale': '=xScale()',\n\t\t\t\t\t'__:yScale': '=yScale()',\n\t\t\t\t\tyMin: '>=yMin()',\n\t\t\t\t\tyMax: '<=yMax()',\n\t\t\t\t\tserieses: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tchartId: '@parent.@parent.@key',\n\t\t\t\t\t\t\tseriesId: '@key',\n\t\t\t\t\t\t\t'__:seriesLabel': '=seriesLabel()',\n\t\t\t\t\t\t\tdata: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t'__:seriesId': '@parent.@parent.seriesId',\n\t\t\t\t\t\t\t\t\t//color: \"$color\",\n\t\t\t\t\t\t\t\t\tx: '$time',\n\t\t\t\t\t\t\t\t\ty: '$cuminc',\n\t\t\t\t\t\t\t\t\tlow: '$low',\n\t\t\t\t\t\t\t\t\thigh: '$high',\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\tnrisk: '$nrisk',\n\t\t\t\t\t\t\t\t\tnevent: '$nevent',\n\t\t\t\t\t\t\t\t\tncensor: '$ncensor'\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t'$time'\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t},\n\t\t\t\t\t\t'$seriesId'\n\t\t\t\t\t],\n\t\t\t\t\t'@done()': '=sortSerieses()'\n\t\t\t\t},\n\t\t\t\t'$chartId'\n\t\t\t]\n\t\t},\n\t\t'=': {\n\t\t\tchartTitle(row) {\n\t\t\t\tif (!self.state?.config?.term) return row.chartId\n\t\t\t\tconst s = self.settings\n\t\t\t\tconst cutoff = self.config.term.q.breaks[0]\n\t\t\t\tif (!row.chartId || row.chartId == '-') {\n\t\t\t\t\treturn cutoff == 5 ? 'CTCAE grade 5' : `CTCAE grade ${cutoff}-5`\n\t\t\t\t}\n\t\t\t\tconst t0 = self.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.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.config?.term2\n\t\t\t\tif (!t2) return context.self.seriesId\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\treturn seriesId\n\t\t\t},\n\t\t\tx(row) {\n\t\t\t\tif (self.settings.hidden?.includes(row.seriesId)) return\n\t\t\t\treturn row.time\n\t\t\t},\n\t\t\tyMin(row) {\n\t\t\t\tif (self.settings.hidden?.includes(row.seriesId)) return\n\t\t\t\treturn self.settings.ciVisible ? row.low : row.cuminc\n\t\t\t},\n\t\t\tyMax(row) {\n\t\t\t\tif (self.settings.hidden?.includes(row.seriesId)) return\n\t\t\t\treturn self.settings.ciVisible ? row.high : row.cuminc\n\t\t\t},\n\t\t\txTickValues(row, context) {\n\t\t\t\tconst s = self.settings\n\t\t\t\tif (s.xTickValues?.length) {\n\t\t\t\t\t// custom x-tick values\n\t\t\t\t\treturn s.xTickValues\n\t\t\t\t} else {\n\t\t\t\t\t// compute x-tick values\n\t\t\t\t\t// uncomment .scale code when the control input is added\n\t\t\t\t\tconst xMin = /*s.scale == 'byChart' ? context.self.xMin : */ context.root.xMin\n\t\t\t\t\tconst xMax = /*s.scale == 'byChart' ? context.self.xMax : */ context.root.xMax\n\t\t\t\t\treturn computeTickValues(xMin, xMax)\n\t\t\t\t}\n\t\t\t},\n\t\t\txScale(row, context) {\n\t\t\t\t// scale axis according to tick values\n\t\t\t\tconst s = self.settings\n\t\t\t\tconst min = Math.min(...context.self.xTickValues)\n\t\t\t\tconst max = Math.max(...context.self.xTickValues)\n\t\t\t\treturn scaleLinear()\n\t\t\t\t\t.domain([min, max])\n\t\t\t\t\t.range([0, s.svgw - s.svgPadding.left - s.svgPadding.right])\n\t\t\t},\n\t\t\tscaledX(row, context) {\n\t\t\t\tconst xScale = context.context.context.context.parent.xScale.clamp(false)\n\t\t\t\treturn xScale(context.self.x)\n\t\t\t},\n\t\t\tyTickValues(row, context) {\n\t\t\t\tconst s = self.settings\n\t\t\t\tif (s.yTickValues?.length) {\n\t\t\t\t\t// custom y-tick values\n\t\t\t\t\treturn s.yTickValues\n\t\t\t\t} else {\n\t\t\t\t\t// compute y-tick values\n\t\t\t\t\t// uncomment .scale code when the control input is added\n\t\t\t\t\tconst yMin = /*s.scale == 'byChart' ? context.self.yMin : */ context.root.yMin\n\t\t\t\t\tconst yMax = /*s.scale == 'byChart' ? context.self.yMax : */ context.root.yMax\n\t\t\t\t\treturn computeTickValues(yMin, yMax)\n\t\t\t\t}\n\t\t\t},\n\t\t\tyScale(row, context) {\n\t\t\t\t// scale axis according to tick values\n\t\t\t\tconst s = self.settings\n\t\t\t\tconst min = Math.min(...context.self.yTickValues)\n\t\t\t\tconst max = Math.max(...context.self.yTickValues)\n\t\t\t\treturn scaleLinear()\n\t\t\t\t\t.domain([max, min])\n\t\t\t\t\t.range([0, s.svgh - s.svgPadding.top - s.svgPadding.bottom])\n\t\t\t},\n\t\t\tscaledY(row, context) {\n\t\t\t\tconst yScale = context.context.context.context.parent.yScale.clamp(false)\n\t\t\t\tconst s = context.self\n\t\t\t\treturn [yScale(s.y), yScale(s.low), yScale(s.high)]\n\t\t\t},\n\t\t\tsortSerieses(result) {\n\t\t\t\tif (!self.refs.bins) return\n\t\t\t\tconst labelOrder = self.refs.bins.map(b => b.label)\n\t\t\t\tresult.serieses.sort((a, b) => labelOrder.indexOf(a.seriesId) - labelOrder.indexOf(b.seriesId))\n\t\t\t}\n\t\t}\n\t})\n\n\treturn pj\n}\n\nfunction computeTickValues(min, max) {\n\t// compute width between ticks for a maximum of 5 ticks\n\tconst tickWidth = (max - min) / 5\n\t// round tick width to the nearest 5\n\tconst log = Math.floor(Math.log10(tickWidth))\n\tconst tickWidth_rnd = Math.round(tickWidth / (5 * 10 ** log)) * (5 * 10 ** log) || 1 * 10 ** log\n\t// compute tick values using tick width\n\tconst tickValues = []\n\tlet tick = min\n\twhile (tick <= Math.min(100, max + tickWidth_rnd)) {\n\t\t// using max + tickWidth_rnd to ensure that\n\t\t// the last tick will be greater than the max\n\t\t// value of the data\n\t\ttickValues.push(tick)\n\t\ttick = tick + tickWidth_rnd\n\t}\n\tif (!tickValues.includes(0)) tickValues.unshift(0)\n\treturn tickValues\n}\n"],
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