npm - @sjcrh/proteinpaint-client - Versions diffs - 2.211.1-0 → 2.212.0 - Mend

@sjcrh/proteinpaint-client 2.211.1-0 → 2.212.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (550) hide show

package/dist/{2dmaf-A4CD7IRB.js → 2dmaf-R23YQDZC.js} RENAMED Viewed

@@ -8,10 +8,10 @@ import {
   renderSandboxFormDiv,
   sayerror,
   to_svg
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import {
   Menu
 } from "./chunk-7XZA2XR2.js";
@@ -1364,4 +1364,4 @@ export {
   d2mafparseinput,
   d2mafui
 };
-//# sourceMappingURL=2dmaf-A4CD7IRB.js.map
+//# sourceMappingURL=2dmaf-R23YQDZC.js.map

package/dist/{AggMatrixInput-4FU3FARW.js → AggMatrixInput-4DIGZZN4.js} RENAMED Viewed

@@ -1,15 +1,15 @@
 import {
   validatePlotConfig
-} from "./chunk-MHDJUMXL.js";
+} from "./chunk-PF5UMQEJ.js";
 import {
   PlotBase,
   appInit,
   capitalizeFirstLetter,
   formatHeaderText
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -403,4 +403,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=AggMatrixInput-4FU3FARW.js.map
+//# sourceMappingURL=AggMatrixInput-4DIGZZN4.js.map

package/dist/{AggregateMatrix-7ODO25TE.js → AggregateMatrix-TF6XXFUN.js} RENAMED Viewed

@@ -4,11 +4,11 @@ import {
   componentInit,
   getPlotConfig,
   validatePlotConfig
-} from "./chunk-MHDJUMXL.js";
-import "./chunk-UODENFH4.js";
+} from "./chunk-PF5UMQEJ.js";
+import "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -38,4 +38,4 @@ export {
   getPlotConfig,
   validatePlotConfig
 };
-//# sourceMappingURL=AggregateMatrix-7ODO25TE.js.map
+//# sourceMappingURL=AggregateMatrix-TF6XXFUN.js.map

package/dist/{AppHeader-F7QNSLZX.js → AppHeader-JB5HPAOQ.js} RENAMED Viewed

@@ -1,17 +1,17 @@
 import {
   makeButton,
   openSandbox
-} from "./chunk-LFTQD2MN.js";
+} from "./chunk-ZKINKYOJ.js";
 import {
   get_tklst
-} from "./chunk-OMVJLJBW.js";
-import "./chunk-LAGNTLWD.js";
-import "./chunk-YDYT5LFU.js";
+} from "./chunk-UWRWFS3K.js";
+import "./chunk-SXYZ274A.js";
+import "./chunk-PCJF5MGF.js";
 import "./chunk-PRZWSBMA.js";
 import "./chunk-MKAF2BHB.js";
 import {
   block_init_default
-} from "./chunk-IHUP4WZT.js";
+} from "./chunk-ZMSTQP6O.js";
 import {
   urlmap_default
 } from "./chunk-4FTH4L3A.js";
@@ -22,12 +22,12 @@ import {
   newSandboxDiv,
   sayerror,
   throwMsgWithFilePathAndFnName
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import {
   string2pos
 } from "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -215,7 +215,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-XCJDVW4D.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-7WZWBQVA.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -814,7 +814,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-XCJDVW4D.js").then((b) => new b.Block(par));
+      import("./block-7WZWBQVA.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -827,4 +827,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-F7QNSLZX.js.map
+//# sourceMappingURL=AppHeader-JB5HPAOQ.js.map

package/dist/{BoxPlot-UOT477UK.js → BoxPlot-47TUXQDP.js} RENAMED Viewed

@@ -20,10 +20,10 @@ import {
   renderTable,
   renderTerm1Label,
   setDescrStatsByTerm
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import {
   Menu
 } from "./chunk-7XZA2XR2.js";
@@ -1205,4 +1205,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=BoxPlot-UOT477UK.js.map
+//# sourceMappingURL=BoxPlot-47TUXQDP.js.map

package/dist/{CorrelationVolcano-7NG7MESL.js → CorrelationVolcano-G7K5JEPM.js} RENAMED Viewed

@@ -9,10 +9,10 @@ import {
   formatHeaderText,
   table2col,
   to_svg
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import {
   Menu
 } from "./chunk-7XZA2XR2.js";
@@ -614,4 +614,4 @@ export {
   getDefaultCorrVolcanoSettings,
   getPlotConfig
 };
-//# sourceMappingURL=CorrelationVolcano-7NG7MESL.js.map
+//# sourceMappingURL=CorrelationVolcano-G7K5JEPM.js.map

package/dist/{Cuminc-MLVPUTBL.js → Cuminc-LBXPOENU.js} RENAMED Viewed

@@ -15,10 +15,10 @@ import {
   renderTerm1Label,
   require_partjson_umd,
   sayerror
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import {
   Menu
 } from "./chunk-7XZA2XR2.js";
@@ -664,6 +664,7 @@ var MassCumInc = class _MassCumInc extends PlotBase {
           legendItems.push({
             seriesId: series.seriesId,
             text: series.seriesLabel,
+            testID: series.seriesId,
             color: this.term2toColor[series.seriesId].adjusted,
             isHidden: this.settings.hidden.includes(series.seriesId)
           });
@@ -1216,4 +1217,4 @@ export {
   cumincInit,
   getPlotConfig
 };
-//# sourceMappingURL=Cuminc-MLVPUTBL.js.map
+//# sourceMappingURL=Cuminc-LBXPOENU.js.map

package/dist/Cuminc-LBXPOENU.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/cuminc/Cuminc.ts", "../plots/cuminc/settings/defaults.ts", "../plots/cuminc/processData.ts"],
+  "sourcesContent": ["import { getCompInit, copyMerge, type ComponentApi, type RxComponent, type AppApi } from '#rx'\nimport { controlsInit, renderTerm1Label } from '#plots/controls.js'\nimport { getT0T2defaultQ } from '#plots/summaryQ.ts'\nimport { fillTermWrapper } from '#termsetting'\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, type Line } from 'd3-shape'\nimport { rgb } from 'd3-color'\nimport { getSeriesTip, htmlLegend, Menu, renderAtRiskG, renderPvalues, sayerror } from '#dom'\nimport Partjson from 'partjson'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\nimport { defaultSettings } from './settings/defaults.ts'\nimport type { CumincSettings } from './settings/Settings.ts'\nimport { computeTickValues } from './processData.ts'\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 implements RxComponent {\n\tstatic type = 'cuminc'\n\n\ttype: string\n\tpj: Partjson\n\tstate: any\n\ttip: Menu\n\tlineFxn: Line<[number, number]>\n\thidePlotTitle: boolean\n\tlegendRenderer: any\n\tlegendClick!: (f: any, f2: any, f3: any) => void\n\tconfig: any\n\tsettings!: CumincSettings\n\tcurrData: any[] = []\n\tuniqueSeriesIds: Set<any> = new Set()\n\ttests: { [chartId: string]: any[] } = {}\n\trefs: any = {}\n\tterm2toColor: { [seriesId: string]: { orig: string; rgb: any; adjusted: string } } = {}\n\tcolorScale: any\n\tlegendData: any[] = []\n\trender: () => void = () => {}\n\n\tconstructor(opts: any, api?: ComponentApi) {\n\t\t// this class is instantiated directly, not as an rx component, so there is no plot api\n\t\tsuper(opts, api)\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: any) => c.scaledX)\n\t\t\t.y((c: any) => 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: any) {\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: any) {\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: any) {\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: any[] = []\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: any = {\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 extends PlotBase implements RxComponent {\n\tstatic type = 'cuminc'\n\n\ttype: string\n\tchartIncrement = 0\n\tloadingWait = 0\n\ttip!: Menu\n\tpj!: any\n\tlineFxn!: any\n\tsettings: any\n\tconfig: any\n\tlegendRenderer: any\n\thiddenRenderer: any\n\tlegendClick: (d: any, x: any, y: any) => void = () => {}\n\thideLegendItem: (d: any) => void = () => {}\n\tdownload: () => void = () => {}\n\trender: () => void = () => {}\n\tmouseover: (event: any) => void = () => {}\n\tmouseout: () => void = () => {}\n\tcomponents: { [name: string]: any } = {}\n\n\tuniqueSeriesIds: Set<any> = new Set()\n\tcurrData: any[] = []\n\ttests: { [chartId: string]: any[] } = {}\n\trefs: any = {}\n\tnoData: string[] = []\n\tlowSampleSize: { [chartId: string]: string[] } = {}\n\tnoEvents: { [chartId: string]: string[] } = {}\n\tterm2toColor: { [seriesId: string]: { orig: string; rgb: any; adjusted: string } } = {}\n\tcolorScale: any\n\tlegendData: any[] = []\n\thiddenData: any[] = []\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = MassCumInc.type\n\t\tthis.chartIncrement = 0\n\t\t// do not transition the loading div on the initial chart load,\n\t\t// toggleLoadingDiv() below resets this to the PlotBase default\n\t\tthis.loadingWait = 0\n\t}\n\n\tasync init(appState: any) {\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 as any).scaledX)\n\t\t\t.y(c => (c as any).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: any) {\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\t;(this.opts.controls as any).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: { label: string; value: string }[] = []\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\tmin: 0,\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\tmin: 0,\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\t\t\t;(this.components.controls as any).on('downloadClick.cuminc', this.download)\n\t\t}\n\t}\n\n\tgetState(appState: any) {\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.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: any = {\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(): string[] {\n\t\tconst hidden: string[] = []\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: any) {\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\tif (chartId in noEvents) noEvents[chartId].push(seriesId)\n\t\t\t\t\t\telse noEvents[chartId] = [seriesId]\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tif (chartId in estimates) estimates[chartId][seriesId] = series\n\t\t\t\t\telse 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\tif (chartId in this.tests) this.tests[chartId].push(d)\n\t\t\t\telse 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: any) {\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: any) {\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: any[] = []\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: any = {\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\ttestID: series.seriesId,\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\t// overrides PlotBase.toggleLoadingDiv(), which also toggles dom.renderedData\n\t// that this plot does not have\n\ttoggleLoadingDiv(display: string = '') {\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(this.loadingWait)\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// only the initial chart load is not transitioned\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: any) {\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', s.orderChartsBy == 'organ-system' ? chart.color : '')\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-' + chart.chartId)\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') as any\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} as any)\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', 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} as any)\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] =\n\t\t\tgetSvgSubElems(\n\t\t\t\tsvg\n\t\t\t\t/*chart*/\n\t\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 (this: any, series: any) {\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-${d.seriesId || ''}`)\n\t\t\t.each(function (this: any, series) {\n\t\t\t\trenderSeries(select(this), series, s)\n\t\t\t})\n\n\t\trenderAxes(xAxis, xTitle, yAxis, yTitle, s, chart)\n\t\trenderAtRiskG({\n\t\t\tg: atRiskG,\n\t\t\ts,\n\t\t\tchart,\n\t\t\tterm2toColor: self.term2toColor,\n\t\t\tonSerieClick: self.legendClick\n\t\t} as any)\n\n\t\tplotRect\n\t\t\t.attr('x', 0)\n\t\t\t.attr('width', s.svgw - s.svgPadding.left - s.svgPadding.right)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('height', s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset)\n\n\t\tsvg.seriesTip.update({\n\t\t\txScale: chart.xScale,\n\t\t\txTitleLabel: s.xTitleLabel,\n\t\t\tdecimals: s.seriesTipDecimals,\n\t\t\tserieses: chart.visibleSerieses.map(s => {\n\t\t\t\tconst seriesLabel = s.seriesLabel ? `${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}-${self.chartIncrement++}`\n\t\t\tclipRect = svg.append('defs').append('clipPath').attr('id', clipId).append('rect')\n\t\t\t// clipG = svg.append('g').attr('class', 'sjpcb-cuminc-clipG')\n\t\t\tmainG = svg.append('g').attr('class', 'sjpcb-cuminc-mainG').attr('data-testid', 'sjpp-cuminc-main-g')\n\t\t\tseriesesG = mainG.append('g').attr('class', 'sjpcb-cuminc-seriesesG').attr('clip-path', `url(#${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\t// clipG = 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 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])(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}, ${pixelOffset})`).call(yTicks)\n\n\t\txTitle.select('text, title').remove()\n\t\t/*const xText =*/ xTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.axisTitleFontSize - 4) +\n\t\t\t\t\t')'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-x-title-text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(s.xTitleLabel)\n\n\t\tconst yTitleLabel = 'Cumulative Incidence (%)'\n\t\tyTitle.select('text, title').remove()\n\n\t\t/*const yText = */ yTitle\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t'translate(' +\n\t\t\t\t\t(-s.svgPadding.left / 2 - s.axisTitleFontSize) +\n\t\t\t\t\t',' +\n\t\t\t\t\t(s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 +\n\t\t\t\t\t')rotate(-90)'\n\t\t\t)\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'sjpp-cuminc-y-title-text')\n\t\t\t.style('text-anchor', 'middle')\n\t\t\t.style('font-size', s.axisTitleFontSize + 'px')\n\t\t\t.text(yTitleLabel)\n\t}\n}\n\nfunction setInteractivity(self: any) {\n\t// const labels = {\n\t// \tcuminc: 'Cumulative incidence',\n\t// \tlow: 'Lower 95% CI',\n\t// \thigh: 'Upper 95% CI'\n\t// }\n\n\t/*** Unused */\n\t// self.mouseover = function (event) {\n\t// \t// const d = event.target.__data__\n\t// \t/*if (event.target.tagName == 'circle') {\n\t// \t\tconst label = labels[d.seriesName]\n\t// \t\tconst x = d.x.toFixed(1)\n\t// \t\tconst y = d.y.toPrecision(2)\n\t// \t\tconst rows = [\n\t// \t\t\t`<tr><td colspan=2 style='text-align: center'>${\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 () => {\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 as MouseEvent).clientX, (event as MouseEvent).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\tif (i == -1) hidden.push(d.seriesId)\n\t\telse 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\nexport async function getPlotConfig(opts: any, app: AppApi) {\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} as any)\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(\n\t\t\t\topts.term2,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term2.bins || opts.term2.q ? undefined : getT0T2defaultQ(true)\n\t\t\t)\n\t\tif (opts.term0)\n\t\t\tawait fillTermWrapper(\n\t\t\t\topts.term0,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term0.bins || opts.term0.q ? undefined : getT0T2defaultQ(true)\n\t\t\t)\n\t} catch (e) {\n\t\tthrow `${e} [cuminc getPlotConfig()]`\n\t}\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: JSON.parse(defaultSettings)\n\t}\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\nfunction getPj(self: any): Partjson {\n\tconst pj = new Partjson({\n\t\ttemplate: {\n\t\t\txMin: '>=x()',\n\t\t\txMax: '<=x()',\n\t\t\tyMin: '>=yMin()',\n\t\t\tyMax: '<=yMax()',\n\t\t\tcharts: [\n\t\t\t\t{\n\t\t\t\t\tchartId: '@key',\n\t\t\t\t\tchartTitle: '=chartTitle()',\n\t\t\t\t\txMin: '>=x()',\n\t\t\t\t\txMax: '<=x()',\n\t\t\t\t\t'__:xTickValues': '=xTickValues()',\n\t\t\t\t\t'__:yTickValues': '=yTickValues()',\n\t\t\t\t\t'__:xScale': '=xScale()',\n\t\t\t\t\t'__:yScale': '=yScale()',\n\t\t\t\t\tyMin: '>=yMin()',\n\t\t\t\t\tyMax: '<=yMax()',\n\t\t\t\t\tserieses: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tchartId: '@parent.@parent.@key',\n\t\t\t\t\t\t\tseriesId: '@key',\n\t\t\t\t\t\t\t'__:seriesLabel': '=seriesLabel()',\n\t\t\t\t\t\t\tdata: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t'__:seriesId': '@parent.@parent.seriesId',\n\t\t\t\t\t\t\t\t\t//color: \"$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\t// const 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(_, 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(_, 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(_, 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(_, 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(_, 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(_, 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(_, 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", "export const defaultSettings = JSON.stringify({\n    controls: {\n        term2: null, // the previous overlay value may be displayed as a convenience for toggling\n        term0: null\n    },\n    cuminc: {\n        minSampleSize: 10, // sent to server-side\n        minAtRisk: 10,\n        atRiskVisible: true,\n        atRiskLabelOffset: -10,\n        seriesTipDecimals: 0,\n        ciVisible: true,\n        radius: 5,\n        fill: '#fff',\n        stroke: '#000',\n        fillOpacity: 0,\n        chartMargin: 10,\n        svgw: 400,\n        svgh: 300,\n        svgPadding: {\n            top: 20,\n            left: 55,\n            right: 20,\n            bottom: 50\n        },\n        axisTitleFontSize: 16,\n        xAxisOffset: 5,\n        yAxisOffset: -5,\n        defaultColor: '#2077b4'\n    }\n})", "/** TODO: Mv any data processing and formatting out of the Cuminc and MassCumInc. \n * Those methods should be encapsulated and tested. See accompanying unit test file. */\n\nexport function computeTickValues(min: number, max: number): number[] {\n\t// guard against invalid/degenerate ranges\n \tif (!Number.isFinite(min) || !Number.isFinite(max)) return [0]\n \tif (max < min) [min, max] = [max, min]\n \tif (max === min) return min === 0 ? [0] : [0, Math.min(100, min)]\n\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 base = 5 * 10 ** log\n\tconst tickWidth_rnd = Math.round(tickWidth / (base)) * (base) || 1 * 10 ** log\n\t// compute tick values using tick width\n\tconst tickValues: number[] = []\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"],
+  "mappings": 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+  "names": ["item", "s", "color", "Partjson"]
+}

package/dist/{DE-D5K7ZSDS.js → DE-JSWA6HXV.js} RENAMED Viewed

@@ -1,19 +1,19 @@
 import {
   appInit
-} from "./chunk-RRV7ISPH.js";
-import "./chunk-U6S3IVWB.js";
+} from "./chunk-TAZQU2LC.js";
+import "./chunk-UYSYZM45.js";
 import "./chunk-WKCVZIN7.js";
-import "./chunk-HVF3XGIM.js";
-import "./chunk-SEX5VXIS.js";
+import "./chunk-O3QKYUDH.js";
+import "./chunk-5WMFEMII.js";
 import "./chunk-W7A4QXZ7.js";
 import "./chunk-X46YA4CB.js";
 import "./chunk-SKMFMGCD.js";
 import "./chunk-BSWVDH75.js";
 import "./chunk-PRZWSBMA.js";
-import "./chunk-UODENFH4.js";
+import "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -86,4 +86,4 @@ async function init(arg, holder, genomes) {
 export {
   init
 };
-//# sourceMappingURL=DE-D5K7ZSDS.js.map
+//# sourceMappingURL=DE-JSWA6HXV.js.map

package/dist/{DEinput-GC57ZRHF.js → DEinput-LEYRVYK6.js} RENAMED Viewed

@@ -13,10 +13,10 @@ import {
   negateFilter,
   renderPreAnalysisData,
   renderTable
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -498,4 +498,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=DEinput-GC57ZRHF.js.map
+//# sourceMappingURL=DEinput-LEYRVYK6.js.map

package/dist/{DM-SX37W5MO.js → DM-332QECUP.js} RENAMED Viewed

@@ -1,19 +1,19 @@
 import {
   appInit
-} from "./chunk-RRV7ISPH.js";
-import "./chunk-U6S3IVWB.js";
+} from "./chunk-TAZQU2LC.js";
+import "./chunk-UYSYZM45.js";
 import "./chunk-WKCVZIN7.js";
-import "./chunk-HVF3XGIM.js";
-import "./chunk-SEX5VXIS.js";
+import "./chunk-O3QKYUDH.js";
+import "./chunk-5WMFEMII.js";
 import "./chunk-W7A4QXZ7.js";
 import "./chunk-X46YA4CB.js";
 import "./chunk-SKMFMGCD.js";
 import "./chunk-BSWVDH75.js";
 import "./chunk-PRZWSBMA.js";
-import "./chunk-UODENFH4.js";
+import "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -87,4 +87,4 @@ async function init(arg, holder, genomes) {
 export {
   init
 };
-//# sourceMappingURL=DM-SX37W5MO.js.map
+//# sourceMappingURL=DM-332QECUP.js.map

package/dist/{DifferentialAnalysis-GL3EXMSS.js → DifferentialAnalysis-JGH2OMTH.js} RENAMED Viewed

@@ -9,12 +9,12 @@ import {
   formatHeaderText,
   getDefaultVolcanoSettings,
   validateVolcanoSettings
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
 import {
   importPlot
-} from "./chunk-6ROUECR6.js";
+} from "./chunk-5WIA4KFA.js";
 import {
   Menu
 } from "./chunk-7XZA2XR2.js";
@@ -236,4 +236,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=DifferentialAnalysis-GL3EXMSS.js.map
+//# sourceMappingURL=DifferentialAnalysis-JGH2OMTH.js.map

package/dist/{Disco-NQFVZ3F7.js → Disco-36PJXFM6.js} RENAMED Viewed

@@ -8,10 +8,10 @@ import {
   renderTable,
   svgLegend,
   table2col
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import {
   Menu
 } from "./chunk-7XZA2XR2.js";
@@ -184,7 +184,7 @@ async function makeSvgraph(fusion, div, genome) {
   await getGm(svpair.a, genome.name, fusion.source.gene);
   await getGm(svpair.b, genome.name, fusion.target.gene);
   wait.remove();
-  const _ = await import("./svgraph-7YACP2JZ.js");
+  const _ = await import("./svgraph-U7MS7YEM.js");
   _.default({
     pairlst: [svpair],
     genome,
@@ -283,7 +283,7 @@ var DiscoInteractions = class {
           }
         ]
       };
-      const _ = await import("./block.init-TJEAFIN6.js");
+      const _ = await import("./block.init-YN4KHHJ2.js");
       await _.default(arg);
     };
     this.colorScaleNumericInputsCallback = async (obj) => {
@@ -3386,4 +3386,4 @@ export {
   discoInit,
   getPlotConfig
 };
-//# sourceMappingURL=Disco-NQFVZ3F7.js.map
+//# sourceMappingURL=Disco-36PJXFM6.js.map

package/dist/{Disco.UI-KDHXODP2.js → Disco.UI-PY2KOGKY.js} RENAMED Viewed

@@ -1,6 +1,6 @@
 import {
   launch
-} from "./chunk-T5LYWAOL.js";
+} from "./chunk-IBZVZZ5J.js";
 import {
   makeBtn,
   makeFileUpload,
@@ -9,18 +9,18 @@ import {
   makeResetBtn,
   makeTextAreaInput
 } from "./chunk-5EBRF6Z7.js";
-import "./chunk-OIRGFH7Q.js";
-import "./chunk-SEX5VXIS.js";
+import "./chunk-A4D2Z2LV.js";
+import "./chunk-5WMFEMII.js";
 import "./chunk-X46YA4CB.js";
 import "./chunk-SKMFMGCD.js";
 import {
   Tabs,
   appear,
   sayerror
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -240,4 +240,4 @@ function backButton(holder, genomes) {
 export {
   init_discoplotUI
 };
-//# sourceMappingURL=Disco.UI-KDHXODP2.js.map
+//# sourceMappingURL=Disco.UI-PY2KOGKY.js.map

package/dist/{DmrPlot-BJXEHPWV.js → DmrPlot-5WMOBZOJ.js} RENAMED Viewed

@@ -1,14 +1,14 @@
 import {
   DmrViewModel,
   getDefaultDMRSettings
-} from "./chunk-JPRCZTWX.js";
+} from "./chunk-WILJJPWV.js";
 import {
   PlotBase,
   table2col
-} from "./chunk-UODENFH4.js";
+} from "./chunk-VHDYIOWU.js";
 import "./chunk-HJ6L54YS.js";
 import "./chunk-KV4W2ACA.js";
-import "./chunk-6ROUECR6.js";
+import "./chunk-5WIA4KFA.js";
 import "./chunk-7XZA2XR2.js";
 import "./chunk-DD3DWHUY.js";
 import "./chunk-EEB5VE2A.js";
@@ -79,7 +79,7 @@ var DmrView = class {
     this.dom = dom;
   }
   async renderBlock(viewData, genomeObj, settings, chr, start, stop, onCoordinateChange) {
-    const { Block } = await import("./block-XCJDVW4D.js");
+    const { Block } = await import("./block-7WZWBQVA.js");
     return new Block({
       holder: this.dom.holder,
       genome: genomeObj,
@@ -359,4 +359,4 @@ export {
   componentInit,
   getPlotConfig
 };
-//# sourceMappingURL=DmrPlot-BJXEHPWV.js.map
+//# sourceMappingURL=DmrPlot-5WMOBZOJ.js.map