@sjcrh/proteinpaint-client 2.135.1 → 2.135.2-0

package/dist/{chunk-3QCGJXNI.js → chunk-IMXYAQRH.js}

@@ -1,19 +1,19 @@
 import {
   downloadSingleSVG
-} from "./chunk-QTWKTJNI.js";
+} from "./chunk-VB6IANQH.js";
 import {
   controlsInit
-} from "./chunk-U6CRL7IJ.js";
+} from "./chunk-PDCHOIX4.js";
 import {
   fillTermWrapper,
   fillTwLst
-} from "./chunk-YCYBH4EW.js";
+} from "./chunk-4FDOZ23V.js";
 import {
   icons
 } from "./chunk-RY7CVONT.js";
 import {
   getCategoricalTermFilter
-} from "./chunk-3DNHZAJC.js";
+} from "./chunk-VBQBPNCJ.js";
 import {
   Menu
 } from "./chunk-ASTFYDAL.js";
@@ -62,7 +62,7 @@ var profilePlot = class {
   isAggregate() {
     if (!this.state.logged) return true;
     if (this.settings.isAggregate) return true;
-    if (this.state.sites?.length > 1 || this.state.user == "admin") return true;
+    if (this.state.sites?.length > 1 || this.state.user == "admin" || this.isRadarFacility) return true;
   }
   async init(appState) {
     const config = appState.plots.find((p) => p.id === this.id);
@@ -204,7 +204,7 @@ var profilePlot = class {
     });
     if (isRadarFacility) {
       if (!this.settings.facilitySite) this.settings.facilitySite = this.sites[0]?.value;
-    } else if (!this.settings.site && !this.settings.sites && this.state.sites?.length == 1) {
+    } else if (!this.settings.site && !this.settings.sites && this.state.sites?.length == 1 && !isAggregate) {
       this.settings.site = this.data.sites?.[0]?.value;
       this.settings.sites = [this.settings.site];
     }
@@ -435,11 +435,10 @@ var profilePlot = class {
     this.filterG.attr("font-size", "0.9em").append("text").attr("text-anchor", "left").style("font-weight", "bold").text(`${title} (n=${this.data.n})`).attr("transform", `translate(0, -5)`);
     for (const tw of this.config.filterTWs) this.addFilterLegendItem(tw.term.name, this.settings[tw.term.id]);
     const hospital = this.data.hospital;
-    if (hospital) {
+    if (this.settings.site) {
       const label = this.sites.find((s) => s.value == this.settings.site).label;
       this.addFilterLegendItem("Facility ID", label);
-      const hospital2 = this.data.hospital;
-      this.addFilterLegendItem("Facility", hospital2);
+      this.addFilterLegendItem("Facility", hospital);
     }
   }
   addFilterLegendItem(filter, value) {
@@ -575,4 +574,4 @@ export {
   getDefaultProfilePlotSettings,
   getProfileLogin
 };
-//# sourceMappingURL=chunk-3QCGJXNI.js.map
+//# sourceMappingURL=chunk-IMXYAQRH.js.map

package/dist/chunk-IMXYAQRH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/profilePlot.js"],
+  "sourcesContent": ["import { downloadSingleSVG } from '../common/svg.download.js'\nimport { controlsInit } from './controls.js'\nimport { fillTermWrapper, fillTwLst } from '#termsetting'\nimport { select } from 'd3-selection'\nimport { getSampleFilter } from '../mass/groups.js'\nimport { Menu } from '#dom/menu'\nimport { icons as icon_functions } from '#dom/control.icons'\nimport { getCategoricalTermFilter } from '#shared/filter.js'\n\n/*\n\nThe profilePlot is the base class for all the profile plots. It handles the common functionality such as setting controls, fetching data, and initializing the plot elements.\nAll the profile plots have the same filters:\n- Region\n- Country\n- Income group\n- Facility type\n- Teaching status\n- Referral status\n- Funding source\n- Hospital volume\n- Year of implementation\n- Sites\n\nThe profileRadarFacility adds at the top of these filters the facility select as here we compare a single facility with the average scores of all the facilities aggregated\n*/\n\nconst orderedIncomes = ['Low income', 'Lower middle income', 'Upper middle income', 'High income']\nconst orderedVolumes = [\n\t'Small (1-25 annual newly diagnoses)',\n\t'Medium (26-80 annual newly diagnoses)',\n\t'Large (81-120 annual newly diagnoses)',\n\t'Very large (>120 annual newly diagnoses)'\n]\n\nexport const ABBREV_COHORT = 0\nexport const FULL_COHORT = 1\nexport class profilePlot {\n\tconstructor() {\n\t\tthis.type = 'profilePlot'\n\t\tthis.downloadCount = 0\n\t\tthis.tip = new Menu({ padding: '4px', offsetX: 10, offsetY: 15 })\n\t\tthis.scoreTerms = []\n\t\tthis.isRadarFacility = false\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\tconst { logged, sites, user } = getProfileLogin(this.app, appState.activeCohort) //later on replace with real login info\n\t\tconst site = sites?.[0]\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tvocab: appState.vocab,\n\t\t\tlogged, //later change to read login info\n\t\t\tsite,\n\t\t\tsites,\n\t\t\tuser,\n\t\t\tactiveCohort: appState.activeCohort\n\t\t}\n\t}\n\n\t//refers to the view where all the filters are shown and not the preselected site\n\tisAggregate() {\n\t\tif (!this.state.logged) return true\n\t\tif (this.settings.isAggregate) return true //marked by the user\n\t\tif (this.state.sites?.length > 1 || this.state.user == 'admin' || this.isRadarFacility) return true //multiple sites selected\n\t}\n\n\tasync init(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tconst state = this.getState(appState)\n\t\tif (this.opts.header) {\n\t\t\tlet chartName = config.chartType.match(/[A-Z][a-z]+/g)\n\t\t\tchartName = chartName.join(' ')\n\t\t\tthis.opts.header\n\t\t\t\t.style('text-transform', 'capitalize')\n\t\t\t\t.text(config.header ? config.header + ` / ${state.user}` : chartName + ` / ${state.user}`)\n\t\t}\n\t\tconst div = this.opts.holder.append('div').style('display', 'inline-block')\n\t\tconst leftDiv = div.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\n\t\tconst rightDiv = div.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\n\t\tconst controlsDiv = leftDiv.append('div').style('display', 'inline-block').style('font-size', '0.9em')\n\t\tconst iconsDiv = leftDiv.append('div').style('margin-left', '6px').style('margin-top', '15px')\n\n\t\tconst holder = rightDiv.insert('div').style('display', 'inline-block')\n\n\t\tconst plotDiv = holder.append('div')\n\t\tthis.dom = {\n\t\t\tcontrolsDiv,\n\t\t\tholder,\n\t\t\ticonsDiv,\n\t\t\trightDiv,\n\t\t\tplotDiv\n\t\t}\n\t\tselect('.sjpp-output-sandbox-content').on('scroll', event => {\n\t\t\tif (this.onMouseOut) this.onMouseOut(event)\n\t\t})\n\t\tthis.dom.rightDiv.on('mousemove', event => this.onMouseOver(event))\n\t\tthis.dom.rightDiv.on('mouseleave', event => this.onMouseOut(event))\n\t\tthis.dom.rightDiv.on('mouseout', event => this.onMouseOut(event))\n\n\t\tdocument.addEventListener('scroll', () => this?.tip?.hide())\n\t\ticon_functions['pdf'](iconsDiv.append('div').style('padding', '0px 5px 15px 5px'), {\n\t\t\ttitle: 'Prints page, select Save as PDF in the options to download as a pdf',\n\t\t\thandler: () => {\n\t\t\t\twindow.print()\n\t\t\t}\n\t\t})\n\t\t//later on show table for the profileForms\n\t\tif (this.type != 'profileBarchart' && this.type != 'profileForms') {\n\t\t\tconst tableIconDiv = iconsDiv.append('div').style('padding-bottom', '15px')\n\t\t\tthis.dom.tableBt = tableIconDiv\n\t\t\t\t.append('button')\n\t\t\t\t.attr('data-testid', 'sjpp-profile-table-button')\n\t\t\t\t.style('border', 'none')\n\t\t\t\t.style('background-color', 'rgb(207, 226, 243)')\n\t\t\ticon_functions['table'](this.dom.tableBt, { title: 'Show table with data' })\n\t\t\tthis.dom.tableBt.on('click', () => {\n\t\t\t\tconst show = !this.settings.showTable\n\t\t\t\tthis.dom.tableBt.style('background-color', show ? 'rgb(207, 226, 243)' : 'transparent')\n\t\t\t\tthis.showTable(show)\n\t\t\t})\n\t\t}\n\t\ticon_functions['restart'](iconsDiv.append('div').style('padding', '0px 5px 15px 5px'), {\n\t\t\ttitle: 'Clear filters',\n\t\t\thandler: async () => {\n\t\t\t\tthis.clearFiltersExcept([])\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: { filter: this.getFilter(), settings: { [this.type]: this.settings } }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\ticon_functions['add'](iconsDiv.append('div').style('padding', '3px'), {\n\t\t\ttitle: 'Open a new plot',\n\t\t\thandler: async () => {\n\t\t\t\tlet config = structuredClone(this.config)\n\t\t\t\tconfig.insertBeforeId = this.id\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tonMouseOut(event) {\n\t\tthis.tip.hide()\n\t}\n\n\tasync showTable(show) {\n\t\tthis.settings.showTable = show\n\t\tawait this.app.dispatch({ type: 'plot_edit', id: this.id, config: { settings: { [this.type]: this.settings } } })\n\t}\n\n\tasync main() {\n\t\tthis.config = JSON.parse(JSON.stringify(this.state.config))\n\t\tthis.settings = this.config.settings[this.type]\n\t\tif (this.dom.tableBt)\n\t\t\tthis.dom.tableBt.style('background-color', this.settings.showTable ? 'rgb(207, 226, 243)' : 'transparent')\n\t}\n\n\tasync setControls(additionalInputs = []) {\n\t\tconst isRadarFacility = this.isRadarFacility\n\t\tconst filters = {}\n\t\tfor (const tw of this.config.filterTWs) {\n\t\t\tconst filter = getCategoricalTermFilter(this.config.filterTWs, this.settings, tw, this.state.termfilter.filter)\n\n\t\t\tif (filter) filters[tw.term.id] = filter\n\t\t}\n\t\tthis.filteredTermValues = await this.app.vocabApi.filterTermValues({\n\t\t\tterms: this.config.filterTWs,\n\t\t\tfilters\n\t\t})\n\t\tthis.regions = this.filteredTermValues[this.config.regionTW.id]\n\t\tthis.countries = this.filteredTermValues[this.config.countryTW.id]\n\t\tthis.incomes = this.filteredTermValues[this.config.incomeTW.id]\n\t\tthis.teachingStates = this.filteredTermValues[this.config.teachingStatusTW.id]\n\t\tthis.referralStates = this.filteredTermValues[this.config.referralStatusTW.id]\n\t\tthis.fundingSources = this.filteredTermValues[this.config.fundingSourceTW.id]\n\t\tthis.hospitalVolumes = this.filteredTermValues[this.config.hospitalVolumeTW.id]\n\t\tthis.yearsOfImplementation = this.filteredTermValues[this.config.yearOfImplementationTW.id]\n\n\t\tthis.incomes.sort((elem1, elem2) => {\n\t\t\tconst i1 = orderedIncomes.indexOf(elem1.value)\n\t\t\tconst i2 = orderedIncomes.indexOf(elem2.value)\n\t\t\tif (i1 < i2) return -1\n\t\t\treturn 1\n\t\t})\n\t\tthis.hospitalVolumes.sort((elem1, elem2) => {\n\t\t\tconst i1 = orderedVolumes.indexOf(elem1.value)\n\t\t\tconst i2 = orderedVolumes.indexOf(elem2.value)\n\t\t\tif (i1 < i2) return -1\n\t\t\treturn 1\n\t\t})\n\t\tthis.types = this.filteredTermValues[this.config.typeTW.id]\n\t\tthis.filter = this.config.filter || this.getFilter()\n\n\t\tconst isAggregate = this.isAggregate()\n\t\tif (this.type != 'profileForms')\n\t\t\tthis.data = await this.app.vocabApi.getProfileScores({\n\t\t\t\tscoreTerms: this.scoreTerms,\n\t\t\t\tfilter: this.filter,\n\t\t\t\tisAggregate,\n\t\t\t\tsites: this.settings.sites,\n\t\t\t\tuserSites: this.state.sites,\n\t\t\t\tfacilityTW: this.config.facilityTW\n\t\t\t})\n\t\telse\n\t\t\tthis.data = await this.app.vocabApi.getProfileFormScores({\n\t\t\t\tscoreTerms: this.scoreTerms,\n\t\t\t\tscScoreTerms: this.scScoreTerms,\n\t\t\t\tfilter: this.filter,\n\t\t\t\tisAggregate,\n\t\t\t\tsites: this.settings.sites,\n\t\t\t\tuserSites: this.state.sites,\n\t\t\t\tfacilityTW: this.config.facilityTW\n\t\t\t})\n\t\tthis.sites = this.data.sites\n\t\tthis.sites.sort((a, b) => {\n\t\t\treturn a.label.localeCompare(b.label)\n\t\t})\n\t\tif (isRadarFacility) {\n\t\t\tif (!this.settings.facilitySite) this.settings.facilitySite = this.sites[0]?.value //set the first site as the facility site\n\t\t} else if (!this.settings.site && !this.settings.sites && this.state.sites?.length == 1 && !isAggregate) {\n\t\t\tthis.settings.site = this.data.sites?.[0]?.value\n\t\t\tthis.settings.sites = [this.settings.site] //set sites to the single site\n\t\t}\n\t\tif (this.settings.sites)\n\t\t\tfor (const site of this.settings.sites) {\n\t\t\t\tconst siteOption = this.sites.find(s => s.value == site)\n\t\t\t\tif (siteOption) siteOption.selected = true //mark selected sites\n\t\t\t}\n\t\tconst chartType = this.type\n\t\tthis.dom.controlsDiv.selectAll('*').remove()\n\t\tlet inputs = []\n\t\tif (this.state.sites?.length == 1 && !isRadarFacility) {\n\t\t\tconst dataInput = {\n\t\t\t\tlabel: 'Data',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType,\n\t\t\t\tsettingsKey: 'isAggregate',\n\t\t\t\tstyles: { display: 'inline-block' },\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: this.state.site, value: false },\n\t\t\t\t\t{ label: 'Aggregate', value: true }\n\t\t\t\t],\n\t\t\t\tcallback: isAggregate => {\n\t\t\t\t\tthis.settings.isAggregate = isAggregate\n\t\t\t\t\tconst id = this.sites.find(s => s.label == this.state.site)?.value\n\t\t\t\t\tisAggregate ? this.setSite('') : this.setSite(id)\n\t\t\t\t}\n\t\t\t}\n\t\t\tinputs.push(dataInput)\n\t\t}\n\t\tif (isAggregate || isRadarFacility) {\n\t\t\tinputs.push(\n\t\t\t\t...[\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Region',\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.regionTW.term.id,\n\t\t\t\t\t\toptions: this.regions,\n\t\t\t\t\t\tcallback: value => this.setRegion(value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Country',\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.countryTW.term.id,\n\t\t\t\t\t\toptions: this.countries,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.countryTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Income group',\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.incomeTW.term.id,\n\t\t\t\t\t\toptions: this.incomes,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.incomeTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Facility type',\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.typeTW.term.id,\n\t\t\t\t\t\toptions: this.types,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.typeTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: this.config.teachingStatusTW.term.name,\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.teachingStatusTW.term.id,\n\t\t\t\t\t\toptions: this.teachingStates,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.teachingStatusTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: this.config.referralStatusTW.term.name,\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.referralStatusTW.term.id,\n\t\t\t\t\t\toptions: this.referralStates,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.referralStatusTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: this.config.fundingSourceTW.term.name,\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.fundingSourceTW.term.id,\n\t\t\t\t\t\toptions: this.fundingSources,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.fundingSourceTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: this.config.hospitalVolumeTW.term.name,\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.hospitalVolumeTW.term.id,\n\t\t\t\t\t\toptions: this.hospitalVolumes,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.hospitalVolumeTW.term.id, value)\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: this.config.yearOfImplementationTW.term.name,\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\tsettingsKey: this.config.yearOfImplementationTW.term.id,\n\t\t\t\t\t\toptions: this.yearsOfImplementation,\n\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.yearOfImplementationTW.term.id, value)\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t)\n\t\t}\n\t\tif (this.state.logged) {\n\t\t\tif (isAggregate && (this.state.sites?.length > 1 || this.state.user == 'admin')) {\n\t\t\t\tconst sitesInput = {\n\t\t\t\t\tlabel: 'Sites',\n\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\tchartType,\n\t\t\t\t\toptions: this.sites,\n\t\t\t\t\tmultiple: true,\n\t\t\t\t\tcallback: values => {\n\t\t\t\t\t\tthis.setSites(values)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tinputs.push(sitesInput)\n\t\t\t}\n\t\t\tif (isRadarFacility) {\n\t\t\t\tthis.sampleData = await this.app.vocabApi.getProfileScores({\n\t\t\t\t\tterms: [...this.twLst, this.config.facilityTW], //added facility term to all the plots to get the hospital name\n\t\t\t\t\tscoreTerms: this.scoreTerms,\n\t\t\t\t\tfilter: this.filter,\n\t\t\t\t\tisAggregate: true,\n\t\t\t\t\tsite: this.settings.facilitySite,\n\t\t\t\t\tuserSites: this.state.sites,\n\t\t\t\t\tfacilityTW: this.config.facilityTW\n\t\t\t\t})\n\t\t\t\tthis.facilitySites = this.sampleData.sites\n\t\t\t\tthis.facilitySites.sort((a, b) => {\n\t\t\t\t\treturn a.label.localeCompare(b.label)\n\t\t\t\t})\n\t\t\t\tthis.facilitySites.find(s => s.value == this.settings.facilitySite).selected = true //mark selected facility site\n\n\t\t\t\tinputs.unshift({\n\t\t\t\t\tlabel: 'Facility site',\n\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\tchartType,\n\t\t\t\t\toptions: this.facilitySites,\n\t\t\t\t\tcallback: value => {\n\t\t\t\t\t\tthis.setFacilitySite(value)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\n\t\tinputs.unshift(...additionalInputs)\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsDiv,\n\t\t\t\tinputs,\n\t\t\t\ttitle: 'Filters'\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on(`downloadClick.${chartType}`, () =>\n\t\t\tdownloadSingleSVG(this.dom.svg, this.getDownloadFilename(), this.dom.holder.node())\n\t\t)\n\t\tthis.components.controls.on(`helpClick.${chartType}`, () => {\n\t\t\tconst activeCohort = this.state.activeCohort\n\t\t\tlet link\n\t\t\tif (activeCohort == ABBREV_COHORT) {\n\t\t\t\tif (chartType == 'profileBarchart')\n\t\t\t\t\tlink = 'https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-abbr-profiledash.pdf'\n\t\t\t\telse if (chartType == 'profilePolar')\n\t\t\t\t\tlink =\n\t\t\t\t\t\t'https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-abbr-profiledash.pdf'\n\t\t\t\telse if (chartType.startsWith('profileRadar'))\n\t\t\t\t\tlink = 'https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-abbr-profiledash.pdf'\n\t\t\t} else if (activeCohort == FULL_COHORT) {\n\t\t\t\tif (chartType == 'profileBarchart')\n\t\t\t\t\tlink = 'https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-full-profiledash.pdf'\n\t\t\t\telse if (chartType == 'profilePolar')\n\t\t\t\t\tlink =\n\t\t\t\t\t\t'https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-full-profiledash.pdf'\n\t\t\t\telse if (chartType.startsWith('profileRadar'))\n\t\t\t\t\tlink = 'https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-full-profiledash.pdf'\n\t\t\t}\n\t\t\tif (link) window.open(link)\n\t\t})\n\t\tthis.filtersCount = 0\n\t}\n\n\tsetFilterValue(key, value) {\n\t\tconst config = this.config\n\t\tthis.settings[key] = value\n\t\tthis.settings.site = '' //always clear site when a filter is changed\n\t\tthis.settings.sites = null //clear sites\n\t\tconfig.filter = this.getFilter()\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: this.config })\n\t}\n\n\tgetFilter() {\n\t\treturn getCategoricalTermFilter(this.config.filterTWs, this.settings, null, this.state.termfilter.filter)\n\t}\n\n\tsetRegion(region) {\n\t\tconst config = this.config\n\t\tthis.settings[config.regionTW.term.id] = region\n\t\tthis.clearFiltersExcept([config.regionTW.term.id])\n\t\tconfig.filter = this.getFilter()\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config })\n\t}\n\n\tclearFiltersExcept(ids) {\n\t\tfor (const tw of this.config.filterTWs) if (!ids.includes(tw.term.id)) this.settings[tw.term.id] = ''\n\t\tthis.settings.site = ''\n\t\tthis.settings.sites = null //clear sites\n\t}\n\n\tsetSite(site) {\n\t\tthis.settings.site = site\n\t\tthis.settings.sites = null //clear sites\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: this.config })\n\t}\n\n\tsetFacilitySite(site) {\n\t\tthis.settings.facilitySite = site\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: this.config })\n\t}\n\n\tsetSites(sites) {\n\t\tif (sites && sites.length == 1) this.settings.site = sites[0] //if only one site selected, set it as the site\n\t\tthis.settings.sites = sites?.map(s => Number(s))\n\t\tif (this.settings.sites.length > 1) this.settings.site = '' //clear site\n\t\telse if (this.settings.sites.length == 1) this.settings.site = this.settings.sites[0] //set site to the single site\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: this.config })\n\t}\n\n\taddFilterLegend() {\n\t\tconst hasFilters = this.config.filterTWs.some(tw => this.settings[tw.term.id]) || this.settings.sites?.length > 0\n\t\tconst title = hasFilters ? 'Filters' : 'No filter applied'\n\t\tthis.filterG\n\t\t\t.attr('font-size', '0.9em')\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'left')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text(`${title} (n=${this.data.n})`)\n\t\t\t.attr('transform', `translate(0, -5)`)\n\t\tfor (const tw of this.config.filterTWs) this.addFilterLegendItem(tw.term.name, this.settings[tw.term.id])\n\t\tconst hospital = this.data.hospital\n\t\tif (this.settings.site) {\n\t\t\tconst label = this.sites.find(s => s.value == this.settings.site).label\n\t\t\tthis.addFilterLegendItem('Facility ID', label)\n\t\t\tthis.addFilterLegendItem('Facility', hospital)\n\t\t}\n\t}\n\n\taddFilterLegendItem(filter, value) {\n\t\tif (!value) return\n\t\tthis.filtersCount++\n\n\t\tconst itemG = this.filterG.append('g').attr('font-size', '0.95em')\n\t\tconst text = itemG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, ${this.filtersCount * 22})`)\n\t\t\t.attr('text-anchor', 'left')\n\t\ttext.append('tspan').attr('font-size', 'bold').text(filter)\n\t\ttext.append('tspan').text(`: ${value ? value : 'None'}`)\n\t}\n\n\taddEndUserImpressionNote(uiG) {\n\t\tuiG.attr('font-size', '0.9em')\n\t\tlet textElem = uiG.append('text').attr('transform', `translate(0, 115)`)\n\t\ttextElem.append('tspan').attr('font-weight', 'bold').text('End-user Impression: ')\n\t\ttextElem.append('tspan').text('It is provided by the local liaison who completed the assessment ')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 140)`)\n\t\t\t.text('in consultation with the PHO medical director or directly by the PHO medical director.')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 165)`)\n\t\t\t.text('The end-user was asked to rate the current status of the domains and subdomains included.')\n\t}\n\n\taddPOCNote(uiG) {\n\t\tuiG.attr('font-size', '0.9em')\n\t\tlet textElem = uiG.append('text').attr('transform', `translate(0, 115)`)\n\t\ttextElem.append('tspan').attr('font-weight', 'bold').text('Point of Care (POC) Staff: ')\n\t\ttextElem.append('tspan').text('All members of the assessment team, ')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 140)`)\n\t\t\t.text('excluding the Site Coordinator. POC staff provide subjective information based ')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 165)`)\n\t\t\t.text('on their experience and perception about service delivery at the PHO facility.')\n\t}\n\n\taddLegendItem(category, description, index) {\n\t\tconst text = this.legendG\n\t\t\t.append('text')\n\t\t\t.attr('font-size', '0.9em')\n\t\t\t.attr('transform', `translate(0, ${index * 20})`)\n\t\t\t.attr('text-anchor', 'left')\n\t\ttext.append('tspan').attr('font-weight', 'bold').text(category)\n\t\ttext.append('tspan').text(`: ${description}`)\n\t}\n\n\tgetDownloadFilename() {\n\t\tthis.downloadCount++\n\t\tlet filename = `${this.type}${this.downloadCount}.svg`\n\t\tfilename = filename.split(' ').join('_')\n\t\treturn filename\n\t}\n\n\tgetPercentage(d) {\n\t\tif (!d) return 0\n\t\tconst score = this.data.term2Score[d.score.term.id]\n\t\treturn score\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance, chartType) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\n\tconst state = chartsInstance.state\n\tconst key = state.activeCohort == FULL_COHORT ? 'full' : 'abbrev'\n\tconst typeConfig = state.termdbConfig?.plotConfigByCohort[key][chartType]\n\tif (typeConfig.options.length == 1) {\n\t\tcreatePlot(typeConfig.options[0], chartType, chartsInstance)\n\t\treturn\n\t}\n\tconst menuDiv = holder.append('div')\n\tfor (const plotConfig of typeConfig.options) {\n\t\tmenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(plotConfig.title)\n\t\t\t.on('click', () => {\n\t\t\t\tcreatePlot(plotConfig, chartType, chartsInstance)\n\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t})\n\t}\n\n\tfunction createPlot(plotConfig, chartType, chartsInstance) {\n\t\tlet config = structuredClone(plotConfig)\n\t\tconfig.chartType = chartType\n\t\tconfig.header = chartType == 'profileRadarFacility' ? 'Facility Radar Graph' : 'Radar Graph'\n\t\tchartsInstance.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tchartType,\n\t\t\tconfig\n\t\t})\n\t}\n}\n\nexport async function getProfilePlotConfig(activeCohort, app, opts) {\n\tconst key = activeCohort == FULL_COHORT ? 'full' : 'abbrev'\n\tconst config = app.vocabApi.termdbConfig?.plotConfigByCohort[key]?.[opts.chartType]\n\tif (!config) throw `No data available for the plot ${opts.chartType} in this dataset`\n\tconst cohortPreffix = activeCohort == FULL_COHORT ? 'F' : 'A'\n\tconfig.facilityTW = { id: cohortPreffix + 'facility' } //All the plots want the facility term to show the hospital name if a site is selected\n\tawait fillTermWrapper(config.facilityTW, app.vocabApi)\n\tawait loadFilterTerms(config, activeCohort, app)\n\treturn structuredClone(config)\n}\n\nexport async function loadFilterTerms(config, activeCohort, app) {\n\tconst cohortPreffix = activeCohort == FULL_COHORT ? 'F' : 'A'\n\tconfig.countryTW = { id: cohortPreffix + 'country' }\n\tconfig.regionTW = { id: cohortPreffix + 'WHO_region' }\n\tconfig.incomeTW = { id: cohortPreffix + 'Income_group' }\n\tconfig.typeTW = { id: cohortPreffix + 'FC_TypeofFacility' }\n\tconfig.teachingStatusTW = { id: cohortPreffix + 'FC_TeachingFacility' }\n\tconfig.referralStatusTW = { id: cohortPreffix + 'FC_ReferralFacility' }\n\tconfig.fundingSourceTW = { id: cohortPreffix + 'FC_FundingSrc' }\n\t//config.annualDiagnosisNumber = {id: 'PO_TotalDxAll'}\n\tconfig.hospitalVolumeTW = { id: cohortPreffix + 'PO_HospitalVolume' }\n\tconfig.yearOfImplementationTW = { id: cohortPreffix + 'Year_implementation' }\n\n\tconst filterTWs = [\n\t\tconfig.countryTW,\n\t\tconfig.regionTW,\n\t\tconfig.incomeTW,\n\t\tconfig.typeTW,\n\t\tconfig.teachingStatusTW,\n\t\tconfig.referralStatusTW,\n\t\tconfig.fundingSourceTW,\n\t\tconfig.hospitalVolumeTW,\n\t\tconfig.yearOfImplementationTW\n\t]\n\tawait fillTwLst(filterTWs, app.vocabApi)\n\tconfig.filterTWs = filterTWs\n}\n\nexport function clearLocalFilters(plot) {\n\tplot.settings = getDefaultProfilePlotSettings()\n}\n\nexport function getDefaultProfilePlotSettings() {\n\treturn {\n\t\tisAggregate: false,\n\t\tshowTable: true\n\t}\n}\n\nexport function getProfileLogin(app, cohort = FULL_COHORT) {\n\tconst auth = app.vocabApi.getClientAuthResult()\n\tif (!auth) return { logged: false, sites: [], user: 'public' }\n\tconst auth_info = cohort == FULL_COHORT ? auth.full : auth.abbrev\n\tconst logged = auth_info?.role != 'public'\n\tif (!auth_info) return { logged: false, sites: [], user: 'public' } //no login info for the cohort, treat it as not logged in, public view for that cohort\n\tconst user = auth_info?.role || 'public'\n\tconst sites = user == 'admin' ? null : auth_info.sites //site only matters if you are not admin\n\treturn { logged, sites, user }\n}\n"],
+  "mappings": 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+  "names": ["config", "isAggregate", "chartType", "chartsInstance"]
+}

package/dist/{chunk-RBRAAJSI.js → chunk-JR37IU5O.js}

@@ -8,7 +8,7 @@ import {
   controlsInit,
   renderTerm1Label,
   term0_term2_defaultQ
-} from "./chunk-U6CRL7IJ.js";
+} from "./chunk-PDCHOIX4.js";
 import {
   fillTermWrapper,
   filterJoin,
@@ -20,10 +20,10 @@ import {
   renderTable,
   svgLegend,
   to_svg
-} from "./chunk-YCYBH4EW.js";
+} from "./chunk-4FDOZ23V.js";
 import {
   isNumericTerm
-} from "./chunk-7Z3NR2LZ.js";
+} from "./chunk-5VX3CXQ3.js";
 import {
   copyMerge,
   getCompInit
@@ -32,7 +32,7 @@ import {
   getColors,
   mclass,
   plotColor
-} from "./chunk-3DNHZAJC.js";
+} from "./chunk-VBQBPNCJ.js";
 import {
   roundValueAuto
 } from "./chunk-5OHXYXLD.js";
@@ -431,14 +431,15 @@ async function listSamples(event, self, seriesId, dataId, chartId) {
   }
   const opts = {
     terms,
-    filter: filterJoin([self.state.termfilter.filter, tvslst])
+    filter: filterJoin([self.state.termfilter.filter, tvslst]),
+    filter0: self.state.termfilter.filter0
   };
   const data = await self.app.vocabApi.getAnnotatedSampleData(opts);
   const rows = [];
   const termIsNumeric = isNumericTerm(self.config.term.term);
   const term2isNumeric = self.config.term2 ? isNumericTerm(self.config.term2.term) : false;
   for (const sample of data.lst) {
-    const sampleName = data.refs.bySampleId[Number(sample.sample)].label;
+    const sampleName = data.refs.bySampleId[sample.sample].label;
     const row = [{ value: sampleName }];
     if (self.config.term.q?.hiddenValues && `${sample[self.config.term.$id].key}` in self.config.term.q.hiddenValues)
       continue;
@@ -475,7 +476,7 @@ async function listSamples(event, self, seriesId, dataId, chartId) {
   menu.show(event.clientX, event.clientY, false);
   function getTvs(termIndex, value) {
     const term = termIndex == 0 ? self.config.term0 : termIndex == 1 ? self.config.term : self.config.term2;
-    const tvs = {
+    let tvs = {
       type: "tvs",
       tvs: {
         term: term.term,
@@ -486,6 +487,33 @@ async function listSamples(event, self, seriesId, dataId, chartId) {
       const bins = self.bins[termIndex];
       tvs.tvs.ranges = [bins.find((bin) => bin.label == value)];
     }
+    if (term.term.type == "geneVariant") {
+      const termdbmclass = self.app.vocabApi.termdbConfig?.mclass;
+      if (termIndex === 1) {
+        const dtTerm = self.chartid2dtterm[chartId];
+        let key;
+        if (termdbmclass) {
+          key = Object.keys(termdbmclass).find((k) => termdbmclass[k].label == value);
+        }
+        if (!key) {
+          key = Object.keys(mclass).find((k) => mclass[k].label == value);
+        }
+        tvs = {
+          type: "tvs",
+          tvs: {
+            term: dtTerm,
+            values: [{ key }],
+            includeNotTested: true
+            // to be able to list not tested samples
+          }
+        };
+      } else {
+        const groups = term.q.customset?.groups;
+        if (!groups || !Array.isArray(groups)) throw "groups[] is missing";
+        const group = groups.find((group2) => group2.name == value);
+        tvs = group.filter;
+      }
+    }
     return tvs;
   }
 }
@@ -520,7 +548,7 @@ function menuoption_select_to_gp(self, tvslst) {
     const item = findItemByTermId(self.state.termfilter.filter, t.tvs.term.id);
     if (!item) lst.push(wrapTvs(t));
   }
-  import("./block-E6ZAGAME.js").then(async (_) => {
+  import("./block-QBZZCTQE.js").then(async (_) => {
     const obj = {
       genome: self.app.opts.genome,
       dslabel: self.state.dslabel
@@ -918,6 +946,7 @@ var Barchart = class {
       const data = results.data;
       this.sampleType = results.sampleType;
       this.bins = results.bins;
+      if (results.chartid2dtterm) this.chartid2dtterm = results.chartid2dtterm;
       this.toggleLoadingDiv("none");
       this.app.vocabApi.syncTermData(this.config, data, this.prevConfig);
       this.currServerData = data;
@@ -1600,4 +1629,4 @@ export {
   getHandlers,
   hideCategory
 };
-//# sourceMappingURL=chunk-RBRAAJSI.js.map
+//# sourceMappingURL=chunk-JR37IU5O.js.map

package/dist/chunk-JR37IU5O.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/barchart.events.js", "../plots/barchart.js"],
+  "sourcesContent": ["import { Menu, renderTable } from '#dom'\nimport { dofetch3 } from '../common/dofetch'\nimport { newpane, export_data } from '../src/client'\nimport { filterJoin, getFilterItemByTag, getNormalRoot, findItemByTermId, normalizeProps } from '#filter'\nimport { rgb } from 'd3-color'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { negateTermLabel } from './barchart'\nimport { mclass } from '#shared/common.js'\n\nexport default function getHandlers(self) {\n\tconst tip = new Menu({ padding: '5px' })\n\tself.dom.tip = tip\n\tconst s = self.settings\n\n\tfunction barLabelClickHandler(event) {\n\t\t// same handler for row label click in horziontal orientation\n\t\t// or col label click in vertical orientation, since\n\t\t// row/column labels only apply to bars\n\t\tconst d = event.target.__data__\n\t\tif (d === undefined) return\n\t\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\t\tconst term = self.config.term\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\tterm: {\n\t\t\t\t\t//Fix for list samples options not working\n\t\t\t\t\t//after hiding a category\n\t\t\t\t\t$id: term?.$id,\n\t\t\t\t\tid: term.id,\n\n\t\t\t\t\tisAtomic: true,\n\t\t\t\t\tterm: term.term,\n\t\t\t\t\tq: getUpdatedQfromClick(d, term, true)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\treturn {\n\t\tchart: {\n\t\t\ttitle(chart) {\n\t\t\t\tif (!self.config.term0) return chart.chartId\n\t\t\t\treturn self.config.term0.term.values && chart.chartId in self.config.term0.term.values\n\t\t\t\t\t? self.config.term0.term.values[chart.chartId].label\n\t\t\t\t\t: chart.chartId\n\t\t\t}\n\t\t},\n\t\tsvg: {\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\tseries: {\n\t\t\tmouseover(event, d) {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tlet percent = self.config.term2 ? (d.total / d.seriesTotal) * 100 : (d.seriesTotal / d.chartTotal) * 100\n\t\t\t\tpercent = percent.toFixed(1)\n\t\t\t\tconst t1 = self.config.term.term\n\t\t\t\tconst t2 = self.config.term2 && self.config.term2.term\n\t\t\t\tconst term1unit = t1.unit\n\t\t\t\tconst seriesLabel =\n\t\t\t\t\t(t1.values && d.seriesId in t1.values ? t1.values[d.seriesId].label : d.seriesId) +\n\t\t\t\t\t(t1.unit ? ' ' + t1.unit : '')\n\t\t\t\tconst dataLabel =\n\t\t\t\t\t(t2 && t2.values && d.dataId in t2.values ? t2.values[d.dataId].label : d.dataId) +\n\t\t\t\t\t(t2 && t2.unit ? ' ' + t2.unit : '')\n\t\t\t\tconst icon = !t2\n\t\t\t\t\t? ''\n\t\t\t\t\t: \"<div style='display:inline-block; width:14px; height:14px; margin: 2px 3px; vertical-align:top; background:\" +\n\t\t\t\t\t  d.color +\n\t\t\t\t\t  \"'>&nbsp;</div>\"\n\t\t\t\tconst rows = [`<tr><td colspan=2 style='padding:3px; text-align:center'>${seriesLabel}</td></tr>`]\n\t\t\t\tif (t2) {\n\t\t\t\t\trows.push(\n\t\t\t\t\t\t`<tr><td colspan=2 style='padding:3px; text-align:center'>${icon} <span>${dataLabel}</span></td></tr>`\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\trows.push(\n\t\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>#Individuals</td><td style='padding:3px; text-align:center'>${d.total}</td></tr>`,\n\t\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>percent</td><td style='padding:3px; text-align:center'>${percent}%</td></tr>`\n\t\t\t\t)\n\n\t\t\t\t//mouse-over p-value and 2x2 table\n\t\t\t\tif (t2) {\n\t\t\t\t\tconst pvalue = d.groupPvalues?.term2tests?.find(x => x.term2id === d.dataId).pvalue\n\t\t\t\t\tconst term1Label = d.groupPvalues.term1Label\n\t\t\t\t\tconst term2Label = d.groupPvalues.term2tests.find(x => x.term2id === d.dataId).term2Label\n\t\t\t\t\tconst tableValues = d.groupPvalues.term2tests.find(x => x.term2id === d.dataId).tableValues\n\t\t\t\t\tconst skipped = d.groupPvalues.term2tests.find(x => x.term2id === d.dataId).skipped\n\n\t\t\t\t\t// when term1 has only 2 categories, Row2 would be the other category instead of \"not Row1\"\n\t\t\t\t\tconst negateTerm1Label = !(\n\t\t\t\t\t\tself.settings.cols.length - self.settings.exclude.cols.length == 2 &&\n\t\t\t\t\t\tself.chartsData.tests[d.chartId].length == 2\n\t\t\t\t\t)\n\t\t\t\t\t\t? negateTermLabel(term1Label)\n\t\t\t\t\t\t: self.chartsData.tests[d.chartId][0].term1Label == term1Label\n\t\t\t\t\t\t? self.chartsData.tests[d.chartId][1].term1Label\n\t\t\t\t\t\t: self.chartsData.tests[d.chartId][0].term1Label\n\n\t\t\t\t\tlet negateTerm2Label = negateTermLabel(term2Label)\n\t\t\t\t\tif (self.settings.rows.length - self.settings.exclude.rows.length == 2) {\n\t\t\t\t\t\t// when term2 has only 2 visible categories, Col2 would be the other category instead of \"not Col1\"\n\t\t\t\t\t\tconst visibleTerm2CatsKeys = self.settings.rows.filter(row => !self.settings.exclude.rows.includes(row))\n\t\t\t\t\t\tconst visibleTerm2Labels = visibleTerm2CatsKeys\n\t\t\t\t\t\t\t.map(catK => self.config.term2?.term?.values?.[catK]?.label)\n\t\t\t\t\t\t\t.filter(x => x != undefined)\n\t\t\t\t\t\tif (visibleTerm2Labels?.length == 2)\n\t\t\t\t\t\t\tnegateTerm2Label = visibleTerm2Labels[0] == term2Label ? visibleTerm2Labels[1] : visibleTerm2Labels[0]\n\t\t\t\t\t}\n\n\t\t\t\t\trows.push(\n\t\t\t\t\t\t`<tr>\n\t\t\t\t\t\t\t<td style='padding:3px; color:#aaa'>p-value</td>\n\t\t\t\t\t\t\t<td style='padding:3px; text-align:center'>${\n\t\t\t\t\t\t\t\tskipped ? 'N/A' : pvalue > 1e-4 ? Number(pvalue.toFixed(4)) : roundValueAuto(Number(pvalue))\n\t\t\t\t\t\t\t}</td>\n\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t<table style=\"margin: 5px; text-align:left; font-size: 0.8em; border-spacing: 5px; border-collapse: separate;\"\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'></td>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${term2Label}</td>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${negateTerm2Label}</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${term1Label}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R1C1}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R1C2}</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td style='color:#aaa'>${negateTerm1Label}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R2C1}</td>\n\t\t\t\t\t\t\t\t<td>${tableValues.R2C2}</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t</table>`\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\tif (!t1.type == 'condition' && (!t2 || !t2.type == 'condition')) {\n\t\t\t\t\trows.push(\n\t\t\t\t\t\t`<tr><td style='padding:3px; color:#aaa'>Percentage</td><td style='padding:3px; text-align:center'>${(\n\t\t\t\t\t\t\t(100 * d.total) /\n\t\t\t\t\t\t\t(t2 ? d.seriesTotal : d.chartTotal)\n\t\t\t\t\t\t).toFixed(1)}%</td></tr>`\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\ttip.show(event.clientX, event.clientY).d.html(`<table class='sja_simpletable'>${rows.join('\\n')}</table>`)\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t},\n\t\t\trectFill(d) {\n\t\t\t\treturn d.color\n\t\t\t},\n\t\t\tstrokeFill(d) {\n\t\t\t\tconst rgbColor = rgb(d.color)\n\t\t\t\tconst stroke = rgbColor.toString() == rgb('white').toString() ? rgbColor.darker() : rgbColor\n\t\t\t\treturn stroke\n\t\t\t},\n\t\t\tclick: self.opts.bar_click_override\n\t\t\t\t? (event, d) => self.opts.bar_click_override(getTermValues(d, self))\n\t\t\t\t: (event, d) => handle_click(event, self, d)\n\t\t},\n\t\tcolLabel: {\n\t\t\ttext: d => {\n\t\t\t\treturn 'label' in d\n\t\t\t\t\t? d.label\n\t\t\t\t\t: self.config.term.values && 'id' in d && d.id in self.config.term.values\n\t\t\t\t\t? self.config.term.values[d.id].label\n\t\t\t\t\t: d\n\t\t\t},\n\t\t\tclick: barLabelClickHandler,\n\t\t\tmouseover: event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\ttip.show(event.clientX, event.clientY).d.html('Click to hide bar')\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\trowLabel: {\n\t\t\ttext: d => {\n\t\t\t\treturn d.label\n\t\t\t\t\t? d.label\n\t\t\t\t\t: self.config.term.values && 'id' in d && d.id in self.config.term.values\n\t\t\t\t\t? self.config.term.values[d.id].label\n\t\t\t\t\t: d\n\t\t\t},\n\t\t\tclick: barLabelClickHandler,\n\t\t\tmouseover: event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\ttip.show(event.clientX, event.clientY).d.html('Click to hide bar')\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\tlegend: {\n\t\t\tonColorClick: e => handleLegendClick(e.target, self),\n\t\t\tclick: e => handleLegendClick(e.target, self),\n\t\t\tmouseover: event => {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tconst d = event.target.__data__\n\t\t\t\tif (d === undefined) return\n\t\t\t\tif (d.isHidden) tip.show(event.clientX, event.clientY).d.html('Click to unhide bar')\n\t\t\t},\n\t\t\tmouseout: () => {\n\t\t\t\ttip.hide()\n\t\t\t}\n\t\t},\n\t\tyAxis: {\n\t\t\ttext: visibleTotal => {\n\t\t\t\tconst type = self.sampleType?.plural_name || 'samples'\n\t\t\t\tconst term = self.config.term\n\t\t\t\tif (s.orientation == 'vertical') {\n\t\t\t\t\t// Do not show the sum of serieses as (n=...) when serieses are 'Sub-condition', 'Most recent grade' or 'Any grade'\n\t\t\t\t\t// because a patient could have multiple 'Sub-condition', 'Most recent grade' or 'Any grade', and as a result could\n\t\t\t\t\t// be counted multiple times.\n\t\t\t\t\treturn s.unit == 'pct'\n\t\t\t\t\t\t? `% of ${type}`\n\t\t\t\t\t\t: `# of ${type} ` +\n\t\t\t\t\t\t\t\t(term.q.bar_by_children || term.q.value_by_most_recent || term.q.value_by_computable_grade\n\t\t\t\t\t\t\t\t\t? ''\n\t\t\t\t\t\t\t\t\t: `(n=${visibleTotal})`)\n\t\t\t\t} else {\n\t\t\t\t\treturn term.q.bar_by_children\n\t\t\t\t\t\t? 'Sub-condition'\n\t\t\t\t\t\t: term.q.value_by_max_grade\n\t\t\t\t\t\t? 'Maximum grade'\n\t\t\t\t\t\t: term.q.value_by_most_recent\n\t\t\t\t\t\t? 'Most recent grade'\n\t\t\t\t\t\t: term.q.value_by_computable_grade\n\t\t\t\t\t\t? 'Any grade'\n\t\t\t\t\t\t: term.type == 'categorical' || !term.unit\n\t\t\t\t\t\t? ''\n\t\t\t\t\t\t: term.unit\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\txAxis: {\n\t\t\ttext: visibleTotal => {\n\t\t\t\tconst type = self.sampleType?.plural_name || 'samples'\n\t\t\t\tconst term = self.config.term\n\t\t\t\tif (s.orientation == 'vertical') {\n\t\t\t\t\treturn term.q.bar_by_children\n\t\t\t\t\t\t? 'Sub-condition'\n\t\t\t\t\t\t: term.q.value_by_max_grade\n\t\t\t\t\t\t? 'Maximum grade'\n\t\t\t\t\t\t: term.q.value_by_most_recent\n\t\t\t\t\t\t? 'Most recent grade'\n\t\t\t\t\t\t: term.q.value_by_computable_grade\n\t\t\t\t\t\t? 'Any grade'\n\t\t\t\t\t\t: term.type == 'categorical' || !term.unit\n\t\t\t\t\t\t? ''\n\t\t\t\t\t\t: term.unit\n\t\t\t\t} else {\n\t\t\t\t\t// Do not show the sum of serieses as (n=...) when serieses are 'Sub-condition', 'Most recent grade' or 'Any grade'\n\t\t\t\t\t// because a patient could have multiple 'Sub-condition', 'Most recent grade' or 'Any grade', and as a result could\n\t\t\t\t\t// be counted multiple times.\n\t\t\t\t\treturn s.unit == 'pct'\n\t\t\t\t\t\t? `% of ${type}`\n\t\t\t\t\t\t: `# of ${type} ` +\n\t\t\t\t\t\t\t\t(term.q.bar_by_children || term.q.value_by_most_recent || term.q.value_by_computable_grade\n\t\t\t\t\t\t\t\t\t? ''\n\t\t\t\t\t\t\t\t\t: `(n=${visibleTotal})`)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction handleColorClick(d, self, color) {\n\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\tconst term = self.config[termNum]\n\tlet dataId = d.dataId\n\tif (term.term.values && !term.term.values?.[dataId])\n\t\tfor (const [key, value] of Object.entries(term.term.values)) if (value.label == d.dataId) dataId = key\n\tif (term.term.values?.[dataId]) term.term.values[dataId].color = color\n\tif (term.term.type == 'geneVariant') {\n\t\tif (!term.term.values) term.term.values = {}\n\t\tterm.term.values[d.dataId] = { label: d.dataId, color }\n\t}\n\tlet binColored = null\n\tif (self.bins[2].length > 0) {\n\t\t//term index: term0: 0, term: 1, term2: 2\n\t\tconst binMatched = self.bins[2].find(bin => bin.label == d.dataId)\n\t\tif (binMatched) {\n\t\t\tbinMatched.color = color\n\t\t\tbinColored = self.bins[2]\n\t\t}\n\t}\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\t[termNum]: {\n\t\t\t\t$id: term.$id,\n\t\t\t\tid: term.id,\n\t\t\t\tisAtomic: true,\n\t\t\t\tterm: term.term,\n\t\t\t\tq: getUpdatedQfromClick(d, term, d.isHidden, binColored)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction handleLegendClick(target, self) {\n\tconst d = target.__data__\n\tif (d === undefined) return\n\tif (!('type' in d)) return\n\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\tconst term = self.config[termNum]\n\tconst isHidden =\n\t\t'isHidden' in d\n\t\t\t? !d.isHidden\n\t\t\t: !(term.q && term.q.hiddenValues && term.q.hiddenValues['dataId' in d ? d.dataId : d.id])\n\tconst tip = self.app.tip\n\tconst menu = tip.clear()\n\tmenu.showunder(target)\n\tconst div = menu.d.append('div')\n\tdiv\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t.text(!isHidden ? 'Show' : 'Hide')\n\t\t.on('click', () => {\n\t\t\tmenu.hide()\n\t\t\thideCategory(d, self, isHidden)\n\t\t})\n\tif (term.q.hiddenValues && Object.keys(term.q.hiddenValues).length > 1)\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show all')\n\t\t\t.on('click', () => {\n\t\t\t\tmenu.hide()\n\t\t\t\tconst config = {}\n\t\t\t\tconst tw = structuredClone(term)\n\t\t\t\tdelete tw.q.hiddenValues\n\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: { [termNum]: tw }\n\t\t\t\t})\n\t\t\t})\n\tconst color = rgb(d.color).formatHex()\n\tif (color != '#ffffff') {\n\t\tconst input = div\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('padding', '0px 10px')\n\t\t\t.text('Color:')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.attr('value', color)\n\t\t\t.on('change', () => {\n\t\t\t\thandleColorClick(d, self, input.node().value)\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t}\n}\n\nexport function hideCategory(d, self, isHidden) {\n\tconst termNum = d.type == 'col' ? 'term' : 'term2'\n\tconst term = self.config[termNum]\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\t[termNum]: {\n\t\t\t\t//Fix for list samples options not working\n\t\t\t\t//after hiding a category\n\t\t\t\t$id: term?.$id,\n\t\t\t\tid: term.id,\n\n\t\t\t\tisAtomic: true,\n\t\t\t\tterm: term.term,\n\t\t\t\tq: getUpdatedQfromClick(d, term, isHidden)\n\t\t\t}\n\t\t}\n\t})\n}\n\nfunction getUpdatedQfromClick(d, term, isHidden = false, binColored = null) {\n\tconst label = 'id' in d ? d.id : d.type == 'col' ? d.seriesId : d.dataId\n\tconst valueId = term.term.values && Object.keys(term.term.values).find(id => term.term.values[id].label === label)\n\tconst id = !valueId ? label : valueId\n\tconst q = JSON.parse(JSON.stringify(term.q))\n\tif (!q.hiddenValues) q.hiddenValues = {}\n\tif (isHidden) q.hiddenValues[id] = 1\n\telse delete q.hiddenValues[id]\n\tif (binColored) q.binColored = binColored\n\treturn q\n}\n\nfunction handle_click(event, self, chart) {\n\tconst d = event.target.__data__ || event.target.parentNode.__data__\n\t// bar label data only has {id,label},\n\t// while bar data has all required data including seriesId\n\tconst term1 = self.config.term.term\n\tconst term2 = self.config.term2 ? self.config.term2.term : null\n\tconst uncomp_term1 = term1.values ? Object.values(term1.values).map(v => v.label) : []\n\tconst uncomp_term2 = term2 && term2.values ? Object.values(term2.values).map(v => v.label) : []\n\tconst term1unit = term1.unit && !uncomp_term1.includes(d.seriesId || d.id) ? ' ' + term1.unit : ''\n\tconst term2unit = term2 && term2.unit && !uncomp_term2.includes(d.dataId || d.id) ? ' ' + term2.unit : ''\n\tconst seriesLabel =\n\t\t(term1.values && d.seriesId in term1.values ? term1.values[d.seriesId].label : d.seriesId ? d.seriesId : d.id) +\n\t\tterm1unit\n\tconst dataLabel =\n\t\t(term2 && term2.values && d.dataId in term2.values ? term2.values[d.dataId].label : d.dataId ? d.dataId : d.id) +\n\t\tterm2unit\n\tconst icon = !term2\n\t\t? ''\n\t\t: \"<div style='display:inline-block; width:14px; height:14px; margin: 2px 3px; vertical-align:top; background:\" +\n\t\t  d.color +\n\t\t  \"'>&nbsp;</div>\"\n\tconst header =\n\t\t`<div style='padding:2px'><b>${term1.name}</b>: ${seriesLabel}</div>` +\n\t\t(d.seriesId && term2 ? `<div style='padding:2px'><b>${term2.name}</b>: ${dataLabel} ${icon}</div>` : '')\n\n\tconst data = d.seriesId || d.seriesId === 0 ? d : { seriesId: d.id, dataId: d.dataId }\n\n\tconst options = []\n\tif (self.opts.bar_click_opts.includes('hide_bar')) {\n\t\toptions.push({\n\t\t\tlabel: d.seriesId ? 'Hide \"' + seriesLabel + '\"' : 'Hide',\n\t\t\tcallback: () => {\n\t\t\t\tconst term = self.config.term\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t$id: term.$id,\n\t\t\t\t\t\t\tid: term.id,\n\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\tq: getUpdatedQfromClick({ id: d.seriesId, type: 'col' }, term, true)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\n\t\tif (d.dataId || d.dataId === 0) {\n\t\t\toptions.push({\n\t\t\t\tlabel: 'Hide \"' + dataLabel + '\" ' + icon,\n\t\t\t\tcallback: () => {\n\t\t\t\t\tconst term2 = self.config.term2\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\tisAtomic: true,\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\t\tisAtomic: true,\n\t\t\t\t\t\t\t\tterm: term2.term,\n\t\t\t\t\t\t\t\tq: getUpdatedQfromClick({ id: d.dataId, type: 'row' }, term2, true)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tif (self.opts.bar_click_opts.includes('add_filter') && (!term2 || !term2.isgenotype)) {\n\t\tconst item = findItemByTermId(self.state.termfilter.filter, self.config.term.term.id)\n\t\tif (!item) {\n\t\t\toptions.push({\n\t\t\t\tlabel: 'Add as filter',\n\t\t\t\tcallback: menuoption_add_filter\n\t\t\t})\n\t\t}\n\t}\n\t//disable sample listing temporarily\n\tif (self.config.displaySampleIds) {\n\t\toptions.push({\n\t\t\tlabel: 'List samples',\n\t\t\tcallback: async () => await listSamples(event, self, d.seriesId, d.dataId, chart.chartId)\n\t\t})\n\t}\n\n\tif (self.opts.bar_click_opts.includes('select_to_gp')) {\n\t\toptions.push({\n\t\t\tlabel: 'Select to GenomePaint',\n\t\t\tcallback: menuoption_select_to_gp\n\t\t})\n\t}\n\n\t// TODO: add to cart\n\t//\n\t// if (self.opts.bar_click_opts.includes('add_to_cart')) {\n\t// \toptions.push({\n\t// \t\tlabel: 'Add group to cart',\n\t// \t\tcallback: menuoption_select_group_add_to_cart\n\t// \t})\n\t// }\n\n\tif (!options.length) return\n\tself.app.tip.clear()\n\tif (header) {\n\t\tself.app.tip.d.append('div').html(header)\n\t}\n\tconst tvslst = getTermValues(data, self)\n\tself.app.tip.d\n\t\t.append('div')\n\t\t.selectAll('div')\n\t\t.data(options)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.html(d => d.label)\n\t\t.on('click', async (event, d) => {\n\t\t\tself.app.tip.hide()\n\t\t\tawait d.callback(self, tvslst)\n\t\t})\n\tself.app.tip.show(event.clientX, event.clientY)\n}\n\nasync function listSamples(event, self, seriesId, dataId, chartId) {\n\tconst tvslst = {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [getTvs(1, seriesId)]\n\t}\n\tconst terms = [self.config.term]\n\tif (self.config.term2) {\n\t\tterms.push(self.config.term2)\n\t\ttvslst.lst.push(getTvs(2, dataId))\n\t}\n\tif (self.config.term0) {\n\t\tterms.push(self.config.term0)\n\t\ttvslst.lst.push(getTvs(0, chartId))\n\t}\n\tconst opts = {\n\t\tterms,\n\t\tfilter: filterJoin([self.state.termfilter.filter, tvslst]),\n\t\tfilter0: self.state.termfilter.filter0\n\t}\n\tconst data = await self.app.vocabApi.getAnnotatedSampleData(opts)\n\tconst rows = []\n\tconst termIsNumeric = isNumericTerm(self.config.term.term)\n\tconst term2isNumeric = self.config.term2 ? isNumericTerm(self.config.term2.term) : false\n\n\tfor (const sample of data.lst) {\n\t\tconst sampleName = data.refs.bySampleId[sample.sample].label\n\t\tconst row = [{ value: sampleName }]\n\t\t/** Don't show hidden values in the results\n\t\t * May not be caught in server request for custom variables\n\t\t * with user supplied keys */\n\t\tif (self.config.term.q?.hiddenValues && `${sample[self.config.term.$id].key}` in self.config.term.q.hiddenValues)\n\t\t\tcontinue\n\t\tif (termIsNumeric) {\n\t\t\tconst value = sample[self.config.term.$id]?.value\n\t\t\trow.push({ value: roundValueAuto(value) })\n\t\t}\n\t\tif (self.config.term2) {\n\t\t\t//Don't show hidden values in the results\n\t\t\tif (\n\t\t\t\tself.config.term2.q?.hiddenValues &&\n\t\t\t\t`${sample[self.config.term2.$id].key}` in self.config.term2.q.hiddenValues\n\t\t\t)\n\t\t\t\tcontinue\n\t\t\tlet value = sample[self.config.term2.$id]\n\t\t\tif (!value) row.push({ value: '' })\n\t\t\telse {\n\t\t\t\tconst label = self.config.term2.term.values?.[value.key]?.label\n\t\t\t\tvalue = term2isNumeric ? roundValueAuto(value.value) : label || value.value\n\t\t\t\trow.push({ value })\n\t\t\t}\n\t\t}\n\t\trows.push(row)\n\t}\n\tconst columns = [{ label: 'Sample' }]\n\tif (termIsNumeric) columns.push({ label: self.config.term.term.name })\n\tif (self.config.term2) columns.push({ label: self.config.term2.term.name })\n\tconst menu = new Menu({ padding: '5px' })\n\tconst div = menu.d.append('div')\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv,\n\t\tshowLines: true,\n\t\tmaxHeight: '40vh',\n\t\tresize: true\n\t})\n\tmenu.show(event.clientX, event.clientY, false)\n\n\tfunction getTvs(termIndex, value) {\n\t\tconst term = termIndex == 0 ? self.config.term0 : termIndex == 1 ? self.config.term : self.config.term2\n\t\tlet tvs = {\n\t\t\ttype: 'tvs',\n\t\t\ttvs: {\n\t\t\t\tterm: term.term,\n\t\t\t\tvalues: [{ key: value }]\n\t\t\t}\n\t\t}\n\t\tif (isNumericTerm(term.term)) {\n\t\t\tconst bins = self.bins[termIndex]\n\t\t\ttvs.tvs.ranges = [bins.find(bin => bin.label == value)]\n\t\t}\n\t\tif (term.term.type == 'geneVariant') {\n\t\t\t// geneVariant term\n\t\t\tconst termdbmclass = self.app.vocabApi.termdbConfig?.mclass\n\t\t\tif (termIndex === 1) {\n\t\t\t\t// term1=geneVariant, chart will be divided by dt term\n\t\t\t\t// get dt term from selected chart and build tvs\n\t\t\t\tconst dtTerm = self.chartid2dtterm[chartId]\n\t\t\t\tlet key\n\t\t\t\tif (termdbmclass) {\n\t\t\t\t\t// custom mclass labels defined in dataset\n\t\t\t\t\tkey = Object.keys(termdbmclass).find(k => termdbmclass[k].label == value)\n\t\t\t\t}\n\t\t\t\tif (!key) {\n\t\t\t\t\tkey = Object.keys(mclass).find(k => mclass[k].label == value)\n\t\t\t\t}\n\t\t\t\ttvs = {\n\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\ttvs: {\n\t\t\t\t\t\tterm: dtTerm,\n\t\t\t\t\t\tvalues: [{ key }],\n\t\t\t\t\t\tincludeNotTested: true // to be able to list not tested samples\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// term0/2=geneVariant, get dt term from groupsetting\n\t\t\t\tconst groups = term.q.customset?.groups\n\t\t\t\tif (!groups || !Array.isArray(groups)) throw 'groups[] is missing'\n\t\t\t\tconst group = groups.find(group => group.name == value)\n\t\t\t\ttvs = group.filter\n\t\t\t}\n\t\t}\n\t\treturn tvs\n\t}\n}\n\nfunction menuoption_add_filter(self, tvslst) {\n\t/*\n\tself: the tree object\n\ttvslst: an array of 1 or 2 term-value setting objects\n\t\tthis is to be added to the obj.termfilter.filter[]\n\t\tif barchart is single-term, tvslst will have only one element\n\t\tif barchart is two-term overlay, tvslst will have two elements, one for term1, the other for term2\n  \t*/\n\tif (!tvslst) return\n\tif (!self.state.termfilter || self.state.nav?.header_mode !== 'with_tabs') {\n\t\t// do not display ui, and do not collect callbacks\n\t\treturn\n\t}\n\tconst filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, 'filterUiRoot')\n\tconst filter = filterJoin([\n\t\tfilterUiRoot,\n\t\t{\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: tvslst.length > 1 ? 'and' : '',\n\t\t\tlst: [...tvslst.map(wrapTvs)]\n\t\t}\n\t])\n\tfilter.tag = 'filterUiRoot'\n\tself.app.dispatch({\n\t\ttype: 'filter_replace',\n\t\tfilter\n\t})\n}\n\nfunction wrapTvs(tvs) {\n\treturn tvs.type === 'tvs' ? tvs : { type: 'tvs', tvs }\n}\n\n/* \t\t\tTODO: add to cart and gp          */\n\nfunction menuoption_listsamples(self, tvslst) {\n\tconst filterRoot = getNormalRoot({\n\t\ttype: 'tvslst',\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\tself.state.termfilter.filter,\n\t\t\t// create a copy of tvslst to not mutate the barchart state,\n\t\t\t// such as when deleting tvs.tvs.term.values below\n\t\t\t...tvslst.map(tvs => wrapTvs(JSON.parse(JSON.stringify(tvs))))\n\t\t]\n\t})\n\t///////////// quick fix to delete term.values{} from stringified filter to reduce url length\n\tnormalizeProps(filterRoot, f => {\n\t\tdelete f.tag\n\t\tif (f.type == 'tvs' && f.tvs && f.tvs.term) delete f.tvs.term.values\n\t})\n\tconst arg = [\n\t\t'getsamples=1',\n\t\t'genome=' + self.app.vocabApi.vocab.genome,\n\t\t'dslabel=' + self.app.vocabApi.vocab.dslabel,\n\t\t'filter=' + encodeURIComponent(JSON.stringify(filterRoot))\n\t]\n\n\tdofetch3('termdb?' + arg.join('&')).then(data => {\n\t\texport_data(data.samples.length + ' samples', [{ text: data.samples.join('\\n') }])\n\t})\n}\n\nfunction menuoption_select_to_gp(self, tvslst) {\n\tconst lst = []\n\tfor (const t of tvslst) {\n\t\tconst f = wrapTvs(t)\n\t\tconst item = findItemByTermId(self.state.termfilter.filter, t.tvs.term.id)\n\t\tif (!item) lst.push(wrapTvs(t))\n\t}\n\n\timport('../src/block').then(async _ => {\n\t\tconst obj = {\n\t\t\tgenome: self.app.opts.genome,\n\t\t\tdslabel: self.state.dslabel\n\t\t}\n\t\tconst pane = newpane({ x: 100, y: 100 })\n\t\tconst filterRoot = getNormalRoot(self.state.termfilter.filter)\n\t\tconst filterUiRoot = getFilterItemByTag(filterRoot, filterUiRoot)\n\t\tif (filterUiRoot && filterUiRoot != filterRoot) delete filterUiRoot.tag\n\t\tfilterRoot.tag = 'filterUiRoot'\n\t\tif (lst.length) {\n\t\t\tfilterRoot.join = 'and'\n\t\t\tfilterRoot.lst.push(...lst)\n\t\t}\n\t\tconst cohortFilter = getFilterItemByTag(filterRoot, 'cohortFilter')\n\t\tif (cohortFilter) {\n\t\t\tcohortFilter.renderAs = 'htmlSelect'\n\t\t\tcohortFilter.selectOptionsFrom = 'selectCohort'\n\t\t}\n\t\tnew _.Block({\n\t\t\thostURL: sessionStorage.getItem('hostURL'),\n\t\t\tholder: pane.body,\n\t\t\tgenome: obj.genome,\n\t\t\tnobox: true,\n\t\t\tchr: obj.genome.defaultcoord.chr,\n\t\t\tstart: obj.genome.defaultcoord.start,\n\t\t\tstop: obj.genome.defaultcoord.stop,\n\t\t\tnativetracks: [obj.genome.tracks.find(i => i.__isgene).name.toLowerCase()],\n\t\t\ttklst: [\n\t\t\t\t{\n\t\t\t\t\ttype: 'mds2',\n\t\t\t\t\tdslabel: obj.dslabel,\n\t\t\t\t\tvcf: {\n\t\t\t\t\t\tnumerical_axis: {\n\t\t\t\t\t\t\tAFtest: {\n\t\t\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t\t\t{ is_termdb: true, filter: filterRoot },\n\t\t\t\t\t\t\t\t\t{ is_population: true, key: 'gnomAD', allowto_adjust_race: true, adjust_race: true }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t})\n}\n\nfunction menuoption_select_group_add_to_cart(self, tvslst) {\n\tif (!tvslst || !tvslst.length) return\n\n\tconst new_group = {}\n\tnew_group.is_termdb = true\n\tnew_group.terms = []\n\n\tfor (const [i, term] of tvslst.entries()) {\n\t\tnew_group.terms.push(term)\n\t}\n\n\tif (!self.selected_groups) {\n\t\tself.selected_groups = []\n\t}\n\n\tself.selected_groups.push(new_group)\n\tself.components.cart.main()\n}\n\nfunction getTermValues(d, self) {\n\t/*\n    d: clicked bar data\n  */\n\tconst termValues = []\n\tif (self.state.nav?.header_mode == 'with_cohortHtmlSelect') {\n\t\t// pass the cohort filter information back to calling app\n\t\t// do not set the renderAs in here since that is decided by the calling app\n\t\tconst cohortFilter = getFilterItemByTag(self.state.termfilter.filter, 'cohortFilter')\n\t\tif (cohortFilter) termValues.push(JSON.parse(JSON.stringify(cohortFilter)))\n\t}\n\n\tconst t1 = self.config.term\n\tconst t1ValKey =\n\t\tt1.term.values && Object.keys(t1.term.values).filter(key => t1.term.values[key].label === d.seriesId)[0]\n\tconst t1ValId = t1.term.values && t1ValKey in t1.term.values ? t1ValKey : d.seriesId\n\tconst t2 = self.config.term2\n\tconst t2ValKey =\n\t\tt2 && t2.term.values && Object.keys(t2.term.values).filter(key => t2.term.values[key].label === d.dataId)[0]\n\tconst t2ValId = t2 && t2.term.values && t2ValKey in t2.term.values ? t2ValKey : d.dataId\n\n\tfor (const term of [t1, t2]) {\n\t\tif (!term) continue\n\t\tconst i = term == t1 ? 1 : 2\n\t\tconst key = term == t1 ? t1ValId : t2ValId\n\t\t// const q = term ? term.q : {}\n\t\tconst q = term.q //self.currServerData.refs.q[i]\n\t\tconst label = !term || !term.term.values ? key : key in term.term.values ? term.term.values[key].label : key\n\n\t\tif (q.type == 'predefined-groupset' || q.type == 'custom-groupset') {\n\t\t\tconst groupset =\n\t\t\t\tq.type == 'predefined-groupset' ? term.term.groupsetting.lst[q.predefined_groupset_idx] : q.customset\n\t\t\tconst group = groupset.groups.find(g => g.name === key)\n\t\t\tconst tvs = { term: term.term, values: group.values, groupset_label: group.name }\n\t\t\tif (term.term.type == 'condition') {\n\t\t\t\ttvs.bar_by_children = term.q.bar_by_children\n\t\t\t\ttvs.bar_by_grade = term.q.bar_by_grade\n\t\t\t\ttvs.value_by_most_recent = term.q.value_by_most_recent\n\t\t\t\ttvs.value_by_max_grade = term.q.value_by_max_grade\n\t\t\t}\n\t\t\ttermValues.push(tvs)\n\t\t} else if (term.term.type == 'condition') {\n\t\t\tif (!t2 || t1.term.id != t2.term.id) {\n\t\t\t\ttermValues.push(\n\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\tvalues: [{ key, label }]\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t}\n\n\t\t\tif (term == t1 && t2 && term.term.id == t2.term.id) {\n\t\t\t\tconst q2 = t2.q\n\t\t\t\tconst term2Label =\n\t\t\t\t\tt2.term.values && d.dataId in t2.term.values ? self.config.term2.values[d.dataId].label : d.dataId\n\n\t\t\t\ttermValues.push(\n\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tterm: term.term,\n\t\t\t\t\t\t\tgrade_and_child: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\tgrade: q2.bar_by_grade ? d.dataId : key,\n\t\t\t\t\t\t\t\t\tgrade_label: q2.bar_by_grade ? term2Label : label,\n\t\t\t\t\t\t\t\t\tchild_id: q2.bar_by_children ? d.dataId : key,\n\t\t\t\t\t\t\t\t\tchild_label: q2.bar_by_children ? term2Label : label\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq2\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t}\n\t\t} else {\n\t\t\tconst bins = self.currServerData.refs.bins[i]\n\t\t\tif (!bins || !bins.length) {\n\t\t\t\t// not associated with numeric bins\n\t\t\t\ttermValues.push({ term: term.term, values: [{ key, label }] })\n\t\t\t} else {\n\t\t\t\tconst range = bins.find(d => d.label == label || d.name == label)\n\t\t\t\tif (range) termValues.push({ term: term.term, ranges: [range] })\n\t\t\t\telse if (term == t1) {\n\t\t\t\t\ttermValues.push({ term: term.term, ranges: [{ value: key }] })\n\t\t\t\t} else if (term == t2) {\n\t\t\t\t\ttermValues.push({ term: term.term, ranges: [{ value: key }] })\n\t\t\t\t} else {\n\t\t\t\t\tthrow 'should not happen'\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\treturn termValues.map(f => wrapTvs(f))\n}\n", "import { getCompInit, copyMerge } from '../rx'\nimport getHandlers from './barchart.events'\nimport barsRenderer from './bars.renderer'\nimport rendererSettings from './bars.settings'\nimport { htmlLegend, svgLegend, renderTable } from '#dom'\nimport { select } from 'd3-selection'\nimport { rgb } from 'd3-color'\nimport { controlsInit, term0_term2_defaultQ, renderTerm1Label } from './controls'\nimport { to_svg } from '../src/client'\nimport { fillTermWrapper } from '#termsetting'\nimport { getColors, mclass, plotColor } from '#shared/common.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\nexport class Barchart {\n\tconstructor(opts) {\n\t\t// rx.getComponentInit() will set this.app, this.id, this.opts\n\t\tthis.type = 'barchart'\n\t\tif (opts?.parentId) this.parentId = opts.parentId\n\t}\n\t//freeze the api of this class. don't want embedder functions to modify it.\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\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\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\tbanner: holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.style('font-size', '16px')\n\t\t\t\t.style('color', '#aaa'),\n\t\t\tbarDiv: holder.append('div'),\n\t\t\tlegendDiv: holder.append('div').style('margin', '5px 5px 15px 5px')\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Barchart')\n\t\tthis.settings = JSON.parse(rendererSettings)\n\n\t\tsetRenderers(this)\n\t\tsetInteractivity(this)\n\n\t\tthis.renderers = {}\n\t\tthis.legendRenderer = htmlLegend(\n\t\t\tthis.dom.legendDiv,\n\t\t\t{\n\t\t\t\tsettings: {\n\t\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t\t},\n\t\t\t\thandlers: this.handlers\n\t\t\t},\n\t\t\tthis.dom.barDiv\n\t\t)\n\t\tthis.controls = {}\n\t\tthis.term2toColor = {}\n\n\t\tif (this.opts.bar_click_override) {\n\t\t\t// will use this as callback to bar click\n\t\t\t// and will not set up bar click menu\n\t\t} else if (!this.opts.bar_click_opts) {\n\t\t\tthis.opts.bar_click_opts = ['hide_bar']\n\t\t\tif (this.app.getState().nav.header_mode === 'with_tabs') this.opts.bar_click_opts.push('add_filter')\n\t\t}\n\t}\n\n\tasync setControls() {\n\t\tconst state = this.state\n\t\tthis.dom.controls.selectAll('*').remove()\n\t\tif (this.opts.controls) {\n\t\t\tthis.opts.controls.on('downloadClick.barchart', 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 inputs = [\n\t\t\t\t{\n\t\t\t\t\ttype: 'term',\n\t\t\t\t\tconfigKey: 'term',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tusecase: { target: 'barchart', detail: 'term' },\n\t\t\t\t\tlabel: renderTerm1Label,\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tmenuOptions: 'edit',\n\t\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t\tconst tw = this.config['term']\n\t\t\t\t\t\tif (!tw) return { skip_samplecounts: true }\n\t\t\t\t\t\tif (tw.term.samplecounts) return { samplecounts: tw.term.samplecounts }\n\t\t\t\t\t\treturn {}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\ttype: 'term',\n\t\t\t\t\tconfigKey: 'term2',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tusecase: { target: 'barchart', detail: 'term2' },\n\t\t\t\t\ttitle: 'Overlay data',\n\t\t\t\t\tlabel: 'Overlay',\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ,\n\t\t\t\t\t// overlay option should always be visible, but must convert unit from log to abs\n\t\t\t\t\t// when an overlay is added\n\t\t\t\t\t//getDisplayStyle: () => (this.settings.unit == 'log' ? 'none' : ''),\n\t\t\t\t\tprocessConfig: config => {\n\t\t\t\t\t\t//config.settings not usually passed for logic check below\n\t\t\t\t\t\tconst s = this.state.config.settings.barchart\n\t\t\t\t\t\tif (!config.settings) config.settings = { barchart: {} }\n\t\t\t\t\t\t//Prevent showing Log option when overlay is selected\n\t\t\t\t\t\tif (config.term2 && s.unit == 'log') config.settings.barchart.unit = 'abs'\n\t\t\t\t\t\t//Revert back to Linear radio when Proportion is selected\n\t\t\t\t\t\t//but the overlay term is removed\n\t\t\t\t\t\tif (!config.term2 && s.unit == 'pct') config.settings.barchart.unit = 'abs'\n\t\t\t\t\t},\n\t\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t\tconst tw = this.config['term2']\n\t\t\t\t\t\tif (!tw) return { skip_samplecounts: true }\n\t\t\t\t\t\tif (tw.term.samplecounts) return { samplecounts: tw.term.samplecounts }\n\t\t\t\t\t\treturn {}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\ttype: 'term',\n\t\t\t\t\tconfigKey: 'term0',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tusecase: { target: 'barchart', detail: 'term0' },\n\t\t\t\t\ttitle: 'Divide by data',\n\t\t\t\t\tlabel: 'Divide by',\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ,\n\t\t\t\t\tgetBodyParams: () => {\n\t\t\t\t\t\tconst tw = this.config['term0']\n\t\t\t\t\t\tif (!tw) return { skip_samplecounts: true }\n\t\t\t\t\t\tif (tw.term.samplecounts) return { samplecounts: tw.term.samplecounts }\n\t\t\t\t\t\treturn {}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Charts layout',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'divideOrientation',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t\t]\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Bar orientation',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'orientation',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t\t]\n\t\t\t\t},\n\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Scale',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'unit',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Linear', value: 'abs' },\n\t\t\t\t\t\t/** Option not available when term2 is present:\n\t\t\t\t\t\t * 1. The scale for the plot renders incorrectly\n\t\t\t\t\t\t * 2. The bars do not appear to be rendering correctly as a result\n\t\t\t\t\t\t * TODOs: Investigate the cause of the rendering issue\n\t\t\t\t\t\t */\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Log',\n\t\t\t\t\t\t\tvalue: 'log',\n\t\t\t\t\t\t\tgetDisplayStyle: (plot, computedDisplay = 'inline-block') => (plot.term2 ? 'none' : computedDisplay)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Proportion',\n\t\t\t\t\t\t\tvalue: 'pct',\n\t\t\t\t\t\t\tgetDisplayStyle: (plot, computedDisplay = 'inline-block') => (plot.term2 ? computedDisplay : 'none')\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Multicolor bars',\n\t\t\t\t\ttitle: 'Color bars using the colors preassigned if available, otherwise generates a color',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'colorBars',\n\t\t\t\t\tboxLabel: 'Yes',\n\t\t\t\t\tgetDisplayStyle: plot => (plot.term2 ? 'none' : 'table-row')\n\t\t\t\t},\n\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Deduplicate',\n\t\t\t\t\ttitle: 'Use separate bars samples that has multiple values or belong to multiple groups',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'dedup',\n\t\t\t\t\tboxLabel: 'Yes',\n\t\t\t\t\tgetDisplayStyle: plot =>\n\t\t\t\t\t\tthis.chartsData.charts.find(c => c.serieses.length != c.dedupedSerieses.length) ? 'table-row' : 'none'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Default color',\n\t\t\t\t\ttitle: 'Default color for bars when there is no overlay',\n\t\t\t\t\ttype: 'color',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t\t\t//getDisplayStyle: plot => (plot.settings.barchart.colorBars || plot.term2 ? 'none' : 'table-row')\n\t\t\t\t}\n\t\t\t]\n\t\t\tif (state.config.term2)\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Show stats table',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'showStatsTable',\n\t\t\t\t\tboxLabel: 'Yes'\n\t\t\t\t})\n\t\t\tconst multipleTestingCorrection = this.app.getState().termdbConfig.multipleTestingCorrection\n\t\t\tif (multipleTestingCorrection) {\n\t\t\t\t// a checkbox to allow users to show or hide asterisks on bars\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Asterisks',\n\t\t\t\t\tboxLabel: 'Visible',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'asterisksVisible',\n\t\t\t\t\ttitle: 'Display the asterisks'\n\t\t\t\t})\n\t\t\t\tconst mtcMethod = multipleTestingCorrection.method\n\t\t\t\tif (!mtcMethod) throw 'no multiple testing correction method specified'\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: `Multiple testing correction (${mtcMethod == 'bon' ? 'Bonferroni' : mtcMethod})`,\n\t\t\t\t\tboxLabel: '',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tsettingsKey: 'multiTestingCorr',\n\t\t\t\t\ttitle: `Perform multiple testing correction (${mtcMethod == 'bon' ? 'Bonferroni' : mtcMethod})`\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tthis.components = {\n\t\t\t\tcontrols: await controlsInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tholder: this.dom.controls.attr('class', 'pp-termdb-plot-controls').style('display', 'inline-block'),\n\t\t\t\t\tinputs\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tthis.components.controls.on('downloadClick.barchart', this.download)\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t\treturn true\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\treturn {\n\t\t\tnav: {\n\t\t\t\theader_mode: appState.nav.header_mode\n\t\t\t},\n\t\t\ttermfilter: parentConfig ? { filter: parentConfig.filter } : appState.termfilter,\n\t\t\tconfig: Object.assign({}, config, {\n\t\t\t\tsettings: {\n\t\t\t\t\tbarchart: config.settings.barchart,\n\t\t\t\t\tcommon: config.settings.common\n\t\t\t\t},\n\t\t\t\tdisplaySampleIds: appState.termdbConfig.displaySampleIds && this.app.vocabApi.hasVerifiedToken()\n\t\t\t}),\n\t\t\tmultipleTestingCorrection: appState.termdbConfig.multipleTestingCorrection,\n\t\t\tbar_click_menu: appState.bar_click_menu || {}\n\t\t}\n\t}\n\n\tasync main() {\n\t\tconst c = this.state.config\n\t\tif (c.chartType != this.type && c.childType != this.type) return\n\t\ttry {\n\t\t\tthis.config = structuredClone(c)\n\t\t\tif (!this.currServerData) this.dom.barDiv.style('max-width', window.innerWidth + 'px')\n\t\t\tthis.prevConfig = this.config || {}\n\t\t\tif (this.dom.header)\n\t\t\t\tthis.dom.header.html(\n\t\t\t\t\tthis.config.term.term.name + ` <span style=\"opacity:.6;font-size:.7em;margin-left:10px;\">BARCHART</span>`\n\t\t\t\t)\n\n\t\t\tthis.toggleLoadingDiv()\n\t\t\tawait this.setControls()\n\n\t\t\tconst reqOpts = this.getDataRequestOpts()\n\t\t\tawait this.getDescrStats()\n\t\t\tconst results = await this.app.vocabApi.getNestedChartSeriesData(reqOpts)\n\t\t\tconst data = results.data\n\t\t\tthis.sampleType = results.sampleType\n\t\t\tthis.bins = results.bins\n\t\t\tif (results.chartid2dtterm) this.chartid2dtterm = results.chartid2dtterm\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthis.app.vocabApi.syncTermData(this.config, data, this.prevConfig)\n\t\t\tthis.currServerData = data\n\t\t\tif (this.currServerData.refs && this.currServerData.refs.q) {\n\t\t\t\tfor (const q of this.currServerData.refs.q) {\n\t\t\t\t\tif (q.error) throw q.error\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tthis.term1toColor = {}\n\t\t\tthis.term2toColor = {} // forget any assigned overlay colors when refreshing a barchart\n\t\t\tthis.updateSettings(this.config)\n\n\t\t\tconst numColors = this.config.term2 ? this.settings.rows?.length : this.settings.cols?.length\n\t\t\tthis.colorScale = getColors(numColors || 0)\n\t\t\tthis.chartsData = this.processData(this.currServerData)\n\t\t\tthis.render()\n\t\t} catch (e) {\n\t\t\tthrow 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 = { term: c.term, filter: this.state.termfilter.filter }\n\t\tif (this.state.termfilter.filter0) opts.filter0 = this.state.termfilter.filter0\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\tasync getDescrStats() {\n\t\t// get descriptive statistics for numerical terms\n\t\tconst terms = [this.config.term]\n\t\tif (this.config.term2) terms.push(this.config.term2)\n\t\tif (this.config.term0) terms.push(this.config.term0)\n\t\tfor (const t of terms) {\n\t\t\tif (isNumericTerm(t.term)) {\n\t\t\t\tconst data = await this.app.vocabApi.getDescrStats(t, this.state.termfilter)\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\tt.q.descrStats = data.values\n\t\t\t}\n\t\t}\n\t}\n\n\tupdateSettings(config) {\n\t\tif (!config) return\n\t\t// translate relevant config keys to barchart settings keys\n\t\tconst obj = this.state\n\t\tconst settings = {\n\t\t\tterm0: config.term0 ? config.term0.term.id : '', // convenient reference to the term id\n\t\t\tterm1: config.term.term.id, // convenient reference to the term2 id\n\t\t\tterm2: config.term2 ? config.term2.term.id : '',\n\t\t\tunit: config.settings.barchart.unit,\n\t\t\torientation: config.settings.barchart.orientation,\n\t\t\tdivideOrientation: config.settings.barchart.divideOrientation,\n\t\t\tasterisksVisible: config.settings.barchart.asterisksVisible,\n\t\t\tmultiTestingCorr: config.settings.barchart.multiTestingCorr,\n\t\t\tdefaultColor: config.settings.barchart.defaultColor,\n\t\t\tcolorBars: config.settings.barchart.colorBars,\n\t\t\tdedup: config.settings.barchart.dedup,\n\t\t\t// normalize bar thickness regardless of orientation\n\t\t\tcolw: config.settings.common.barwidth,\n\t\t\trowh: config.settings.common.barwidth,\n\t\t\tcolspace: config.settings.common.barspace,\n\t\t\trowspace: config.settings.common.barspace\n\t\t}\n\n\t\t/* mayResetHidden() was added before to prevent showing empty chart due to automatic hiding uncomputable categories\n\t\tthis has following problems:\n\t\t1. when term1=diaggrp and term2=hrtavg, uncomputable categories from term2 can show up by default.\n\t\t2. inconsistent behavior: when term1=agedx, term2=hrtavg the uncomputable categories are hidden by default\n\n\t\tside effect of disabling this function can cause empty chart, but seems to be minor given above\n\t\t*/\n\t\t//this.mayResetHidden(this.config.term, this.config.term2, this.config.term0)\n\n\t\tthis.setExclude(this.config.term, this.config.term2)\n\t\tObject.assign(this.settings, settings, this.currServerData.refs || {}, {\n\t\t\texclude: this.settings.exclude\n\t\t})\n\n\t\tthis.settings.cols = this.settings.dedup ? this.currServerData.refs.dedupCols : this.currServerData.refs.cols\n\t\tthis.settings.numCharts = this.currServerData.charts ? this.currServerData.charts.length : 0\n\t\tif (!config.term2 && this.settings.unit == 'pct') {\n\t\t\tthis.settings.unit = 'abs'\n\t\t}\n\t}\n\n\tmayResetHidden(term, term2, term0) {\n\t\tconst combinedTermIds = (term && term.term.id) + ';;' + (term2 && term2.term.id) + ';;' + (term0 && term0.term.id)\n\t\tif (combinedTermIds === this.currCombinedTermIds) return\n\t\t// only reset hidden if terms have changed\n\t\tfor (const chart of this.currServerData.charts) {\n\t\t\tif (term.q && term.q.hiddenValues) {\n\t\t\t\tthis.mayEditHiddenValues(term, chart.serieses.length, 'term')\n\t\t\t}\n\t\t\tif (term2 && term2.q && term2.q.hiddenValues) {\n\t\t\t\tfor (const series of chart.serieses) {\n\t\t\t\t\tthis.mayEditHiddenValues(term2, series.data.length, 'term2')\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.currCombinedTermIds = combinedTermIds\n\t}\n\n\tmayEditHiddenValues(term, numAvailable, termNum) {\n\t\tconst numHidden = Object.keys(term.q.hiddenValues).filter(key => term.q.hiddenValues[key]).length\n\t\tif (numHidden < numAvailable) return\n\t\t/*\n\t\t\tif all the serieses are assigned to be hidden on first render,\n\t\t\tshow the usually hidden values instead to avoid confusion\n\t\t\twith an empty plot\n\t\t*/\n\t\tfor (const key in term.q.hiddenValues) {\n\t\t\tif (!term.q.hiddenValues[key]) return\n\t\t\tdelete term.q.hiddenValues[key]\n\t\t}\n\t\t// since config.[term | term2 | term0] are copies of appState,\n\t\t// must save the changes to q.hiddenValues in the stored state\n\t\t// for consistent behavior in later app.dispatch or barchart updates\n\t\tthis.app.save({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: {\n\t\t\t\t[termNum]: term\n\t\t\t}\n\t\t})\n\t}\n\n\tsetExclude(term, term2) {\n\t\t// a non-numeric term.id is used directly as seriesId or dataId\n\t\tthis.settings.exclude.cols = Object.keys(term.q?.hiddenValues || {})\n\t\t\t.filter(id => term.q.hiddenValues[id])\n\t\t\t.map(id => {\n\t\t\t\treturn term.term.type == 'categorical'\n\t\t\t\t\t? id\n\t\t\t\t\t: this.settings.cols?.includes(id)\n\t\t\t\t\t? id\n\t\t\t\t\t: term.term.values[id]?.label\n\t\t\t\t\t? term.term.values[id].label\n\t\t\t\t\t: id\n\t\t\t})\n\n\t\tthis.settings.exclude.rows = !term2?.q?.hiddenValues\n\t\t\t? []\n\t\t\t: Object.keys(term2.q.hiddenValues)\n\t\t\t\t\t.filter(id => term2.q.hiddenValues[id])\n\t\t\t\t\t.map(id =>\n\t\t\t\t\t\tterm2.term.type == 'categorical'\n\t\t\t\t\t\t\t? id\n\t\t\t\t\t\t\t: this.settings.rows?.includes(id)\n\t\t\t\t\t\t\t? id\n\t\t\t\t\t\t\t: term2.term.values[id]?.label\n\t\t\t\t\t\t\t? term2.term.values[id].label\n\t\t\t\t\t\t\t: id\n\t\t\t\t\t)\n\t}\n\n\tprocessData(chartsData) {\n\t\tthis.seriesOrder = this.setMaxVisibleTotals(chartsData)\n\t\tif (!chartsData.charts.length) {\n\t\t\tthis.seriesOrder = []\n\t\t} else if (chartsData.refs.useColOrder) {\n\t\t\tthis.seriesOrder = this.settings.cols\n\t\t}\n\n\t\tconst rows = chartsData.refs.rows\n\n\t\tthis.barSorter = (a, b) => this.seriesOrder.indexOf(a) - this.seriesOrder.indexOf(b)\n\t\tthis.overlaySorter = chartsData.refs.useRowOrder\n\t\t\t? (a, b) => rows.indexOf(a.dataId) - rows.indexOf(b.dataId)\n\t\t\t: (a, b) =>\n\t\t\t\t\tthis.totalsByDataId[b.dataId] > this.totalsByDataId[a.dataId]\n\t\t\t\t\t\t? 1\n\t\t\t\t\t\t: this.totalsByDataId[b.dataId] < this.totalsByDataId[a.dataId]\n\t\t\t\t\t\t? -1\n\t\t\t\t\t\t: a.dataId < b.dataId\n\t\t\t\t\t\t? -1\n\t\t\t\t\t\t: 1\n\n\t\tthis.visibleCharts = chartsData.charts.filter(chart => chart.visibleSerieses.length)\n\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\tconst chartsTests = chartsData.tests\n\n\t\t//get term1 and term2 labels\n\t\tfor (const chartId in chartsTests) {\n\t\t\tconst chartTests = chartsTests[chartId]\n\t\t\tfor (const t1c of chartTests) {\n\t\t\t\tconst t1label =\n\t\t\t\t\tt1.term.values && t1c.term1comparison in t1.term.values\n\t\t\t\t\t\t? t1.term.values[t1c.term1comparison].label\n\t\t\t\t\t\t: t1c.term1comparison\n\t\t\t\tt1c.term1Label = t1label\n\n\t\t\t\tfor (const t2t of t1c.term2tests) {\n\t\t\t\t\tconst t2label =\n\t\t\t\t\t\tt2.term.values && t2t.term2id in t2.term.values ? t2.term.values[t2t.term2id].label : t2t.term2id\n\t\t\t\t\tt2t.term2Label = t2label\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn chartsData\n\t}\n\n\tsetMaxVisibleTotals(chartsData) {\n\t\t// chartsData = this.currServerData\n\t\tthis.totalsByDataId = {}\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\t// this will prioritize sorting series totals in the first chart,\n\t\t// then serieses in the subsequent chart that are not already in the first chart, and so on\n\t\tconst visibleTotalsByChartSeriesId = {}\n\t\tlet maxVisibleAcrossCharts = 0\n\t\tfor (const chart of chartsData.charts) {\n\t\t\tif (!chart.settings) chart.settings = JSON.parse(rendererSettings)\n\t\t\tObject.assign(chart.settings, this.settings)\n\t\t\tchart.visibleTotal = 0\n\t\t\tconst serieses = this.settings.dedup ? chart.dedupedSerieses : chart.serieses\n\t\t\tchart.visibleSerieses = serieses.filter(series => {\n\t\t\t\tif (chart.settings.exclude.cols.includes(series.seriesId)) return false\n\t\t\t\tseries.visibleData = series.data.filter(d => !chart.settings.exclude.rows.includes(d.dataId))\n\t\t\t\tseries.visibleTotal = series.visibleData.reduce((sum, a) => sum + a.total, 0)\n\t\t\t\tif (!series.visibleTotal) return false\n\t\t\t\tchart.visibleTotal += series.visibleTotal\n\t\t\t\tif (!(series.seriesId in visibleTotalsByChartSeriesId))\n\t\t\t\t\tvisibleTotalsByChartSeriesId[series.seriesId] = series.visibleTotal\n\t\t\t\tfor (const data of series.data) {\n\t\t\t\t\tdata.seriesId = series.seriesId\n\t\t\t\t\tif (\n\t\t\t\t\t\t(t1.term.type == 'geneVariant' && t1.q.type == 'values') ||\n\t\t\t\t\t\t(t2?.term.type == 'geneVariant' && t2?.q.type == 'values')\n\t\t\t\t\t) {\n\t\t\t\t\t\t// term1 or term2 is a geneVariant term not using groupsetting\n\t\t\t\t\t\t// need specialized processing\n\t\t\t\t\t\tif (!(data.dataId in this.totalsByDataId)) {\n\t\t\t\t\t\t\tthis.totalsByDataId[data.dataId] = {}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.totalsByDataId[data.dataId][chart.chartId] = this.totalsByDataId[data.dataId][chart.chartId]\n\t\t\t\t\t\t\t? this.totalsByDataId[data.dataId][chart.chartId] + data.total\n\t\t\t\t\t\t\t: 0 + data.total\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (!(data.dataId in this.totalsByDataId)) {\n\t\t\t\t\t\t\tthis.totalsByDataId[data.dataId] = 0\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.totalsByDataId[data.dataId] += data.total\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn true\n\t\t\t})\n\t\t\tchart.settings.colLabels = chart.visibleSerieses.map(series => {\n\t\t\t\tconst id = series.seriesId\n\t\t\t\tconst label = t1.term.values && id in t1.term.values ? t1.term.values[id].label : id\n\t\t\t\tconst af = series && 'AF' in series ? ', AF=' + series.AF : ''\n\t\t\t\tconst ntotal =\n\t\t\t\t\tt2 && t2.term.type == 'condition' && t2.q.value_by_computable_grade ? '' : `, n=${series.visibleTotal}`\n\t\t\t\treturn {\n\t\t\t\t\tid,\n\t\t\t\t\tlabel: label + af + ntotal\n\t\t\t\t}\n\t\t\t})\n\t\t\tchart.maxVisibleSeriesTotal = chart.visibleSerieses.reduce((max, series) => {\n\t\t\t\treturn series.visibleTotal > max ? series.visibleTotal : max\n\t\t\t}, 0)\n\t\t\tif (chart.maxVisibleSeriesTotal > maxVisibleAcrossCharts) {\n\t\t\t\tmaxVisibleAcrossCharts = chart.maxVisibleSeriesTotal\n\t\t\t}\n\t\t}\n\t\tfor (const chart of chartsData.charts) {\n\t\t\tchart.maxVisibleAcrossCharts = maxVisibleAcrossCharts\n\t\t}\n\n\t\treturn Object.keys(visibleTotalsByChartSeriesId).sort(\n\t\t\t(a, b) => visibleTotalsByChartSeriesId[b] - visibleTotalsByChartSeriesId[a]\n\t\t)\n\t}\n\n\tsortStacking(series, chart, chartsData) {\n\t\tthis.term1toColor[series.seriesId] = this.settings.colorBars\n\t\t\t? this.getColor(this.config.term, series.seriesId, this.bins?.[1])\n\t\t\t: this.settings.defaultColor\n\n\t\tseries.visibleData.sort(this.overlaySorter)\n\t\tlet seriesLogTotal = 0\n\t\tfor (const result of series.visibleData) {\n\t\t\tresult.colgrp = '-'\n\t\t\tresult.rowgrp = '-'\n\t\t\tresult.chartId = chart.chartId\n\t\t\tresult.seriesId = series.seriesId\n\t\t\tif (chartsData.tests) {\n\t\t\t\t// statistical tests result exist\n\t\t\t\t// put the pvalues corresponding to series.seriesId to result.groupPvalues\n\t\t\t\tresult.groupPvalues = chartsData.tests[chart.chartId].find(x => x.term1comparison === series.seriesId)\n\t\t\t}\n\t\t\tresult.seriesTotal = series.total\n\t\t\tresult.chartTotal = chart.visibleTotal\n\t\t\tresult.logTotal = Math.log10(result.total)\n\t\t\tseriesLogTotal += result.logTotal\n\t\t\tthis.setTerm2Color(result)\n\t\t\tresult.color = this.term2toColor[result.dataId] || this.term1toColor[series.seriesId]\n\t\t}\n\t\tif (seriesLogTotal > chart.maxSeriesLogTotal) {\n\t\t\tchart.maxSeriesLogTotal = seriesLogTotal\n\t\t}\n\t\t// assign color to hidden data for use in legend\n\t\tfor (const result of series.data) {\n\t\t\tif (result.color) continue\n\t\t\tthis.setTerm2Color(result)\n\t\t\tresult.color = this.term2toColor[result.dataId] || this.term1toColor[series.seriesId]\n\t\t}\n\t}\n\n\tsetTerm2Color(result) {\n\t\tif (!this.config.term2) return\n\t\tthis.term2toColor[result.dataId] = this.getColor(this.config.term2, result.dataId, this.bins?.[2])\n\t}\n\n\tgetColor(t, label, bins) {\n\t\tif (!t.term) return\n\t\tif (t.term.values) {\n\t\t\tfor (const [key, v] of Object.entries(t.term.values)) {\n\t\t\t\tif (!v.color) continue\n\t\t\t\tif (key === label) return v.color\n\t\t\t\tif (v.label === label) return v.color\n\t\t\t}\n\t\t}\n\t\tconst bin = bins?.find(bin => bin.label == label)\n\t\tif (bin?.color) return bin.color\n\n\t\tif (t.term.type == 'geneVariant' && t.q.type == 'values') return this.getMutationColor(label)\n\n\t\treturn rgb(this.colorScale(label)).toString()\n\t}\n\n\t// should move this outside of setTerm2Color(),\n\t// otherwise it will get *** recreated on every call *** to setTerm2Color()\n\tgetMutationColor(label) {\n\t\t// for (const [key, mc] of Object.entries(mclass)) if (mc.label == label) return mc.color\n\n\t\t// key is not used in loop above, can do this instead\n\t\tfor (const mc of Object.values(mclass)) if (mc.label === label && mc.color) return mc.color\n\n\t\t// can loop on the object directly\n\t\tfor (const key in mclass) {\n\t\t\tif (mclass[key].label === label && mclass[key].color) return mclass[key].color\n\t\t}\n\t}\n\n\t/*\n\t  when term1 or term2 is a geneVariant term, return legendGrps: \n\t\t[ \n\t\t\t[\n\t\t\t\t{\n\t\t\t\t\tname: \"...\", \n\t\t\t\t\titems: [...]\n\t\t\t\t},\n\t\t\t\t...\n\t\t\t],\n\t\t\t... \n\t\t]\n\t*/\n\tgetLegendGrps() {\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\tif (\n\t\t\t(t1.term.type == 'geneVariant' && t1.q.type == 'values') ||\n\t\t\t(t2?.term.type == 'geneVariant' && t2?.q.type == 'values')\n\t\t) {\n\t\t\tconst legendGrps = []\n\t\t\tfor (const chart of this.chartsData.charts) {\n\t\t\t\tlegendGrps.push(this.getOneLegendGrps(chart))\n\t\t\t}\n\t\t\treturn legendGrps\n\t\t}\n\t\treturn this.getOneLegendGrps()\n\t}\n\n\t//Used by getLegendGrps to get one legendGrps\n\tgetOneLegendGrps(chart) {\n\t\tconst legendGrps = []\n\t\tconst s = this.settings\n\t\tconst t1 = this.config.term\n\t\tconst t2 = this.config.term2\n\t\tconst headingStyle = 'color: #aaa; font-weight: 400'\n\n\t\t// descriptive statistics\n\t\tif (t1.q.descrStats) {\n\t\t\t// term1 has descriptive stats\n\t\t\tconst items = t1.q.descrStats.map(stat => {\n\t\t\t\treturn {\n\t\t\t\t\ttext: `${stat.label}: ${stat.value}`,\n\t\t\t\t\tnoIcon: true\n\t\t\t\t}\n\t\t\t})\n\t\t\t// title of descriptive stats should include the term1 name if term2 is present\n\t\t\tconst title = t2 ? `Descriptive statistics: ${t1.term.name}` : 'Descriptive statistics'\n\t\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\t\tlegendGrps.push({ name, items })\n\t\t}\n\t\tif (t2?.q.descrStats) {\n\t\t\t// term2 has descriptive stats\n\t\t\tconst items = t2.q.descrStats.map(stat => {\n\t\t\t\treturn {\n\t\t\t\t\ttext: `${stat.label}: ${stat.value}`,\n\t\t\t\t\tnoIcon: true\n\t\t\t\t}\n\t\t\t})\n\t\t\t// title of descriptive stats will include the term2 name\n\t\t\t// because two terms are present\n\t\t\tconst title = `Descriptive statistics: ${t2.term.name}`\n\t\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\t\tlegendGrps.push({ name, items })\n\t\t}\n\n\t\tif (s.cols && s.exclude.cols.length) {\n\t\t\tconst reducer = (sum, b) => sum + b.total\n\t\t\tconst items = s.exclude.cols\n\t\t\t\t.filter(collabel => s.cols.includes(collabel)) // && (!t1.term.values || collabel in t1.term.values))\n\t\t\t\t.flatMap(collabel => {\n\t\t\t\t\tconst filter = c => c.seriesId == collabel\n\t\t\t\t\tconst total =\n\t\t\t\t\t\tt2?.term?.type == 'condition'\n\t\t\t\t\t\t\t? 0\n\t\t\t\t\t\t\t: (t1.term.type == 'geneVariant' && t1.q.type == 'values') ||\n\t\t\t\t\t\t\t  (t2?.term.type == 'geneVariant' && t2?.q.type == 'values')\n\t\t\t\t\t\t\t? chart.serieses.filter(filter).reduce(reducer, 0)\n\t\t\t\t\t\t\t: this.currServerData.charts.reduce((sum, chart) => {\n\t\t\t\t\t\t\t\t\treturn sum + chart.serieses.filter(filter).reduce(reducer, 0)\n\t\t\t\t\t\t\t  }, 0)\n\t\t\t\t\tif (!total && !t2?.term?.type) return []\n\t\t\t\t\tconst label = t1.term.values && collabel in t1.term.values ? t1.term.values[collabel].label : collabel\n\t\t\t\t\tconst ntotal = total ? ', n=' + total : ''\n\t\t\t\t\treturn [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tid: collabel,\n\t\t\t\t\t\t\ttext: label + ntotal,\n\t\t\t\t\t\t\tcolor: '#fff',\n\t\t\t\t\t\t\ttextColor: '#000',\n\t\t\t\t\t\t\tborder: '1px solid #333',\n\t\t\t\t\t\t\t//inset: total ? \"n=\"+total : '',\n\t\t\t\t\t\t\tnoIcon: true,\n\t\t\t\t\t\t\ttype: 'col',\n\t\t\t\t\t\t\tisHidden: true,\n\t\t\t\t\t\t\thiddenOpacity: 1\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t\t.sort(this.barSorter)\n\n\t\t\tif (items.length) {\n\t\t\t\tconst name = t2 ? t1.term.name : 'Other categories'\n\t\t\t\tlegendGrps.push({\n\t\t\t\t\tname: `<span style=\"${headingStyle}\">${name}</span>`,\n\t\t\t\t\titems\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (s.rows /*&& s.rows.length > 1*/ && !s.hidelegend && t2 && this.term2toColor) {\n\t\t\tconst value_by_label =\n\t\t\t\tt2.term.type != 'condition' || !t2.q\n\t\t\t\t\t? ''\n\t\t\t\t\t: t2.q.value_by_max_grade\n\t\t\t\t\t? 'max. grade'\n\t\t\t\t\t: t2.q.value_by_most_recent\n\t\t\t\t\t? 'most recent'\n\t\t\t\t\t: ''\n\t\t\tlegendGrps.push({\n\t\t\t\tname:\n\t\t\t\t\t`<span style=\"${headingStyle}\">` + t2.term.name + (value_by_label ? ', ' + value_by_label : '') + '</span>',\n\t\t\t\titems: s.rows\n\t\t\t\t\t.flatMap(d => {\n\t\t\t\t\t\tconst total = chart ? this.totalsByDataId[d]?.[chart.chartId] : this.totalsByDataId[d]\n\t\t\t\t\t\tif (!total) return []\n\t\t\t\t\t\tconst ntotal = total ? ', n=' + total : ''\n\t\t\t\t\t\tconst label = t2.term.values && d in t2.term.values ? t2.term.values[d].label : d\n\t\t\t\t\t\treturn [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tdataId: d,\n\t\t\t\t\t\t\t\ttext: label + ntotal,\n\t\t\t\t\t\t\t\tcolor: this.term2toColor[d],\n\t\t\t\t\t\t\t\ttype: 'row',\n\t\t\t\t\t\t\t\tisHidden: s.exclude.rows.includes(d)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t})\n\t\t\t\t\t.sort(this.overlaySorter)\n\t\t\t})\n\t\t}\n\t\tif (t2 && this.state.multipleTestingCorrection) {\n\t\t\t// the dataset requires multiple testing correction and therefore needs to show this legend of Statistical Significance\n\t\t\t// calculate total number of unskipped tests\n\t\t\tlet testNum = 0\n\t\t\tfor (const chartId in this.chartsData.tests) {\n\t\t\t\ttestNum += this.chartsData.tests[chartId].reduce((a, b) => a + b.term2tests.filter(a => !a.skipped).length, 0)\n\t\t\t}\n\t\t\tconst items =\n\t\t\t\ttestNum > 1 && this.state.config.settings.barchart.multiTestingCorr\n\t\t\t\t\t? [{ text: `* p-value < (0.05 / ${testNum} tests)`, noEditColor: true }]\n\t\t\t\t\t: [{ text: `* p-value < 0.05`, noEditColor: true }]\n\t\t\tlegendGrps.push({\n\t\t\t\tname: `<span style=\"${headingStyle}\">&nbsp;</span>`,\n\t\t\t\titems\n\t\t\t})\n\t\t}\n\n\t\treturn legendGrps\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 barInit = getCompInit(Barchart)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = barInit\n\nfunction setRenderers(self) {\n\tself.render = function () {\n\t\tconst charts = self.dom.barDiv.selectAll('.pp-sbar-div').data(self.visibleCharts, chart => chart.chartId)\n\n\t\tcharts.exit().each(self.exitChart)\n\t\tcharts.each(self.updateChart)\n\t\tcharts.enter().append('div').each(self.addChart)\n\n\t\tself.dom.holder.selectAll('.pp-chart-title').style('display', self.visibleCharts.length < 2 ? 'none' : 'block')\n\t\tconst grps = self.getLegendGrps()\n\t\tself.legendRenderer(grps)\n\n\t\tif (!self.visibleCharts.length) {\n\t\t\tconst clickLegendMessage =\n\t\t\t\tself.settings.exclude.cols.length || self.settings.exclude.rows.length\n\t\t\t\t\t? `<br/><span>click on a legend label below to display the barchart</span>`\n\t\t\t\t\t: ''\n\t\t\tself.dom.banner\n\t\t\t\t.html(`<span>No visible barchart data to render</span>${clickLegendMessage}`)\n\t\t\t\t.style('display', 'block')\n\t\t\tself.dom.legendDiv.selectAll('*').remove()\n\t\t} else {\n\t\t\tself.dom.banner.text('').style('display', 'none')\n\t\t}\n\t}\n\n\tself.exitChart = function (chart) {\n\t\tdelete self.renderers[chart.chartId]\n\t\tselect(this).remove()\n\t}\n\n\tself.updateChart = function (chart) {\n\t\t// this.dom.legendDiv.remove(\"*\")\n\t\tchart.settings.cols.sort(self.barSorter)\n\t\tchart.maxAcrossCharts = self.chartsData.maxAcrossCharts\n\t\tchart.handlers = self.handlers\n\t\tchart.maxSeriesLogTotal = 0\n\t\tchart.visibleSerieses.forEach(series => self.sortStacking(series, chart, self.chartsData))\n\t\tself.renderers[chart.chartId](chart)\n\n\t\tconst div = select(this)\n\t\tdiv.style(\n\t\t\t'display',\n\t\t\tself.state.config.settings.barchart.divideOrientation == 'horizontal' ? 'inline-block' : 'block'\n\t\t)\n\n\t\tdiv.select('.pp-sbar-div-chartLengends').selectAll('*').remove()\n\t\tif (self.chartsData.tests && self.chartsData.tests[chart.chartId] && self.config.settings.barchart.showStatsTable) {\n\t\t\t//chart has pvalues\n\t\t\tgeneratePvalueTable(chart, div)\n\t\t}\n\t}\n\n\tself.addChart = function (chart, i) {\n\t\tconst div = select(this)\n\t\t\t.attr('class', 'pp-sbar-div')\n\t\t\t.style(\n\t\t\t\t'display',\n\t\t\t\tself.state.config.settings.barchart.divideOrientation == 'horizontal' ? 'inline-block' : 'block'\n\t\t\t)\n\t\t\t.style('padding', '20px')\n\t\t\t.style('vertical-align', 'top')\n\t\tself.renderers[chart.chartId] = barsRenderer(self, select(this))\n\t\t//self.updateChart.call(this, chart)\n\t\tchart.settings.cols.sort(self.barSorter)\n\t\tchart.maxAcrossCharts = self.chartsData.maxAcrossCharts\n\t\tchart.handlers = self.handlers\n\t\tchart.maxSeriesLogTotal = 0\n\t\tchart.visibleSerieses.forEach(series => self.sortStacking(series, chart, self.chartsData))\n\t\tself.renderers[chart.chartId](chart)\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-sbar-div-chartLengends')\n\t\t\t.attr('data-testid', 'sjpcb-bars-chartLengends')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin', '10px 10px 10px 30px')\n\t\t\t.style('display', 'none')\n\n\t\tif (self.chartsData.tests && self.chartsData.tests[chart.chartId] && self.config.settings.barchart.showStatsTable) {\n\t\t\t//chart has pvalues\n\t\t\tgeneratePvalueTable(chart, div)\n\t\t}\n\t}\n\n\t/*\n\tA function to generate a p-value table for Chi-squared/Fisher's exact tests\n\t*/\n\tfunction generatePvalueTable(chart, div) {\n\t\tconst holder = div\n\t\t\t.select('.pp-sbar-div-chartLengends')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('text-align', 'center')\n\t\t\t.append('div')\n\t\t// sort term1 categories based on self.chartsData.refs.cols\n\t\t// const cols = self.settings.dedup ?  self.chartsData.refs.cols\n\t\tself.chartsData.tests[chart.chartId].sort(function (a, b) {\n\t\t\treturn self.settings.cols.indexOf(a.term1comparison) - self.settings.cols.indexOf(b.term1comparison)\n\t\t})\n\n\t\t// sort term2 categories based on self.chartsData.refs.rows\n\t\tfor (const t1c of self.chartsData.tests[chart.chartId]) {\n\t\t\tt1c.term2tests.sort(function (a, b) {\n\t\t\t\treturn self.chartsData.refs.rows.indexOf(a.term2id) - self.chartsData.refs.rows.indexOf(b.term2id)\n\t\t\t})\n\t\t}\n\t\tconst columns = [\n\t\t\t{ label: 'Row 1' },\n\t\t\t{ label: 'Row 2' },\n\t\t\t{ label: 'Column 1' },\n\t\t\t{ label: 'Column 2' },\n\t\t\t{ label: 'P-value' }\n\t\t]\n\t\tconst noSkipped = self.chartsData.tests[chart.chartId].every(term1 =>\n\t\t\tterm1.term2tests.every(term2 => !term2.skipped)\n\t\t)\n\t\tconst rows = []\n\n\t\tconst visibleTests = self.chartsData.tests[chart.chartId].filter(term1Data =>\n\t\t\tchart.visibleSerieses.some(visibleTerm1 => visibleTerm1.seriesId === term1Data.term1comparison)\n\t\t)\n\t\tfor (const [index, term1] of visibleTests.entries()) {\n\t\t\tif (visibleTests.length == 2 && index == 1) {\n\t\t\t\t// when term1 has only 2 categories, then only a single category needs to be tested in the\n\t\t\t\t// association test (because the other category will get tested in that same test).\n\t\t\t\tbreak\n\t\t\t}\n\t\t\tconst visibleTerm1Data = chart.visibleSerieses.find(\n\t\t\t\tvisibleTerm1 => visibleTerm1.seriesId === term1.term1comparison\n\t\t\t)\n\t\t\tconst visibleTerm2Data = term1.term2tests.filter(term2Data =>\n\t\t\t\tvisibleTerm1Data.visibleData.some(visibleTerm2 => visibleTerm2.dataId === term2Data.term2id)\n\t\t\t)\n\t\t\tfor (const [index2, term2] of visibleTerm2Data.entries()) {\n\t\t\t\tif (chart.settings.rows.length - chart.settings.exclude.rows.length == 2 && index2 == 1) {\n\t\t\t\t\t// when term2 has only 2 visible categories, then only a single category needs to be tested in the\n\t\t\t\t\t// association test (because the other category will get tested in that same test).\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tlet negateTerm2Label = negateTermLabel(term2.term2Label)\n\t\t\t\tif (chart.settings.rows.length - chart.settings.exclude.rows.length == 2) {\n\t\t\t\t\t// when term2 has only 2 visible categories, Col2 would be the other category instead of \"not Col1\"\n\t\t\t\t\tconst visibleTerm2CatsKeys = chart.settings.rows.filter(row => !chart.settings.exclude.rows.includes(row))\n\t\t\t\t\tconst visibleTerm2Labels = visibleTerm2CatsKeys\n\t\t\t\t\t\t.map(catK => self.config.term2?.term?.values?.[catK]?.label)\n\t\t\t\t\t\t.filter(x => x != undefined)\n\t\t\t\t\tif (visibleTerm2Labels?.length == 2)\n\t\t\t\t\t\tnegateTerm2Label = visibleTerm2Labels[0] == term2.term2Label ? visibleTerm2Labels[1] : visibleTerm2Labels[0]\n\t\t\t\t}\n\n\t\t\t\trows.push([\n\t\t\t\t\t{ value: `${term1.term1Label}` },\n\t\t\t\t\t// when term1 has only 2 categories, Row2 would be the other category instead of \"not Row1\"\n\t\t\t\t\t{ value: visibleTests.length == 2 ? visibleTests[1].term1Label : negateTermLabel(term1.term1Label) },\n\t\t\t\t\t{ value: term2.term2Label },\n\t\t\t\t\t{ value: negateTerm2Label },\n\t\t\t\t\t//if both chi-square and Fisher's exact tests were used. for the tests computed by Fisher's exact test, add a superscript letter 'a' after the pvalue.\n\t\t\t\t\t{\n\t\t\t\t\t\thtml: term2.skipped\n\t\t\t\t\t\t\t? 'N/A'\n\t\t\t\t\t\t\t: term2.pvalue > 1e-4\n\t\t\t\t\t\t\t? roundValueAuto(Number(term2.pvalue))\n\t\t\t\t\t\t\t: roundValueAuto(Number(term2.pvalue))\n\t\t\t\t\t}\n\t\t\t\t])\n\t\t\t}\n\t\t}\n\t\t//adding a title for the pvalue table\n\t\t//title is \"Group comparisons (Fisher's exact test)\" if all tests are Fisher's exact test, otherwise title is 'Group comparisons (Chi-square test)'\n\t\tconst title = holder\n\t\t\t.append('div')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('padding-bottom', '0.5em')\n\t\t\t.html(\"2x2 Association test (Fisher's exact test)\")\n\t\t\t.style('font-size', '0.9em')\n\n\t\tconst table = holder.append('div').style('font-size', '0.9em')\n\n\t\trenderTable({\n\t\t\tcolumns,\n\t\t\trows,\n\t\t\tdiv: table,\n\t\t\tshowLines: false,\n\t\t\tmaxWidth: '70vw',\n\t\t\tmaxHeight: `${chart.svgh - 100}px`,\n\t\t\tresize: true\n\t\t})\n\n\t\t//footnote: superscript letter 'a' indicates the pvalue was computed by Fisher's exact test\n\t\ttable\n\t\t\t.append('div')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.style('text-align', 'left')\n\t\t\t.style('font-size', '10px')\n\t\t\t.style('font-weight', 'normal')\n\t\t\t.html(noSkipped ? '' : 'N/A: association test skipped because of limited sample size <br>')\n\t}\n}\n\nfunction setInteractivity(self) {\n\tself.handlers = getHandlers(self)\n\n\tself.download = function () {\n\t\tif (!self.state) return\n\t\t// has to be able to handle multichart view\n\t\tconst mainGs = []\n\t\tconst translate = { x: undefined, y: undefined }\n\t\tconst titles = []\n\t\tlet maxw = 0,\n\t\t\tmaxh = 0,\n\t\t\ttboxh = 0\n\t\tlet prevY = 0,\n\t\t\tnumChartsPerRow = 0\n\n\t\tself.dom.barDiv.selectAll('.sjpcb-bars-mainG').each(function () {\n\t\t\tmainGs.push(this)\n\t\t\tconst bbox = this.getBBox()\n\t\t\tif (bbox.width > maxw) maxw = bbox.width\n\t\t\tif (bbox.height > maxh) maxh = bbox.height\n\t\t\tconst divY = Math.round(this.parentNode.parentNode.getBoundingClientRect().y)\n\t\t\tif (!numChartsPerRow) {\n\t\t\t\tprevY = divY\n\t\t\t\tnumChartsPerRow++\n\t\t\t} else if (Math.abs(divY - prevY) < 5) {\n\t\t\t\tnumChartsPerRow++\n\t\t\t}\n\t\t\tconst xy = select(this)\n\t\t\t\t.attr('transform')\n\t\t\t\t.split('translate(')[1]\n\t\t\t\t.split(')')[0]\n\t\t\t\t.split(',')\n\t\t\t\t.map(d => +d.trim())\n\t\t\tif (translate.x === undefined || xy[0] > translate.x) translate.x = +xy[0]\n\t\t\tif (translate.y === undefined || xy[1] > translate.y) translate.y = +xy[1]\n\n\t\t\tconst title = this.parentNode.parentNode.firstChild\n\t\t\tconst tbox = title.getBoundingClientRect()\n\t\t\tif (tbox.width > maxw) maxw = tbox.width\n\t\t\tif (tbox.height > tboxh) tboxh = tbox.height\n\t\t\ttitles.push({ text: title.innerText, styles: window.getComputedStyle(title) })\n\t\t})\n\n\t\t// add padding between charts\n\t\tmaxw += 30\n\t\tmaxh += 30\n\n\t\tconst svg = document.createElementNS('http://www.w3.org/2000/svg', 'svg')\n\n\t\tconst svgSel = select(svg)\n\t\t\t.style('display', 'block')\n\t\t\t.style('opacity', 1)\n\t\t\t.attr('width', numChartsPerRow * maxw)\n\t\t\t.attr('height', Math.floor(mainGs.length / numChartsPerRow) * maxh)\n\n\t\tconst svgStyles = window.getComputedStyle(document.querySelector('.pp-bars-svg'))\n\t\tfor (const prop of svgStyles) {\n\t\t\tif (prop.startsWith('font')) svgSel.style(prop, svgStyles.getPropertyValue(prop))\n\t\t}\n\n\t\tmainGs.forEach((g, i) => {\n\t\t\tconst mainG = g.cloneNode(true)\n\t\t\tconst colNum = i % numChartsPerRow\n\t\t\tconst rowNum = Math.floor(i / numChartsPerRow)\n\t\t\tconst corner = { x: colNum * maxw + translate.x, y: rowNum * maxh + translate.y }\n\t\t\tconst title = select(svg)\n\t\t\t\t.append('text')\n\t\t\t\t.attr('transform', 'translate(' + corner.x + ',' + corner.y + ')')\n\t\t\t\t.text(titles[i].text)\n\t\t\tfor (const prop of titles[i].styles) {\n\t\t\t\tif (prop.startsWith('font')) title.style(prop, titles[i].styles.getPropertyValue(prop))\n\t\t\t}\n\n\t\t\tselect(mainG).attr('transform', 'translate(' + corner.x + ',' + (corner.y + tboxh) + ')')\n\t\t\tsvg.appendChild(mainG)\n\t\t})\n\n\t\t// svg + legend must be attached to DOM in order for getBBox() to work within svgLegendRenderer\n\t\tconst hiddenDiv = select('body').append('div').style('opacity', 0)\n\t\thiddenDiv.node().appendChild(svg)\n\n\t\tself.svgLegendRenderer = svgLegend({\n\t\t\tholder: svgSel.append('g'),\n\t\t\trectFillFxn: d => d.color,\n\t\t\ticonStroke: '#aaa'\n\t\t})\n\n\t\tconst s = self.settings\n\t\tconst svg0 = self.dom.barDiv.select('svg').node().getBoundingClientRect()\n\t\tlet data = self.getLegendGrps()\n\t\tdata.forEach(d => {\n\t\t\td.name = d.name.replace(/<[^>]*>?/gm, '')\n\t\t\tif (d.items) d.items = d.items.filter(c => !c.isHidden)\n\t\t})\n\t\tdata = data.filter(d => d.items.length && !d.name.includes('tatistic'))\n\t\tconst fontsize = 14\n\t\tself.svgLegendRenderer(data, {\n\t\t\tsettings: Object.assign(\n\t\t\t\t{\n\t\t\t\t\tontop: false,\n\t\t\t\t\tlineh: 25,\n\t\t\t\t\tpadx: 5,\n\t\t\t\t\tpadleft: 0, //150,\n\t\t\t\t\tpadright: 20,\n\t\t\t\t\tpadbtm: 30,\n\t\t\t\t\tfontsize,\n\t\t\t\t\ticonh: fontsize - 2,\n\t\t\t\t\ticonw: fontsize - 2,\n\t\t\t\t\thangleft: 1,\n\t\t\t\t\tlinesep: false\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tsvgw: self.visibleCharts.length * svg0.width,\n\t\t\t\t\tsvgh: svg0.height,\n\t\t\t\t\tdimensions: {\n\t\t\t\t\t\txOffset: 50\n\t\t\t\t\t},\n\t\t\t\t\tpadleft: 50\n\t\t\t\t}\n\t\t\t)\n\t\t})\n\n\t\tconst box = self.dom.legendDiv.node().getBoundingClientRect()\n\t\tselect(svg).attr('height', svg0.height + box.height + 30)\n\t\tif (box.width > svg0.width) select(svg).attr('width', box.width)\n\t\thiddenDiv.remove()\n\n\t\tconst svg_name = self.config.term.term.name + ' barchart'\n\t\tto_svg(svg, svg_name, { apply_dom_styles: true })\n\t}\n}\n\nexport function getDefaultBarSettings(app) {\n\treturn {\n\t\torientation: 'horizontal',\n\t\tdivideOrientation: 'horizontal', // maintain horizontal as default charts layout\n\t\tunit: 'abs',\n\t\toverlay: 'none',\n\t\tdivideBy: 'none',\n\t\trowlabelw: 250,\n\t\tasterisksVisible: app?.getState()?.termdbConfig?.multipleTestingCorrection ? true : false,\n\t\tmultiTestingCorr: app?.getState()?.termdbConfig?.multipleTestingCorrection?.applyByDefault ? true : false,\n\t\tdefaultColor: plotColor,\n\t\tcolorBars: false,\n\t\tdedup: false,\n\t\tshowStatsTable: true\n\t}\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'barchart getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tconsole.log('Error reading config: ' + JSON.stringify(opts))\n\t\tconsole.error(e)\n\t\tthrow `${e} [barchart getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\tcommon: {\n\t\t\t\tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t\tuse_percentage: false,\n\t\t\t\tbarheight: 300, // maximum bar length\n\t\t\t\tbarwidth: 20, // bar thickness\n\t\t\t\tbarspace: 2 // space between two bars\n\t\t\t},\n\t\t\tbarchart: getDefaultBarSettings(app)\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\n// a function used by generatePvalueTable to negate a term label\n// TODO: add more conditions for better negation than \"not termLable\"\nexport function negateTermLabel(termLabel) {\n\tconst termLabelStr = String(termLabel)\n\tif (termLabelStr.toUpperCase().startsWith('NOT ')) {\n\t\treturn termLabelStr.substring(4) // Remove the \"not\" prefix\n\t} else {\n\t\treturn 'not ' + termLabelStr // Otherwise, add \"not\" prefix\n\t}\n}\n"],
+  "mappings": 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+}