@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/chunk-N5VBIEH5.js

@@ -1,1412 +0,0 @@
-import {
-  importPlot
-} from "./chunk-FOXJTDTH.js";
-import {
-  maxGESampleCutoff,
-  maxSampleCutoff
-} from "./chunk-SN5QKRXO.js";
-import {
-  GeneExpChartMenu,
-  GeneSetEditUI,
-  appInit,
-  fillTermWrapper,
-  filterInit,
-  filterJoin,
-  filterPromptInit,
-  get$id,
-  getFilterItemByTag,
-  getNormalRoot,
-  make_radios,
-  negateFilter,
-  renderTable,
-  sayerror,
-  table2col
-} from "./chunk-UT6W4ZZL.js";
-import {
-  dofetch3
-} from "./chunk-5TDKRZN5.js";
-import {
-  NumericModes,
-  TermTypes,
-  isNumericTerm,
-  termType2label
-} from "./chunk-RYRCMHYR.js";
-import {
-  getColors
-} from "./chunk-ECKWM4HB.js";
-import {
-  Menu
-} from "./chunk-NXOWHUR4.js";
-import {
-  getCompInit
-} from "./chunk-FYTZCTJC.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-
-// mass/charts.js
-var MassCharts = class {
-  constructor(opts = {}) {
-    this.type = "charts";
-    setRenderers(this);
-  }
-  async init(appState) {
-    this.dom = {
-      holder: this.opts.holder,
-      tip: new Menu({ padding: "0px" }),
-      tooltip: new Menu({ padding: "4px" })
-    };
-    this.makeButtons(appState);
-  }
-  // TODO later add reactsTo() to react to filter change
-  getState(appState) {
-    const state = {
-      vocab: appState.vocab,
-      // TODO delete it as vocabApi should be used instead
-      activeCohort: appState.activeCohort,
-      termfilter: appState.termfilter,
-      currentCohortChartTypes: getCurrentCohortChartTypes(appState),
-      termdbConfig: appState.termdbConfig
-    };
-    if (appState?.termfilter?.filter) {
-      state.filter = getNormalRoot(appState.termfilter.filter);
-    }
-    return state;
-  }
-  main() {
-    this.dom.btns.style("display", (d) => this.state.currentCohortChartTypes.includes(d.chartType) ? "" : "none");
-  }
-  getBtnLabel_dict(state) {
-    return state.termdbConfig.queries ? "Data Variables" : "Data Dictionary";
-  }
-  getBtnLabel_regression(state) {
-    const lst = getCurrentCohortChartTypes(state);
-    if (!lst.includes("regression")) return "";
-    const ms = [];
-    if (lst.includes("linear")) ms.push("linear");
-    if (lst.includes("logistic")) ms.push("logistic");
-    if (lst.includes("cox")) ms.push("cox");
-    if (ms.length > 1) return "Regression Analysis";
-    return `${ms[0] == "linear" ? "Linear" : ms[0] == "cox" ? "Cox" : "Logistic"} Regression`;
-  }
-  getBtnLabel_sampleScatter(state) {
-    const lst = getCurrentCohortChartTypes(state);
-    if (state.termdbConfig.scatterplots?.length == 1 && !lst.includes("dynamicScatter")) {
-      return state.termdbConfig.scatterplots[0].name;
-    }
-    return "Sample Scatter";
-  }
-  getBtnLabel_report(state) {
-    return state.termdbConfig.plotConfigByCohort?.default?.report?.name || "Report";
-  }
-  getBtnLabel_summarizeMutationTerm(state, phrase) {
-    if (!state.termdbConfig.queries) return "Not supported!";
-    const t = [];
-    if (state.termdbConfig.queries.snvindel) t.push("Mutation");
-    if (state.termdbConfig.queries.cnv) t.push("CNV");
-    if (state.termdbConfig.queries.svfusion) t.push("Fusion");
-    return `${t.length > 2 ? "Alterations" : t.join("/")} vs ${phrase}`;
-  }
-};
-var chartsInit = getCompInit(MassCharts);
-function getActiveCohortStr(appState) {
-  if (appState?.termdbConfig?.selectCohort?.values) {
-    if (!Number.isInteger(appState.activeCohort)) throw "appState.activeCohort is not integer array index";
-    const activeCohortObject = appState.termdbConfig.selectCohort.values[appState.activeCohort];
-    if (!activeCohortObject) throw "appState.activeCohort array index out of bound";
-    return [...activeCohortObject.keys].sort().join(",");
-  }
-  return "";
-}
-function getCurrentCohortChartTypes(appState) {
-  const activeCohortStr = getActiveCohortStr(appState);
-  const chartTypesByCohort = structuredClone(appState.termdbConfig?.supportedChartTypes || {});
-  return chartTypesByCohort[activeCohortStr] || ["summary"];
-}
-function getChartTypeList(self, state) {
-  const buttons = [
-    ////////////////////// PROFILE PLOTS START //////////////////////
-    {
-      label: "Polar",
-      chartType: "profilePolar",
-      clickTo: self.prepPlot,
-      config: { chartType: "profilePolar" }
-    },
-    {
-      label: "Barchart",
-      clickTo: self.prepPlot,
-      chartType: "profileBarchart",
-      config: { chartType: "profileBarchart" }
-    },
-    {
-      label: "Facility Radar",
-      chartType: "profileRadarFacility",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Radar",
-      chartType: "profileRadar",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Templates",
-      chartType: "profileForms",
-      clickTo: self.showTree_select1term,
-      usecase: { target: "profileForms", detail: "tw" },
-      config: { chartType: "profileForms" }
-    },
-    ////////////////////// PROFILE PLOTS END //////////////////////
-    //       rest are general plots applicable to all ds
-    {
-      label: self.getBtnLabel_dict(state),
-      clickTo: self.prepPlot,
-      chartType: "dictionary",
-      config: {
-        chartType: "dictionary"
-      }
-    },
-    {
-      // currently only used by gdc, so hardcoding correlation input label
-      // may allow for other labels if used by other datasets
-      label: "Correlation Input",
-      clickTo: self.prepPlot,
-      chartType: "summaryInput",
-      config: {
-        chartType: "summaryInput"
-      }
-    },
-    {
-      label: self.getBtnLabel_report(state),
-      chartType: "report",
-      clickTo: self.plotCreate,
-      config: { chartType: "report" }
-    },
-    {
-      label: "Sample View",
-      clickTo: self.prepPlot,
-      chartType: "sampleView",
-      config: {
-        chartType: "sampleView"
-      }
-    },
-    {
-      label: self.getBtnLabel_sampleScatter(state),
-      chartType: "sampleScatter",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Run Chart",
-      chartType: "runChart",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Frequency Chart",
-      chartType: "frequencyChart",
-      clickTo: self.showTree_select1term,
-      usecase: { target: "frequencyChart", detail: "term" }
-    },
-    {
-      label: "Cumulative Incidence",
-      chartType: "cuminc",
-      clickTo: self.showTree_select1term,
-      usecase: { target: "cuminc", detail: "term" }
-    },
-    {
-      label: "Survival",
-      chartType: "survival",
-      clickTo: self.showTree_select1term,
-      usecase: { target: "survival", detail: "term" }
-    },
-    {
-      label: self.getBtnLabel_regression(state),
-      chartType: "regression",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Sample Matrix",
-      chartType: "matrix",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Genome Browser",
-      chartType: "genomeBrowser",
-      clickTo: self.loadChartSpecificMenu
-    },
-    // Commenting out this button since DE does not work without specifying two groups
-    //{
-    //	label: 'Differential Expression',
-    //	chartType: 'DEanalysis',
-    //	clickTo: self.loadChartSpecificMenu
-    //},
-    {
-      label: "Data Download",
-      clickTo: self.prepPlot,
-      chartType: "dataDownload",
-      config: {
-        chartType: "dataDownload",
-        terms: []
-      }
-    },
-    {
-      label: "Facet Table",
-      clickTo: self.loadChartSpecificMenu,
-      chartType: "facet",
-      config: {
-        chartType: "facet"
-      }
-    },
-    {
-      label: "Brain Imaging",
-      clickTo: self.loadChartSpecificMenu,
-      chartType: "brainImaging",
-      config: {
-        chartType: "brainImaging"
-      }
-    },
-    {
-      label: "Chat",
-      clickTo: self.loadChartSpecificMenu,
-      chartType: "chat",
-      config: {
-        chartType: "chat"
-      }
-    },
-    {
-      label: "Single Cell Plot",
-      clickTo: self.prepPlot,
-      chartType: "singleCellPlot",
-      config: {
-        chartType: "singleCellPlot"
-      }
-    },
-    {
-      //This chart may be later on extended to support other gene expression data types
-      label: "Gene Expression",
-      chartType: "geneExpression",
-      clickTo: self.showGenesetEditUI,
-      usecase: { target: "geneExpression" }
-    },
-    {
-      label: "Metabolite Intensity",
-      chartType: "metaboliteIntensity",
-      clickTo: self.showTree_selectlst,
-      usecase: { target: "metaboliteIntensity", detail: "term" },
-      updateActionBySelectedTerms: (action, termlst) => {
-        const twlst = termlst.map((term) => ({
-          term: structuredClone(term),
-          q: { mode: NumericModes.continuous }
-        }));
-        if (twlst.length == 1) {
-          action.config.chartType = "summary";
-          action.config.term = twlst[0];
-          return;
-        }
-        if (twlst.length == 2) {
-          action.config.chartType = "summary";
-          action.config.term = twlst[0];
-          action.config.term2 = twlst[1];
-          return;
-        }
-        action.config.chartType = "hierCluster";
-        action.config.dataType = TermTypes.METABOLITE_INTENSITY;
-        action.config.termgroups = [{ name: "Metabolite Intensity Cluster", lst: twlst, type: "hierCluster" }];
-      }
-    },
-    {
-      label: state.termdbConfig.numericDictTermCluster?.appName || "Numeric Dictionary Term cluster",
-      chartType: "numericDictTermCluster",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Mutation Signature",
-      chartType: "mutationSignature",
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Correlation Volcano",
-      chartType: "correlationVolcano",
-      usecase: { target: "correlationVolcano", detail: "numeric" },
-      clickTo: self.showTree_select1term
-    },
-    {
-      label: "GRIN2",
-      chartType: "grin2",
-      config: { chartType: "grin2" },
-      clickTo: self.prepPlot
-    },
-    {
-      label: self.getBtnLabel_summarizeMutationTerm(state, "Disease Type"),
-      chartType: "summarizeMutationDiagnosis",
-      // type names of other similar charts should all begin with `summarize` to indcate they are based on summary plot
-      usecase: { target: "summarizeMutationDiagnosis" },
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: self.getBtnLabel_summarizeMutationTerm(state, "Survival"),
-      chartType: "summarizeMutationSurvival",
-      usecase: { target: "summarizeMutationSurvival" },
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "CNV vs GeneExp",
-      // this is limited to cnv, and could be generalized to include snvindel/fusion
-      chartType: "summarizeCnvGeneexp",
-      usecase: { target: "summarizeCnvGeneexp" },
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "GeneExp vs Survival",
-      chartType: "summarizeGeneexpSurvival",
-      usecase: { target: "summarizeGeneexpSurvival" },
-      clickTo: self.loadChartSpecificMenu
-    },
-    {
-      label: "Alpha Genome",
-      chartType: "alphaGenome",
-      usecase: { target: "alphaGenome" },
-      clickTo: self.prepPlot,
-      config: { chartType: "alphaGenome" }
-    }
-  ];
-  for (const field in state?.termdbConfig.renamedChartTypes || []) {
-    const btn = buttons.find((b) => b.chartType === field);
-    if (btn) {
-      btn.label = state.termdbConfig.renamedChartTypes[field];
-    }
-  }
-  return buttons;
-}
-function setRenderers(self) {
-  self.makeButtons = function(state) {
-    const chartTypeList = getChartTypeList(self, state);
-    self.dom.btns = self.dom.holder.selectAll("button").data(chartTypeList).enter().append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").html((d) => d.label).on("click", function(event, chart) {
-      self.dom.tip.clear().showunder(this);
-      chart.clickTo(chart);
-    }).on("mouseover", (e, d) => {
-      if (d.tooltip) self.dom.tooltip.clear().showunder(e.target).d.text(d.tooltip);
-    }).on("mouseleave", (e, d) => {
-      if (d.tooltip) self.dom.tooltip.hide();
-    });
-  };
-  self.showTree_select1term = async (chart) => {
-    if (chart.usecase.label) {
-      self.dom.tip.d.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).html(chart.usecase.label);
-    }
-    const action = {
-      type: "plot_create",
-      id: getId(),
-      config: { chartType: chart.chartType, activeCohort: self.state.activeCohort }
-    };
-    if (chart.parentId) action.parentId = chart.parentId;
-    const termdb = await import("./app-JPURIGQW.js");
-    termdb.appInit({
-      vocabApi: self.app.vocabApi,
-      holder: self.dom.tip.d.append("div"),
-      state: {
-        activeCohort: self.state.activeCohort,
-        nav: {
-          header_mode: "search_only"
-        },
-        tree: { usecase: chart.usecase }
-      },
-      tree: {
-        click_term: (term) => {
-          const tw = term.term ? term : { term };
-          action.config[chart.usecase.detail] = tw;
-          self.dom.tip.hide();
-          self.app.dispatch(action);
-        }
-      }
-    });
-  };
-  self.showGenesetEditUI = async (chart) => {
-    const app = self.app;
-    const additionalItems = [];
-    if (app.vocabApi.termdbConfig?.queries?.rnaseqGeneCount) {
-      additionalItems.push(
-        {
-          //Section heading
-          text: "Differential Gene Expression Analysis"
-        },
-        {
-          /** TODO: In the future, may replace these instructions
-           * with DA button that is in development. */
-          label: "View Instructions",
-          isSubmenu: true,
-          callback: (holder) => {
-            const message = `For Differential Gene Expression Analysis, please follow steps:
-		<ol>
-		<li>Navigate to the <span style="opacity:.5">GROUPS</span> tab at the top, and create two groups.</li>
-		<li>Create a new variable from the two groups and click on the new variable button.</li>
-		<li>Select <span class=sja_menuoption style="font-size:.8em">Differential Gene Expression Analysis</span> from the menu options and run the analysis.</li>
-		</ol>`;
-            holder.append("div").style("padding", "10px").html(message);
-          }
-        }
-      );
-    }
-    new GeneExpChartMenu(app, self.dom.tip, additionalItems);
-  };
-  self.showTree_selectlst = async (chart) => {
-    if (chart.usecase?.label) {
-      self.dom.tip.d.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).html(chart.usecase.label);
-    }
-    const action = {
-      type: "plot_create",
-      id: getId(),
-      config: { chartType: chart.chartType }
-      // NOTE if chartType is intermediary, action will be updated on term selection
-    };
-    const termdb = await import("./app-JPURIGQW.js");
-    self.dom.submenu = self.dom.tip.d.append("div");
-    termdb.appInit({
-      holder: self.dom.submenu,
-      vocabApi: self.app.vocabApi,
-      state: {
-        activeCohort: self.state.activeCohort,
-        nav: {
-          header_mode: "search_only"
-        },
-        tree: { usecase: chart.usecase }
-      },
-      tree: {
-        submit_lst: (termlst) => {
-          const data = chart.processSelection ? chart.processSelection(termlst) : termlst;
-          action.config[chart.usecase.detail] = data;
-          if (chart.updateActionBySelectedTerms) chart.updateActionBySelectedTerms(action, termlst);
-          self.dom.tip.hide();
-          self.app.dispatch(action);
-        }
-      }
-    });
-  };
-  self.loadChartSpecificMenu = async (chart) => {
-    self.dom.tip.clear();
-    const _ = await importPlot(chart.chartType);
-    _.makeChartBtnMenu(self.dom.tip.d, self, chart.chartType);
-  };
-  self.prepPlot = function(chart) {
-    self.dom.tip.hide();
-    const action = { type: "plot_prep", config: chart.config, id: getId() };
-    self.app.dispatch(action);
-  };
-  self.plotCreate = function(chart) {
-    self.dom.tip.hide();
-    const action = { type: "plot_create", config: chart.config, id: getId() };
-    self.app.dispatch(action);
-  };
-}
-var idPrefix = "_CHART_AUTOID_";
-var id = Date.now();
-function getId() {
-  return idPrefix + id++;
-}
-
-// mass/groups.js
-var colorScale = getColors(5);
-var MassGroups = class {
-  constructor(opts = {}) {
-    this.type = "groups";
-    this.selectedGroupsIdx = /* @__PURE__ */ new Set();
-  }
-  async init() {
-    this.dom = {
-      holder: this.opts.holder.append("div").style("margin", "10px")
-    };
-    initUI(this);
-    this.tip = new Menu({ padding: "0px" });
-    this.tip2 = new Menu({ padding: "0px", offsetX: 250, offsetY: -34, parent_menu: this.tip.d.node() });
-    this.tip3 = new Menu({ padding: "0px" });
-  }
-  getState(appState) {
-    const state = {
-      termfilter: appState.termfilter,
-      groups: rebaseGroupFilter(appState),
-      customTerms: appState.customTerms,
-      currentCohortChartTypes: getCurrentCohortChartTypes(appState),
-      matrixplots: this.app.vocabApi.termdbConfig.matrixplots
-    };
-    return state;
-  }
-  async main() {
-    await updateUI(this);
-  }
-  //////////////// rest are app-specific logic
-  getMassFilter() {
-    if (!this.state.termfilter.filter || this.state.termfilter.filter.lst.length == 0) {
-      return { type: "tvslst", in: true, join: "", lst: [] };
-    }
-    const f = getNormalRoot(structuredClone(this.state.termfilter.filter));
-    return f;
-  }
-  async groups2samplelst(groups) {
-    const samplelstGroups = [];
-    const processedSamples = /* @__PURE__ */ new Set(), overlap = [];
-    for (const g of groups) {
-      const samples = await this.app.vocabApi.getFilteredSampleList(
-        filterJoin([g.filter, this.state.termfilter.filter])
-      );
-      const items = [];
-      for (const sample of samples) {
-        const item = { sampleId: sample.id };
-        if ("name" in sample) {
-          item.sample = sample.name;
-        }
-        if (!processedSamples.has(sample.id)) items.push(item);
-        else {
-          for (const pg of samplelstGroups) {
-            const i = pg.items.findIndex((i2) => i2.sampleId === sample.id);
-            if (i !== -1) overlap.push(...pg.items.splice(i, 1));
-          }
-        }
-        processedSamples.add(item.sampleId);
-      }
-      if (items.length) samplelstGroups.push({ name: g.name, items, color: g.color });
-    }
-    if (overlap.length) {
-      const ok = confirm(
-        'Overlap detected: 1 or more samples belong to >1 groups. A new group will be created for these "overlap" samples.'
-      );
-      if (!ok) return;
-      samplelstGroups.push({ name: "Group overlap", items: overlap });
-    }
-    if (groups.length == 1) {
-      const samples = await this.app.vocabApi.getFilteredSampleList(
-        filterJoin([negateFilter(groups[0].filter), this.state.termfilter.filter])
-      );
-      if (!samples.length) throw "0 samples for the other group";
-      const items = [];
-      for (const sample of samples) {
-        const item = { sampleId: sample.id };
-        if ("name" in sample) {
-          item.sample = sample.name;
-        }
-        items.push(item);
-      }
-      samplelstGroups.push({ name: "Not in " + groups[0].name, items, color: "#ccc" });
-    }
-    return getSamplelstTW2(samplelstGroups);
-  }
-  updateLaunchButton() {
-    this.dom.newTermSpan.style("display", "none");
-    this.dom.noGroupSelected.style("display", "none");
-    if (this.state.groups.length == 0) return;
-    if (this.state.groups.length == 1) {
-      this.dom.newTermSpan.style("display", "");
-      this.dom.launchButton.text(`Create variable using "${this.state.groups[0].name}"`);
-      this.dom.newTermNameInput.property("value", this.state.groups[0].name + " vs others");
-      return;
-    }
-    const lst = [...this.selectedGroupsIdx];
-    if (lst.length == 0) {
-      this.dom.noGroupSelected.style("display", "");
-      return;
-    }
-    this.dom.newTermSpan.style("display", "");
-    if (lst.length == 1) {
-      this.dom.launchButton.text(`Create  variable using "${this.state.groups[lst[0]]?.name}"`);
-      this.dom.newTermNameInput.property("value", this.state.groups[lst[0]].name + " vs others");
-      return;
-    }
-    this.dom.launchButton.text(`Create variable using ${lst.length} groups`);
-    this.dom.newTermNameInput.property("value", lst.map((i) => this.state.groups[i].name).join(" vs "));
-  }
-  displayCustomTerms() {
-    this.dom.customTermDiv.selectAll("*").remove();
-    if (this.state.customTerms.length == 0) {
-      this.dom.customTermDiv.append("div").text("No custom variables. Use above controls to create new ones. Custom variables are added to dictionary.").style("font-size", ".8em");
-      return;
-    }
-    this.dom.customTermDiv.append("div").style("margin-bottom", "10px").style("font-size", ".8em").text("Following custom variables are available in all charts where variables are used. Click one to delete.");
-    for (const { name, tw } of this.state.customTerms) {
-      const div = this.dom.customTermDiv.append("div");
-      div.text(name).attr("class", "sja_filter_tag_btn").style("padding", "3px 6px").style("border-radius", "6px").style("margin-right", "5px").on("click", (event) => {
-        const deleteCallback = () => this.app.vocabApi.deleteCustomTerm(name);
-        this.showGroupsMenu(event, tw, deleteCallback);
-      });
-    }
-  }
-  newId() {
-    this.lastId = get$id();
-    return this.lastId;
-  }
-  showGroupsMenu(event, tw, deleteCallback) {
-    const samplelstTW = structuredClone(tw);
-    this.tip.clear().showunder(event.target);
-    const menuDiv = this.tip.d.append("div");
-    const id2 = this?.lastId;
-    const groupsInfo = menuDiv.append("div");
-    const table = table2col({ holder: groupsInfo });
-    table.table.style("scale", 0.9).style("margin-left", "0px");
-    for (const [grpKey, grp] of Object.entries(tw.term.values)) {
-      const colorSquare = grp.color ? `<span style="display:inline-block; width:12px; height:12px; background-color:${grp.color}" ></span>` : `<span style="display:inline-block; width:11px; height:11px; background-color:${"#fff"}; border: 0.1px solid black" ></span>`;
-      const [c1, c2] = table.addRow();
-      c1.html(`${colorSquare} ${grp.label}`);
-      c2.html(`${grp.othersGroupSampleNum || grp.list.length} samples`);
-    }
-    if (this.state.currentCohortChartTypes.includes("DA") && samplelstTW.q.groups.length == 2)
-      addDiffAnalysisPlotMenuItem(menuDiv, this, samplelstTW);
-    addSummarizeOptions(menuDiv, this, samplelstTW, id2);
-    mayAddHierClusterPlotMenuItem("geneExpression", menuDiv, "Gene expression", this.tip2, samplelstTW, id2, this, true);
-    mayAddMatrixMenuItems(menuDiv, "Matrix", this.tip2, samplelstTW, id2, this, this.state, true, () => this.newId);
-    mayAddSamplescatterOption(menuDiv, this, samplelstTW);
-    mayAddGenomebrowserOption(menuDiv, this, samplelstTW);
-    menuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Delete variable").on("click", (event2) => {
-      deleteCallback();
-      this.tip.hide();
-    });
-  }
-};
-var groupsInit = getCompInit(MassGroups);
-function addSummarizeOptions(menuDiv, self, samplelstTW, id2) {
-  const d = menuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Summarize");
-  d.on("click", async () => {
-    showTree(
-      d,
-      (term) => {
-        const tw = { term };
-        if (isNumericTerm(term)) tw.q = { mode: "continuous" };
-        openSummaryPlot(tw, samplelstTW, self.app, id2, () => self.newId);
-      },
-      self.app,
-      self.tip2
-    );
-  });
-  d.insert("div").html("\u203A").style("float", "right");
-  if (self.state.currentCohortChartTypes.includes("survival"))
-    addPlotMenuItem("survival", menuDiv, "Compare survival", self.tip2, samplelstTW, id2, self, true);
-  if (self.state.currentCohortChartTypes.includes("cuminc"))
-    addPlotMenuItem("cuminc", menuDiv, "Compare cumulative incidence", self.tip2, samplelstTW, id2, self, true);
-}
-function mayAddGenomebrowserOption(menuDiv, self, samplelstTW) {
-  if (!self.state.currentCohortChartTypes.includes("genomeBrowser")) return;
-  if (!self.app.vocabApi.termdbConfig.queries?.snvindel) return;
-  if (self.app.vocabApi.termdbConfig.queries.snvindel.details) return;
-  if (samplelstTW.q.groups.length != 2) return;
-  menuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Compare mutations").on("click", () => {
-    self.tip.hide();
-    self.tip2.hide();
-    self.tip3.hide();
-    const [f1, f2] = makeFiltersFromTwoSampleGroups(samplelstTW);
-    const config = {
-      chartType: "genomeBrowser",
-      snvindel: { shown: true, filter: f1 },
-      // code filter in 1st tk
-      subMds3Tks: [{ filterObj: f2 }]
-      // code filter in 2nd tk
-    };
-    self.app.dispatch({
-      type: "plot_create",
-      config
-    });
-  });
-}
-function makeFiltersFromTwoSampleGroups(tw) {
-  const [g1, g2] = tw.q.groups;
-  if (!g1 || !g2) throw "not 2 groups in tw.q.groups[]";
-  return [
-    {
-      in: g1.in,
-      join: "",
-      type: "tvslst",
-      lst: [
-        {
-          type: "tvs",
-          tvs: {
-            term: {
-              name: g1.name,
-              type: "samplelst",
-              values: {
-                [g1.name]: {
-                  key: g1.name,
-                  label: g1.name,
-                  list: g1.values
-                }
-              }
-            }
-          }
-        }
-      ]
-    },
-    {
-      in: g2.in,
-      join: "",
-      type: "tvslst",
-      lst: [
-        {
-          type: "tvs",
-          tvs: {
-            term: {
-              name: g2.name,
-              type: "samplelst",
-              values: {
-                [g2.name]: {
-                  key: g2.name,
-                  label: g2.name,
-                  list: g2.values
-                }
-              }
-            }
-          }
-        }
-      ]
-    }
-  ];
-}
-function mayAddSamplescatterOption(menuDiv, self, samplelstTW) {
-  if (!self.app.vocabApi.termdbConfig.scatterplots) return;
-  for (const plot of self.app.vocabApi.termdbConfig.scatterplots) {
-    if (plot.colorTW)
-      menuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Overlay on ${plot.name}`).on("click", () => {
-        self.tip2.hide();
-        let config = {
-          chartType: "sampleScatter",
-          name: plot.name
-        };
-        if (plot.sampleCategory)
-          config.sampleCategory = {
-            tw: structuredClone(plot.sampleCategory.tw),
-            order: plot.sampleCategory.order,
-            defaultValue: plot.sampleCategory.defaultValue
-          };
-        if (plot.sampleType) config.sampleType = plot.sampleType;
-        config.colorTW = structuredClone(samplelstTW);
-        if (plot.settings) config.settings = structuredClone(plot.settings);
-        self.app.dispatch({
-          type: "plot_create",
-          config
-        });
-        self.tip.hide();
-      });
-  }
-}
-function addDiffAnalysisPlotMenuItem(div, self, samplelstTW) {
-  if (self.app.vocabApi.termdbConfig.queries?.rnaseqGeneCount) {
-    const itemDiv = div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Differential ${termType2label(TermTypes.GENE_EXPRESSION)} Analysis`).on("click", async (e) => {
-      const groups = [];
-      for (const group of samplelstTW.q.groups) {
-        if (group.values && group.values.length > 0) {
-          groups.push(group);
-        } else {
-          throw "group does not contain samples for differential analysis";
-        }
-      }
-      const body = {
-        genome: self.app.vocabApi.vocab.genome,
-        dslabel: self.app.vocabApi.vocab.dslabel,
-        samplelst: { groups },
-        filter: self.state.termfilter.filter,
-        filter0: self.state.termfilter.filter0,
-        preAnalysis: true
-      };
-      const preAnalysisData = await dofetch3("termdb/DE", { body });
-      const tip = self.tip2;
-      if (!preAnalysisData?.data) {
-        tip.clear().showunderoffset(itemDiv.node());
-        sayerror(tip.d.append("div"), "Error retrieving pre-analysis data");
-        throw new Error("no data returned from pre-analysis request");
-      }
-      const numControl = preAnalysisData.data[samplelstTW.q.groups[0].name];
-      const numCase = preAnalysisData.data[samplelstTW.q.groups[1].name];
-      if (numControl + numCase > maxSampleCutoff) {
-        if (preAnalysisData.data.alert)
-          preAnalysisData.data.alert += ` | Sample size ${numControl + numCase} exceeds max sample size of ${maxSampleCutoff}. Please reduce sample size.`;
-        else
-          preAnalysisData.data.alert = `Sample size ${numControl + numCase} exceeds max sample size of ${maxSampleCutoff}. Please reduce sample size.`;
-      }
-      tip.clear().showunderoffset(itemDiv.node());
-      const menuDiv = tip.d.append("div");
-      const table = table2col({ holder: menuDiv });
-      table.table.style("margin-left", "5px").style("padding", "5px 10px");
-      {
-        const controlGColor = samplelstTW.term.values[samplelstTW.q.groups[0].name].color;
-        const colorSquareCtrl = controlGColor ? `<span style="display:inline-block; width:12px; height:12px; background-color:${controlGColor}" ></span>` : `<span style="display:inline-block; width:11px; height:11px; background-color:${"#fff"}; border: 0.1px solid black" ></span>`;
-        const [c1, c2] = table.addRow();
-        c1.html(
-          `<span style="font-size:.8em;font-weight:bold">CONTROL</span> ${colorSquareCtrl} ${samplelstTW.q.groups[0].name}`
-        );
-        c2.html(`${numControl} samples`);
-      }
-      {
-        const caseGColor = samplelstTW.term.values[samplelstTW.q.groups[1].name].color;
-        const colorSquareCase = caseGColor ? `<span style="display:inline-block; width:12px; height:12px; background-color:${caseGColor}" ></span>` : `<span style="display:inline-block; width:11px; height:11px; background-color:${"#fff"}; border: 0.1px solid black" ></span>`;
-        const [c1, c2] = table.addRow();
-        c1.html(
-          `<span style="font-size:.8em;font-weight:bold">CASE</span> ${colorSquareCase} ${samplelstTW.q.groups[1].name}`
-        );
-        c2.html(`${numCase} samples`);
-      }
-      const alertDiv = menuDiv.append("div");
-      if (preAnalysisData.data.alert) {
-        sayerror(alertDiv, preAnalysisData.data.alert);
-      }
-      const sample_size_limit = 8;
-      if (!preAnalysisData.data.alert) {
-        const options = numControl + numCase >= maxGESampleCutoff ? [{ label: "Wilcoxon", value: "wilcoxon" }] : numControl <= sample_size_limit && numCase <= sample_size_limit ? [
-          { label: "edgeR", value: "edgeR" },
-          { label: "Limma", value: "limma" }
-        ] : [
-          { label: "edgeR", value: "edgeR" },
-          { label: "Wilcoxon", value: "wilcoxon" },
-          { label: "Limma", value: "limma" }
-        ];
-        const launchDEDiv = menuDiv.append("div").style("margin", "8px 5px").style("padding", "5px 10px");
-        const radioRow = launchDEDiv.append("tr");
-        let selectedMethod = options[0].value;
-        radioRow.append("td").html("Method").attr("aria-label", "DE Method").attr("class", "sja-termdb-config-row-label").style("padding", "5px");
-        const cell = radioRow.append("td");
-        const radioBtnDiv = cell.append("div");
-        make_radios({
-          holder: radioBtnDiv,
-          inputName: `de-method-${Date.now()}`,
-          options: options.map((o, i) => ({
-            ...o,
-            title: `${o.label} method`,
-            checked: i === 0
-            // preselect first option
-          })),
-          styles: {
-            display: "inline-block",
-            padding: "0 12px 0 0"
-          },
-          callback: (v) => selectedMethod = v
-        });
-        launchDEDiv.append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text(`Run Differential ${termType2label(TermTypes.GENE_EXPRESSION)} Analysis`).on("click", async () => {
-          const config = {
-            chartType: "differentialAnalysis",
-            state: self.state,
-            samplelst: { groups },
-            termType: TermTypes.GENE_EXPRESSION,
-            tw: samplelstTW,
-            settings: { volcano: { method: selectedMethod } }
-          };
-          tip.hide();
-          self.tip.hide();
-          self.app.dispatch({
-            type: "plot_create",
-            config
-          });
-        });
-      }
-    });
-  }
-  if (self.app.vocabApi.termdbConfig.allowedTermTypes?.includes(TermTypes.METABOLITE_INTENSITY)) {
-    div.append("div").text("DA should support metabolite");
-  }
-  div.append("div").html(
-    `<span style="font-size:.8em;font-weight:bold">CASE</span> ${samplelstTW.q.groups[1].name}
-		&nbsp;
-		<span style="font-size:.8em;font-weight:bold">CONTROL</span> ${samplelstTW.q.groups[0].name}`
-  ).style("font-size", "0.8em").style("opacity", 0.8).style("padding", "3px 3px 3px 10px");
-}
-function initUI(self) {
-  self.dom.filterTableDiv = self.dom.holder.append("div").style("margin-bottom", "10px");
-  const btnRow = self.dom.holder.append("div");
-  self.dom.addNewGroupBtnHolder = btnRow.append("span").style("margin-right", "20px");
-  self.dom.newTermSpan = btnRow.append("span");
-  self.dom.newTermSpan.append("span").style("padding-left", "15px").text("Add variable:");
-  self.dom.newTermNameInput = self.dom.newTermSpan.append("input").attr("type", "text");
-  self.dom.launchButton = self.dom.newTermSpan.append("span").attr("class", "sja_menuoption").on("click", () => clickLaunchBtn(self));
-  self.dom.noGroupSelected = btnRow.append("span").text("No groups selected").style("opacity", 0.5);
-  self.dom.customTermDiv = self.dom.holder.append("div").style("margin", "20px").style("border-left", "solid 1px black").style("padding", "10px");
-}
-async function updateUI(self) {
-  if (!self.filterPrompt) {
-    self.filterPrompt = await filterPromptInit({
-      holder: self.dom.addNewGroupBtnHolder,
-      vocabApi: self.app.vocabApi,
-      emptyLabel: "Add group",
-      termdbConfig: self.app.vocabApi.termdbConfig,
-      callback: (f) => {
-        addNewGroup(self.app, f, self.state.groups);
-      },
-      debug: self.opts.debug
-    });
-  }
-  self.filterPrompt.main(self.getMassFilter());
-  const groups = structuredClone(self.state.groups);
-  if (!groups.length) {
-    self.updateLaunchButton();
-    self.dom.filterTableDiv.style("display", "none");
-    self.displayCustomTerms();
-    return;
-  }
-  self.dom.filterTableDiv.style("display", "").selectAll("*").remove();
-  const tableArg = {
-    div: self.dom.filterTableDiv,
-    columns: [
-      {},
-      // blank column to add delete buttons
-      {
-        label: "NAME",
-        editCallback: async (i, cell) => {
-          const newName = cell.value;
-          const index = self.state.groups.findIndex((group) => group.name == newName);
-          if (index != -1) {
-            alert(`Group named ${newName} already exists`);
-            updateUI(self);
-          } else
-            await self.app.dispatch({
-              type: "rename_group",
-              index: i,
-              newName: cell.value
-            });
-        }
-      },
-      {
-        label: "COLOR",
-        editCallback: async (i, cell) => {
-          await self.app.dispatch({
-            type: "change_color_group",
-            index: i,
-            newColor: cell.color
-          });
-        }
-      },
-      { label: "#SAMPLE" },
-      { label: "FILTER" }
-    ],
-    rows: [],
-    striped: false,
-    // no alternating row bg color so delete button appears more visible
-    showLines: false
-  };
-  for (const g of groups) {
-    tableArg.rows.push([
-      {},
-      // blank cell to add delete button
-      { value: g.name },
-      // to allow click to show <input>
-      { color: g.color },
-      { value: "Loading..." },
-      // sample count is lazily retrieved to not to hold up table rendering
-      {}
-      // blank cell to show filter ui
-    ]);
-  }
-  self.selectedGroupsIdx.clear();
-  if (groups.length == 1) {
-    self.selectedGroupsIdx.add(0);
-  } else {
-    tableArg.noButtonCallback = (i, node) => {
-      if (node.checked) self.selectedGroupsIdx.add(i);
-      else self.selectedGroupsIdx.delete(i);
-      self.updateLaunchButton();
-    };
-    tableArg.selectedRows = [];
-    for (let i = 0; i < groups.length; i++) {
-      tableArg.selectedRows.push(i);
-      self.selectedGroupsIdx.add(i);
-    }
-  }
-  renderTable(tableArg);
-  for (const [i, row] of tableArg.rows.entries()) {
-    row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
-      const group2 = groups[i];
-      self.app.vocabApi.deleteGroup(group2.name);
-    });
-    const group = groups[i];
-    filterInit({
-      holder: row[4].__td,
-      vocabApi: self.app.vocabApi,
-      termdbConfig: self.app.vocabApi.termdbConfig,
-      callback: (f) => {
-        if (!f || f.lst.length == 0) {
-          const i2 = groups.findIndex((g) => g.name == group.name);
-          groups.splice(i2, 1);
-        } else {
-          group.filter = f;
-        }
-        self.app.dispatch({
-          type: "app_refresh",
-          state: { groups }
-        });
-      }
-    }).main(group.filter);
-    self.app.vocabApi.getFilteredSampleCount(groups[i].filter).then((n) => row[3].__td.text(n));
-  }
-  self.updateLaunchButton();
-  self.displayCustomTerms();
-}
-async function clickLaunchBtn(self) {
-  const groups = [];
-  for (const i of self.selectedGroupsIdx) {
-    const g = self.state.groups[i];
-    if (g) groups.push(g);
-  }
-  if (groups.length == 0) throw "No groups, should not happen";
-  const name = self.dom.newTermNameInput.property("value");
-  const tw = await self.groups2samplelst(groups);
-  if (!tw) return;
-  tw.term.name = name;
-  self.app.vocabApi.addCustomTerm({ name, tw });
-  self.dom.newTermSpan.style("display", "none");
-}
-function rebaseGroupFilter(s) {
-  if (!s.termfilter?.filter || s.termfilter.filter.lst.length == 0) {
-    return s.groups;
-  }
-  const groups = [];
-  for (const g of s.groups) {
-    const f = getNormalRoot(structuredClone(s.termfilter.filter));
-    const f2 = getFilterItemByTag(g.filter, "filterUiRoot");
-    if (!f2) {
-      groups.push(g);
-      continue;
-    }
-    f.lst.push(f2);
-    f.join = f.lst.length > 1 ? "and" : "";
-    const g2 = {
-      name: g.name,
-      filter: f,
-      color: g.color
-    };
-    groups.push(g2);
-  }
-  return groups;
-}
-async function openPlot(chartType, term, term2, app, id2, newId) {
-  let config = {
-    chartType,
-    term,
-    term2
-  };
-  if (id2) config.insertBefore = id2;
-  if (newId) config.id = newId();
-  await app.dispatch({
-    type: "plot_create",
-    config
-  });
-}
-async function openSummaryPlot(tw, samplelstTW, app, id2, newId) {
-  const config = {
-    chartType: "summary",
-    childType: tw.q?.mode == "continuous" ? "violin" : "barchart",
-    term: tw,
-    term2: samplelstTW
-  };
-  if (id2) config.insertBefore = id2;
-  if (newId) config.id = newId();
-  await app.dispatch({
-    type: "plot_create",
-    config
-  });
-}
-async function showTree(div, callback, app, tip, treeState = { tree: { usecase: { target: "default", detail: "term" } } }) {
-  const activeCohort = app.getState().activeCohort;
-  const state = { activeCohort, ...treeState };
-  tip.clear().showunderoffset(div.node());
-  appInit({
-    holder: tip.d,
-    vocabApi: app.vocabApi,
-    state,
-    tree: {
-      click_term: (term) => {
-        callback(term);
-        tip.hide();
-        if (tip.dnode.parent_menu) tip.dnode.parent_menu.style.display = "none";
-      }
-    }
-  });
-}
-function addPlotMenuItem(chartType, div, text, tip, samplelstTW, id2, parent, openOnTop = false) {
-  const d = div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(text).on("click", (e) => {
-    const state = { tree: { usecase: { target: chartType, detail: "term" } } };
-    if (chartType == "survival") state.nav = { header_mode: "hide_search" };
-    showTree(
-      d,
-      (term) => {
-        openPlot(chartType, term, samplelstTW, parent.app, id2, openOnTop ? () => parent.newId : null);
-      },
-      parent.app,
-      tip,
-      state
-    );
-  });
-  d.insert("div").html("\u203A").style("float", "right");
-}
-function mayAddHierClusterPlotMenuItem(chartType, div, text, tip, samplelstTW, id2, parent, openOnTop = false) {
-  if (!parent.state.currentCohortChartTypes.includes("geneExpression")) return;
-  const itemDiv = div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(text).on("click", () => {
-    tip.clear().showunderoffset(itemDiv.node());
-    new GeneSetEditUI({
-      holder: tip.d,
-      genome: parent.app.opts.genome,
-      geneList: [],
-      vocabApi: parent.app.vocabApi,
-      mode: TermTypes.GENE_EXPRESSION,
-      callback: async ({ geneList, groupName }) => {
-        const group = { name: groupName, lst: [], type: "hierCluster" };
-        const lst = group.lst.filter((tw) => tw.term.type != "geneExpression");
-        const tws = await Promise.all(
-          geneList.map(async (d) => {
-            const gene = d.symbol || d.gene;
-            const unit = parent.app.vocabApi.termdbConfig.queries.geneExpression?.unit || "Gene Expression";
-            const name = `${gene} ${unit}`;
-            const term = { gene, name, type: "geneExpression" };
-            let tw = group.lst.find((tw2) => tw2.term.name == d.symbol || tw2.term.name == d.gene);
-            if (!tw) {
-              tw = { term, q: {} };
-            }
-            return tw;
-          })
-        );
-        tip.hide();
-        if (tip.dnode.parent_menu) tip.dnode.parent_menu.style.display = "none";
-        if (tws.length == 1) {
-          const tw = tws[0];
-          parent.app.dispatch({
-            type: "plot_create",
-            config: {
-              chartType: "summary",
-              term: tw,
-              term2: samplelstTW
-            }
-          });
-          return;
-        }
-        if (tws.length == 2) {
-          const tw = tws[0];
-          const tw2 = tws[1];
-          parent.app.dispatch({
-            type: "plot_create",
-            config: {
-              chartType: "summary",
-              term: tw,
-              term2: tw2,
-              colorTW: samplelstTW
-            }
-          });
-          return;
-        }
-        group.lst = [...lst, ...tws];
-        parent.app.dispatch({
-          type: "plot_create",
-          config: {
-            chartType: "hierCluster",
-            termgroups: [group],
-            dataType: TermTypes.GENE_EXPRESSION,
-            divideBy: samplelstTW,
-            settings: { hierCluster: { yDendrogramHeight: 0, clusterSamples: false } }
-          }
-        });
-      }
-    });
-  });
-  itemDiv.insert("div").html("\u203A").style("float", "right");
-}
-function mayAddMatrixMenuItems(div, text, tip, samplelstTW, id2, parent, state, openOnTop = false, newId) {
-  if (!state.currentCohortChartTypes.includes("matrix")) return;
-  const preBuiltMatrix = state.matrixplots;
-  const hasSnvIndel = parent.app.vocabApi.termdbConfig?.queries?.snvindel;
-  if (!preBuiltMatrix && !hasSnvIndel) return;
-  const itemDiv = div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(text).on("click", () => {
-    tip.clear().showunderoffset(itemDiv.node());
-    if (preBuiltMatrix) {
-      const preBuiltMatrixDiv = tip.d.append("div");
-      for (const plot of preBuiltMatrix) {
-        preBuiltMatrixDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text("Divide " + plot.name).on("click", async () => {
-          const config = await parent.app.vocabApi.getMatrixByName(plot.name);
-          config.divideBy = samplelstTW;
-          config.insertBefore = id2;
-          config.settings.matrix.colw = 0;
-          if (newId) config.id = newId();
-          parent.app.dispatch({
-            type: "plot_create",
-            config
-          });
-          tip.hide();
-          tip.dnode.parent_menu.style.display = "none";
-        });
-      }
-    }
-    if (hasSnvIndel) {
-      const newMatrixDiv = tip.d.append("div");
-      new GeneSetEditUI({
-        holder: newMatrixDiv,
-        genome: parent.app.opts.genome,
-        geneList: [],
-        mode: TermTypes.GENE_VARIANT,
-        vocabApi: parent.app.vocabApi,
-        callback: async ({ geneList, groupName }) => {
-          tip.hide();
-          tip.dnode.parent_menu.style.display = "none";
-          const group = { name: groupName, lst: [] };
-          const lst = group.lst.filter((tw) => tw.term.type != "geneVariant");
-          const tws = await Promise.all(
-            geneList.map(async (d) => {
-              const term = {
-                gene: d.symbol || d.gene,
-                name: d.symbol || d.gene,
-                type: "geneVariant"
-              };
-              let tw = group.lst.find((tw2) => tw2.term.name == d.symbol || tw2.term.name == d.gene);
-              if (!tw) {
-                tw = { term };
-                await fillTermWrapper(tw, parent.app.vocabApi);
-              } else if (!tw.$id) {
-                tw.$id = await get$id(parent.app.vocabApi.getTwMinCopy({ term }));
-              }
-              return tw;
-            })
-          );
-          group.lst = [...lst, ...tws];
-          parent.app.dispatch({
-            type: "plot_create",
-            config: {
-              chartType: "matrix",
-              termgroups: [group],
-              dataType: TermTypes.GENE_VARIANT,
-              divideBy: samplelstTW
-            }
-          });
-        }
-      });
-    }
-  });
-  itemDiv.insert("div").html("\u203A").style("float", "right");
-}
-function addNewGroup(app, filter, groups) {
-  groups = JSON.parse(JSON.stringify(groups));
-  let name = "New group";
-  let i = 0;
-  while (1) {
-    const name2 = name + (i == 0 ? "" : " " + i);
-    if (!groups.find((g) => g.name == name2)) break;
-    i++;
-  }
-  name = name + (i == 0 ? "" : " " + i);
-  const newGroup = {
-    name,
-    filter,
-    color: rgb(colorScale(groups.length)).formatHex()
-  };
-  groups.push(newGroup);
-  app.dispatch({
-    type: "app_refresh",
-    state: { groups }
-  });
-}
-function getSamplelstTWFromIds(ids) {
-  if (!ids) throw "getSamplelstTWFromIds: ids is empty";
-  if (!Array.isArray(ids)) throw "getSamplelstTWFromIds: ids must be an array";
-  const name = "group";
-  const values = ids.map((id2) => {
-    return { sampleId: id2 };
-  });
-  const qgroup = {
-    name,
-    in: true,
-    values
-  };
-  const tw = {
-    isAtomic: true,
-    term: { name, type: "samplelst", values: { [name]: { key: name, list: values } } },
-    q: {
-      groups: [qgroup]
-    }
-  };
-  return tw;
-}
-function getSamplelstFilter(ids) {
-  const tw = getSamplelstTWFromIds(ids);
-  const filter = getFilter(tw);
-  return filter;
-}
-function getFilter(samplelstTW) {
-  let i = 0;
-  let noEdit = true;
-  for (const field in samplelstTW.term.values) {
-    const values = samplelstTW.q.groups[i].values;
-    samplelstTW.term.values[field].list = values;
-    if (values[0] && "sample" in values[0]) noEdit = false;
-    i++;
-  }
-  const filter = {
-    type: "tvslst",
-    in: true,
-    join: "",
-    lst: [
-      {
-        type: "tvs",
-        tvs: { term: samplelstTW.term },
-        noEdit
-      }
-    ]
-  };
-  return filter;
-}
-function getSamplelstTW2(groups) {
-  const values = {};
-  const qgroups = [];
-  for (const group of groups) {
-    const samples = getGroupSamples(group);
-    const qgroup = {
-      name: group.name,
-      in: true,
-      values: samples
-    };
-    qgroups.push(qgroup);
-    values[group.name] = { key: group.name, label: group.name, color: group.color, list: samples };
-  }
-  return {
-    isAtomic: true,
-    term: { name: "groups", type: "samplelst", values },
-    q: { groups: qgroups }
-  };
-}
-function getSamplelstTW(groups, name = groups.length == 1 ? "group" : "groups", notIn = true) {
-  const values = {};
-  const qgroups = [];
-  let samples;
-  for (const group of groups) {
-    samples = getGroupSamples(group);
-    const qgroup = {
-      name: group.name,
-      in: true,
-      values: samples
-    };
-    qgroups.push(qgroup);
-    values[group.name] = { key: group.name, label: group.name, color: group.color, list: samples };
-  }
-  if (groups.length == 1 && notIn) {
-    const name2 = "Not in " + groups[0].name;
-    values[name2] = { key: name2, label: name2, color: "#aaa", list: samples, in: false };
-    qgroups.push({
-      name: name2,
-      in: false,
-      values: samples
-    });
-  }
-  const tw = {
-    isAtomic: true,
-    term: { name, type: "samplelst", values },
-    q: { groups: qgroups }
-  };
-  return tw;
-}
-function getGroupSamples(group) {
-  const values = [];
-  for (const item of group.items) {
-    const value = { sampleId: item.sampleId };
-    if ("sample" in item) {
-      value.sample = item.sample;
-    }
-    values.push(value);
-  }
-  return values;
-}
-
-export {
-  chartsInit,
-  getCurrentCohortChartTypes,
-  groupsInit,
-  rebaseGroupFilter,
-  openPlot,
-  openSummaryPlot,
-  addNewGroup,
-  getSamplelstFilter,
-  getFilter,
-  getSamplelstTW
-};
-//# sourceMappingURL=chunk-N5VBIEH5.js.map