@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/GeneExpInput-DWB7OYT2.js

@@ -0,0 +1,335 @@
+import {
+  GeneSetEditUI,
+  PlotBase,
+  Tabs,
+  addGeneSearchbox,
+  getCurrentCohortChartTypes,
+  getGEunit,
+  getSCGEunit,
+  sayerror
+} from "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import {
+  importPlot
+} from "./chunk-3QBZ2Y77.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import {
+  GENE_EXPRESSION,
+  SINGLECELL_GENE_EXPRESSION,
+  typeGroup
+} from "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/GeneExpInput.ts
+var GeneExpInput = class _GeneExpInput extends PlotBase {
+  static {
+    this.type = "GeneExpInput";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _GeneExpInput.type;
+    this.opts = opts;
+    this.components = {
+      plots: {}
+    };
+    const termProperties = opts?.termProperties || {};
+    this.makeTerm = (term) => ({ ...term, ...termProperties, type: this.termType, unit: this.unit });
+    const spawnConfig = opts?.spawnConfig || {};
+    this.makeConfig = (config) => {
+      const tmp = { ...config, ...spawnConfig };
+      if (this.termType === SINGLECELL_GENE_EXPRESSION) tmp.hidePlotFilter = true;
+      return tmp;
+    };
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    const subplots = appState.plots.filter((p) => p.parentId === this.id);
+    return {
+      config,
+      termdbConfig: appState.termdbConfig,
+      subplots
+    };
+  }
+  async init(appState) {
+    const state = this.getState(appState);
+    this.genome = this.app.opts.genome;
+    this.termType = state.config.termType;
+    this.unit = this.getUnit();
+    this.dom = this.initDom();
+    const chartTypes = new Set(getCurrentCohortChartTypes(appState));
+    this.tabs = [
+      {
+        label: "One gene",
+        isVisible: () => true,
+        callback: (event, tab) => {
+          this.renderGeneSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Two genes",
+        isVisible: () => true,
+        callback: (event, tab) => {
+          this.renderTwoGeneSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Hierarchical clustering",
+        isVisible: () => chartTypes.has("matrix") && this.termType === GENE_EXPRESSION,
+        // hierarchical clustering doesn't support scge
+        callback: (event, tab) => {
+          this.renderGeneMultiSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: `Differential ${typeGroup[this.termType].toLowerCase()} analysis`,
+        //Only enabling for gene expression for now
+        chartType: "DEinput",
+        isVisible: () => false,
+        // TODO: Sorting out server response error in another PR.
+        // Will enable when fixed. For now hiding from UI to avoid confusion.
+        // isVisible: () => chartTypes.has('DA') && this.termType === GENE_EXPRESSION,
+        callback: async (event, tab) => {
+          await this.app.dispatch({
+            type: "plot_create",
+            parentId: this.id,
+            config: {
+              chartType: "DEinput",
+              parentId: this.id
+            }
+          });
+          delete tab.callback;
+        }
+      }
+    ];
+    const chartTabs = new Tabs({
+      holder: this.dom.tabs,
+      tabs: this.tabs,
+      tabsPosition: "vertical"
+    });
+    await chartTabs.main();
+  }
+  getUnit() {
+    return this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi);
+  }
+  initDom() {
+    const headerText = this.opts.headerText ? `${this.opts.headerText} ` : "";
+    const dom = {
+      header: {
+        title: this.opts.header.append("span").text(headerText).attr("data-testid", "sjpp-gene-exp-input-headerText"),
+        plot: this.opts.header.append("span").text(typeGroup[this.termType].toUpperCase()).style("font-size", "0.7em").style("opacity", "0.6").attr("data-testid", "sjpp-gene-exp-input-termType")
+      },
+      tabs: this.opts.holder.append("div").style("margin", "10px").attr("data-testid", "sjpp-gene-exp-input-tabs-wrapper")
+    };
+    return dom;
+  }
+  async main() {
+    const state = this.getState(this.app.getState());
+    for (const subplot of state.subplots || []) {
+      if (!this.components.plots[subplot.id]) await this.initSubplotInTab(subplot);
+    }
+  }
+  renderGeneSelect(tab) {
+    const row = tab.contentHolder.style("padding", "15px");
+    row.append("span").style("padding", "5px").text("Select a gene:");
+    const geneSearch = addGeneSearchbox({
+      row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        const tw = {
+          term: this.makeTerm({
+            gene: geneSearch.geneSymbol,
+            name: `${geneSearch.geneSymbol} ${this.unit}`
+          })
+        };
+        const config = this.makeConfig({
+          chartType: "summary",
+          term: tw
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  /** Guide the user to select the first gene then
+   * a second to launch the summary plot on submit.*/
+  renderTwoGeneSelect(tab) {
+    const term = {};
+    const term2 = {};
+    const holder = tab.contentHolder.style("padding", "10px");
+    const gene1row = holder.append("div").style("padding", "5px");
+    const gene2row = holder.append("div").style("padding", "5px").style("display", "none");
+    const submitButton = holder.append("button").attr("type", "button").attr("disabled", true);
+    gene1row.append("span").text("Select the first gene:");
+    const geneSearch1 = addGeneSearchbox({
+      row: gene1row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        gene2row.style("display", "block");
+        if (!geneSearch1.geneSymbol) throw new Error("First gene result is required");
+        term.gene = geneSearch1.geneSymbol;
+        term.name = `${geneSearch1.geneSymbol} ${this.unit}`;
+      }
+    });
+    gene2row.append("span").text("Select the second gene:");
+    const geneSearch2 = addGeneSearchbox({
+      row: gene2row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        if (!geneSearch2.geneSymbol) throw new Error("Second gene result is required");
+        term2.gene = geneSearch2.geneSymbol;
+        term2.name = `${geneSearch2.geneSymbol} ${this.unit}`;
+        submitButton.attr("disabled", null);
+      }
+    });
+    submitButton.text("Submit").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").on("click", async () => {
+      if (!term.name || !term.gene) {
+        sayerror(holder, "Missing first gene. Please provide a valid gene.");
+        return;
+      }
+      if (!term2.name || !term2.gene) {
+        sayerror(holder, "Missing second gene. Please provide a valid gene.");
+        return;
+      }
+      const config = this.makeConfig({
+        chartType: "summary",
+        term: { term: this.makeTerm(term) },
+        term2: { term: this.makeTerm(term2) }
+      });
+      await this.dispatchEdits(config);
+    });
+  }
+  // /** Render the GeneSetEdit UI for selection and then
+  //  * launch the hierarchical clustering on submit.*/
+  renderGeneMultiSelect(tab) {
+    const holder = tab.contentHolder.style("padding", "10px");
+    const grpWrapper = holder.append("div").style("padding", "10px");
+    grpWrapper.append("span").style("font-weight", "bold").text("Group name:");
+    let customName = "New custom group";
+    const input = grpWrapper.append("input").style("margin", "2px 5px").style("width", "210px").attr("placeholder", "Group Name").on("input", () => {
+      customName = input.property("value");
+    });
+    new GeneSetEditUI({
+      holder: holder.append("div"),
+      /** running hier clustering and the editing group
+       * is the group used for clustering pass this mode
+       * value to inform ui to support the optional button
+       * "top variably exp gene" this is hardcoded for
+       * the purpose of gene expression and should be improved. */
+      genome: this.genome,
+      mode: "geneExpression",
+      vocabApi: this.app.vocabApi,
+      callback: async ({ geneList, name }) => {
+        if (geneList.length <= 2) {
+          return alert("At least three genes are required for hierarchical clustering. Please select more genes.");
+        }
+        const group = {
+          name: name || customName,
+          lst: [],
+          type: "hierCluster"
+        };
+        const tws = await Promise.all(
+          geneList.map((d) => {
+            const gene = d.symbol || d.gene;
+            const name2 = `${gene} ${this.unit}`;
+            const term = this.makeTerm({ gene, name: name2 });
+            return { term, q: {} };
+          })
+        );
+        group.lst = [...tws];
+        const config = this.makeConfig({
+          chartType: "hierCluster",
+          termgroups: [group],
+          //TODO: Need to allow singleCellGeneExpression as well
+          dataType: GENE_EXPRESSION
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  async initSubplotInTab(subplot) {
+    const holder = this.tabs.find((tab) => tab.chartType === subplot.chartType)?.contentHolder;
+    if (!holder) throw new Error(`No tab found for chart type ${subplot.chartType}`);
+    const opts = Object.assign({}, subplot, {
+      holder,
+      app: this.app,
+      parentId: this.id,
+      id: subplot.id
+    });
+    const { componentInit: componentInit2 } = await importPlot(opts.chartType);
+    this.components.plots[subplot.id] = await componentInit2(opts);
+  }
+  async dispatchEdits(config) {
+    await this.app.dispatch({
+      type: "app_refresh",
+      subactions: [
+        {
+          type: "plot_create",
+          config
+        },
+        {
+          type: "plot_delete",
+          id: this.id
+        }
+      ]
+    });
+  }
+};
+var geneExpInputInit = getCompInit(GeneExpInput);
+var componentInit = geneExpInputInit;
+var enabledTermTypes = /* @__PURE__ */ new Set([GENE_EXPRESSION, SINGLECELL_GENE_EXPRESSION]);
+function getPlotConfig(opts) {
+  if (!opts?.termType) throw new Error("termType is required in opts");
+  if (!enabledTermTypes.has(opts.termType)) throw new Error(`Invalid termType: ${opts.termType}`);
+  const config = {
+    chartType: "GeneExpInput",
+    termType: opts.termType,
+    hidePlotFilter: true
+  };
+  return copyMerge(config, opts);
+}
+export {
+  GeneExpInput,
+  componentInit,
+  geneExpInputInit,
+  getPlotConfig
+};
+//# sourceMappingURL=GeneExpInput-DWB7OYT2.js.map

package/dist/GeneExpInput-DWB7OYT2.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/GeneExpInput.ts"],
+  "sourcesContent": ["import { PlotBase } from './PlotBase.ts'\nimport { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { GENE_EXPRESSION, SINGLECELL_GENE_EXPRESSION, typeGroup } from '#shared/terms.js'\nimport { getGEunit } from '../tw/geneExpression'\nimport { getSCGEunit } from '../tw/singleCellGeneExpression'\nimport { addGeneSearchbox, GeneSetEditUI, Menu, sayerror, Tabs } from '#dom'\nimport type { ClientGenome } from '../types/clientGenome'\nimport { getCurrentCohortChartTypes } from '../mass/charts.js'\nimport { importPlot } from '#plots/importPlot.js'\n\ntype GeneExpInputOpts = {\n\t/** sandbox header\n\t * Normally this is optional but there's no reason to launch this plot\n\t * sans sandbox. */\n\theader: any\n\t/** Optional text to display in the header before the term type */\n\theaderText?: string\n\ttermProperties?: { [key: string]: any }\n\tspawnConfig?: { [key: string]: any }\n}\n\n/** Transient plot for users to pick gene(s) of interest and launch\n * the appropriate plot. */\nexport class GeneExpInput extends PlotBase implements RxComponent {\n\tstatic type = 'GeneExpInput'\n\n\ttype: string\n\tcomponents: { plots: { [key: string]: any } }\n\tgenome!: ClientGenome\n\ttermType!: string\n\t/** termType dependent */\n\tunit!: string\n\tdom!: { [index: string]: any }\n\ttabs!: any\n\t/** Helper function to create term with any additional properties */\n\tmakeTerm: (term: any) => object\n\t/** Helper function to create config or the spawning plot with\n\t * any additional properties. Used in the violin, scatter, and hierCluster */\n\tmakeConfig: (config: any) => object\n\n\tconstructor(opts: GeneExpInputOpts, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = GeneExpInput.type\n\t\tthis.opts = opts\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\n\t\tconst termProperties = opts?.termProperties || {}\n\t\tthis.makeTerm = term => ({ ...term, ...termProperties, type: this.termType, unit: this.unit })\n\n\t\tconst spawnConfig = opts?.spawnConfig || {}\n\t\tthis.makeConfig = config => {\n\t\t\tconst tmp = { ...config, ...spawnConfig }\n\t\t\t/** TODO: Single cell terms cannot be filtered. */\n\t\t\tif (this.termType === SINGLECELL_GENE_EXPRESSION) tmp.hidePlotFilter = true\n\t\t\treturn tmp\n\t\t}\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst subplots = appState.plots.filter(p => p.parentId === this.id)\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tsubplots\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tthis.genome = this.app.opts.genome\n\t\tthis.termType = state.config.termType\n\t\tthis.unit = this.getUnit()\n\t\tthis.dom = this.initDom()\n\n\t\tconst chartTypes = new Set(getCurrentCohortChartTypes(appState))\n\n\t\tthis.tabs = [\n\t\t\t{\n\t\t\t\tlabel: 'One gene',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: (event, tab) => {\n\t\t\t\t\tthis.renderGeneSelect(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Two genes',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: (event, tab) => {\n\t\t\t\t\tthis.renderTwoGeneSelect(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Hierarchical clustering',\n\t\t\t\tisVisible: () => chartTypes.has('matrix') && this.termType === GENE_EXPRESSION, // hierarchical clustering doesn't support scge\n\t\t\t\tcallback: (event, tab) => {\n\t\t\t\t\tthis.renderGeneMultiSelect(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Differential ${typeGroup[this.termType].toLowerCase()} analysis`,\n\t\t\t\t//Only enabling for gene expression for now\n\t\t\t\tchartType: 'DEinput',\n\t\t\t\tisVisible: () => false,\n\t\t\t\t// TODO: Sorting out server response error in another PR.\n\t\t\t\t// Will enable when fixed. For now hiding from UI to avoid confusion.\n\t\t\t\t// isVisible: () => chartTypes.has('DA') && this.termType === GENE_EXPRESSION,\n\t\t\t\tcallback: async (event, tab) => {\n\t\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tparentId: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'DEinput',\n\t\t\t\t\t\t\tparentId: this.id\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tconst chartTabs = new Tabs({\n\t\t\tholder: this.dom.tabs,\n\t\t\ttabs: this.tabs,\n\t\t\ttabsPosition: 'vertical'\n\t\t})\n\t\tawait chartTabs.main()\n\t}\n\n\tgetUnit() {\n\t\treturn this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi)\n\t}\n\n\tinitDom() {\n\t\tconst headerText = this.opts.headerText ? `${this.opts.headerText} ` : ''\n\t\tconst dom: { [index: string]: any } = {\n\t\t\theader: {\n\t\t\t\ttitle: this.opts.header.append('span').text(headerText).attr('data-testid', 'sjpp-gene-exp-input-headerText'),\n\t\t\t\tplot: this.opts.header\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.text(typeGroup[this.termType].toUpperCase())\n\t\t\t\t\t.style('font-size', '0.7em')\n\t\t\t\t\t.style('opacity', '0.6')\n\t\t\t\t\t.attr('data-testid', 'sjpp-gene-exp-input-termType')\n\t\t\t},\n\t\t\ttabs: this.opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.attr('data-testid', 'sjpp-gene-exp-input-tabs-wrapper')\n\t\t}\n\n\t\treturn dom\n\t}\n\n\tasync main() {\n\t\tconst state = this.getState(this.app.getState())\n\n\t\tfor (const subplot of state.subplots || []) {\n\t\t\tif (!this.components.plots[subplot.id]) await this.initSubplotInTab(subplot)\n\t\t}\n\t}\n\n\trenderGeneSelect(tab) {\n\t\tconst row = tab.contentHolder.style('padding', '15px')\n\t\trow.append('span').style('padding', '5px').text('Select a gene:')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\trow,\n\t\t\tgenome: this.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\tconst tw = {\n\t\t\t\t\tterm: this.makeTerm({\n\t\t\t\t\t\tgene: geneSearch.geneSymbol,\n\t\t\t\t\t\tname: `${geneSearch.geneSymbol} ${this.unit}`\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tconst config = this.makeConfig({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: tw\n\t\t\t\t})\n\t\t\t\tawait this.dispatchEdits(config)\n\t\t\t}\n\t\t})\n\t}\n\n\t/** Guide the user to select the first gene then\n\t * a second to launch the summary plot on submit.*/\n\trenderTwoGeneSelect(tab) {\n\t\tconst term: any = {}\n\t\tconst term2: any = {}\n\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\n\t\tconst gene1row = holder.append('div').style('padding', '5px')\n\t\tconst gene2row = holder.append('div').style('padding', '5px').style('display', 'none')\n\t\tconst submitButton = holder.append('button').attr('type', 'button').attr('disabled', true)\n\n\t\tgene1row.append('span').text('Select the first gene:')\n\t\tconst geneSearch1 = addGeneSearchbox({\n\t\t\trow: gene1row,\n\t\t\tgenome: this.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\tgene2row.style('display', 'block')\n\t\t\t\tif (!geneSearch1.geneSymbol) throw new Error('First gene result is required')\n\t\t\t\tterm.gene = geneSearch1.geneSymbol\n\t\t\t\tterm.name = `${geneSearch1.geneSymbol} ${this.unit}`\n\t\t\t}\n\t\t})\n\n\t\tgene2row.append('span').text('Select the second gene:')\n\t\tconst geneSearch2 = addGeneSearchbox({\n\t\t\trow: gene2row,\n\t\t\tgenome: this.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\tif (!geneSearch2.geneSymbol) throw new Error('Second gene result is required')\n\t\t\t\tterm2.gene = geneSearch2.geneSymbol\n\t\t\t\tterm2.name = `${geneSearch2.geneSymbol} ${this.unit}`\n\t\t\t\tsubmitButton.attr('disabled', null)\n\t\t\t}\n\t\t})\n\n\t\tsubmitButton\n\t\t\t.text('Submit')\n\t\t\t.style('border', 'none')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('padding', '10px 15px')\n\t\t\t.on('click', async () => {\n\t\t\t\tif (!term.name || !term.gene) {\n\t\t\t\t\tsayerror(holder, 'Missing first gene. Please provide a valid gene.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!term2.name || !term2.gene) {\n\t\t\t\t\tsayerror(holder, 'Missing second gene. Please provide a valid gene.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\tconst config = this.makeConfig({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: { term: this.makeTerm(term) },\n\t\t\t\t\tterm2: { term: this.makeTerm(term2) }\n\t\t\t\t})\n\t\t\t\tawait this.dispatchEdits(config)\n\t\t\t})\n\t}\n\t// /** Render the GeneSetEdit UI for selection and then\n\t//  * launch the hierarchical clustering on submit.*/\n\trenderGeneMultiSelect(tab) {\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\t\tconst grpWrapper = holder.append('div').style('padding', '10px')\n\t\tgrpWrapper.append('span').style('font-weight', 'bold').text('Group name:')\n\n\t\tlet customName: string = 'New custom group'\n\t\tconst input = grpWrapper\n\t\t\t.append('input')\n\t\t\t.style('margin', '2px 5px')\n\t\t\t.style('width', '210px')\n\t\t\t.attr('placeholder', 'Group Name')\n\t\t\t.on('input', () => {\n\t\t\t\tcustomName = input.property('value')\n\t\t\t})\n\n\t\tnew GeneSetEditUI({\n\t\t\tholder: holder.append('div'),\n\t\t\t/** running hier clustering and the editing group\n\t\t\t * is the group used for clustering pass this mode\n\t\t\t * value to inform ui to support the optional button\n\t\t\t * \"top variably exp gene\" this is hardcoded for\n\t\t\t * the purpose of gene expression and should be improved. */\n\t\t\tgenome: this.genome,\n\t\t\tmode: 'geneExpression',\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tcallback: async ({ geneList, name }) => {\n\t\t\t\tif (geneList.length <= 2) {\n\t\t\t\t\treturn alert('At least three genes are required for hierarchical clustering. Please select more genes.')\n\t\t\t\t}\n\n\t\t\t\tconst group: { name: string; lst: { [index: string]: any }[]; type: string } = {\n\t\t\t\t\tname: name || customName,\n\t\t\t\t\tlst: [],\n\t\t\t\t\ttype: 'hierCluster'\n\t\t\t\t}\n\t\t\t\tconst tws = await Promise.all(\n\t\t\t\t\tgeneList.map((d: any) => {\n\t\t\t\t\t\tconst gene: string = d.symbol || d.gene\n\t\t\t\t\t\tconst name = `${gene} ${this.unit}`\n\t\t\t\t\t\tconst term = this.makeTerm({ gene, name })\n\t\t\t\t\t\treturn { term, q: {} }\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t\t\tgroup.lst = [...tws]\n\n\t\t\t\tconst config = this.makeConfig({\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\ttermgroups: [group],\n\t\t\t\t\t//TODO: Need to allow singleCellGeneExpression as well\n\t\t\t\t\tdataType: GENE_EXPRESSION\n\t\t\t\t})\n\n\t\t\t\tawait this.dispatchEdits(config)\n\t\t\t}\n\t\t})\n\t}\n\n\tasync initSubplotInTab(subplot) {\n\t\tconst holder = this.tabs.find(tab => tab.chartType === subplot.chartType)?.contentHolder\n\t\tif (!holder) throw new Error(`No tab found for chart type ${subplot.chartType}`)\n\n\t\tconst opts = Object.assign({}, subplot, {\n\t\t\tholder,\n\t\t\tapp: this.app,\n\t\t\tparentId: this.id,\n\t\t\tid: subplot.id\n\t\t})\n\n\t\tconst { componentInit } = await importPlot(opts.chartType)\n\t\tthis.components.plots[subplot.id] = await componentInit(opts)\n\t}\n\n\tasync dispatchEdits(config) {\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'app_refresh',\n\t\t\tsubactions: [\n\t\t\t\t{\n\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\tconfig\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\tid: this.id\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t}\n}\n\nexport const geneExpInputInit = getCompInit(GeneExpInput)\nexport const componentInit = geneExpInputInit\n\n//Sanity check\nconst enabledTermTypes = new Set([GENE_EXPRESSION, SINGLECELL_GENE_EXPRESSION])\n\nexport function getPlotConfig(opts) {\n\tif (!opts?.termType) throw new Error('termType is required in opts')\n\tif (!enabledTermTypes.has(opts.termType)) throw new Error(`Invalid termType: ${opts.termType}`)\n\n\tconst config = {\n\t\tchartType: 'GeneExpInput',\n\t\ttermType: opts.termType,\n\t\thidePlotFilter: true\n\t}\n\n\treturn copyMerge(config, opts)\n}\n"],
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+}