@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/GeneExpInput-Q42COANS.js

@@ -1,366 +0,0 @@
-import {
-  GeneSetEditUI,
-  PlotBase,
-  addGeneSearchbox,
-  getCurrentCohortChartTypes,
-  getGEunit,
-  getSCGEunit,
-  sayerror
-} from "./chunk-SA7APTJR.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import {
-  importPlot
-} from "./chunk-SKREEF3H.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-UI7OCM2A.js";
-import "./chunk-YZK37YCC.js";
-import "./chunk-7EMWHCVW.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-QH6W3NVF.js";
-import {
-  GENE_EXPRESSION,
-  SINGLECELL_GENE_EXPRESSION,
-  SSGSEA,
-  typeGroup
-} from "./chunk-NOEAT6CX.js";
-import "./chunk-4UWS5Y3N.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.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 ${typeGroup[this.termType].toLowerCase()} analysis`,
-        //Only enabling for gene expression for now
-        chartType: "DEinput",
-        isVisible: () => chartTypes.has("DA") && this.termType === GENE_EXPRESSION,
-        callback: async (event, tab) => {
-          await this.app.dispatch({
-            type: "plot_create",
-            parentId: this.id,
-            config: {
-              chartType: "DEinput",
-              parentId: this.id,
-              /** ' ' overrides the default 'hide_search' mode in DEInput.
-               * 'hide_search' by default expands all terms. */
-              header_mode: " "
-            }
-          });
-          delete tab.callback;
-        }
-      },
-      {
-        label: typeGroup[SSGSEA],
-        isVisible: () => {
-          return this.termType === GENE_EXPRESSION && state.termdbConfig?.allowedTermTypes?.includes(SSGSEA);
-        },
-        callback: async (event, tab) => {
-          await this.renderSSGSEA(tab);
-          delete tab.callback;
-        }
-      }
-    ];
-    const chartTabs = new Tabs({
-      holder: this.dom.tabs,
-      tabs: this.tabs,
-      tabsPosition: "vertical"
-    });
-    await chartTabs.main();
-  }
-  getUnit() {
-    return this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi);
-  }
-  initDom() {
-    const headerText = this.opts.headerText ? `${this.opts.headerText} ` : "";
-    const dom = {
-      header: {
-        title: this.opts.header.append("span").style("padding-right", "5px").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 renderSSGSEA(tab) {
-    const holder = tab.contentHolder.style("padding", "10px");
-    const _ = await import("./ssGSEA-7T6S3DSE.js");
-    const searchHandler = new _.SearchHandler();
-    await searchHandler.init({
-      holder,
-      app: this.app,
-      genomeObj: this.genome,
-      callback: async (term) => {
-        const config = this.makeConfig({
-          chartType: "summary",
-          term: { term }
-        });
-        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-Q42COANS.js.map

package/dist/GeneExpInput-Q42COANS.js.map

@@ -1,7 +0,0 @@
-{
-  "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, SSGSEA, 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 ${typeGroup[this.termType].toLowerCase()} analysis`,\n\t\t\t\t//Only enabling for gene expression for now\n\t\t\t\tchartType: 'DEinput',\n\t\t\t\tisVisible: () => chartTypes.has('DA') && this.termType === GENE_EXPRESSION,\n\t\t\t\tcallback: async (event, tab) => {\n\t\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tparentId: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'DEinput',\n\t\t\t\t\t\t\tparentId: this.id,\n\t\t\t\t\t\t\t/** ' ' overrides the default 'hide_search' mode in DEInput.\n\t\t\t\t\t\t\t * 'hide_search' by default expands all terms. */\n\t\t\t\t\t\t\theader_mode: ' '\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: typeGroup[SSGSEA],\n\t\t\t\tisVisible: () => {\n\t\t\t\t\treturn this.termType === GENE_EXPRESSION && state.termdbConfig?.allowedTermTypes?.includes(SSGSEA)\n\t\t\t\t},\n\t\t\t\tcallback: async (event, tab) => {\n\t\t\t\t\tawait this.renderSSGSEA(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tconst chartTabs = new Tabs({\n\t\t\tholder: this.dom.tabs,\n\t\t\ttabs: this.tabs,\n\t\t\ttabsPosition: 'vertical'\n\t\t})\n\t\tawait chartTabs.main()\n\t}\n\n\tgetUnit() {\n\t\treturn this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi)\n\t}\n\n\tinitDom() {\n\t\tconst headerText = this.opts.headerText ? `${this.opts.headerText} ` : ''\n\t\tconst dom: { [index: string]: any } = {\n\t\t\theader: {\n\t\t\t\ttitle: this.opts.header\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('padding-right', '5px')\n\t\t\t\t\t.text(headerText)\n\t\t\t\t\t.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 renderSSGSEA(tab) {\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\t\tconst _ = await import('../termdb/handlers/ssGSEA.ts')\n\t\tconst searchHandler = new _.SearchHandler()\n\t\tawait searchHandler.init({\n\t\t\tholder,\n\t\t\tapp: this.app,\n\t\t\tgenomeObj: this.genome,\n\t\t\tcallback: async term => {\n\t\t\t\tconst config = this.makeConfig({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: { term: term }\n\t\t\t\t})\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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