@sjcrh/proteinpaint-client 2.191.3 → 2.191.4

package/dist/SC-M6RGALZM.js

@@ -0,0 +1,936 @@
+import {
+  PlotBase,
+  digestMessage,
+  getGEunit,
+  make_radios,
+  newSandboxDiv,
+  renderTable
+} 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 "./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 {
+  dofetch3
+} from "./chunk-7EMWHCVW.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-QH6W3NVF.js";
+import {
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-NOEAT6CX.js";
+import {
+  TermTypeGroups
+} from "./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/sc/model/SCModel.ts
+var SCModel = class {
+  constructor(app, id) {
+    this.app = app;
+    this.id = id;
+    this.state = this.app.getState();
+  }
+  /********** Single Cell SAMPLES for rendering the table ********
+   * The table data does not update. Should only need to run once. */
+  async getSampleData() {
+    const body = this.getSampleRequestOpts();
+    return await dofetch3("termdb/singlecellSamples", { body });
+  }
+  //May involve more complicated logic later
+  getSampleRequestOpts() {
+    return {
+      genome: this.state.vocab.genome,
+      dslabel: this.state.vocab.dslabel,
+      filter0: this.state.termfilter.filter0 || null
+    };
+  }
+  //Fetches optional name for ds defined columns
+  async getColumnLabels(dsScSamples) {
+    if (!dsScSamples || !dsScSamples.sampleColumns) return;
+    const colsCopy = structuredClone(dsScSamples.sampleColumns);
+    for (const col of colsCopy) {
+      let label = col.termid;
+      try {
+        label = (await this.app.vocabApi.getterm(col.termid)).name;
+      } catch (e) {
+        if (e.message) {
+        }
+      }
+      col.label = label;
+    }
+    return colsCopy;
+  }
+  /********** Single Cell DATA for rendering plots ********
+   * This is for the plot buttons. Returns an array plots with found files or
+   * available data. */
+  async getData() {
+    const body = this.getDataRequestOpts();
+    if (!body) return;
+    return await dofetch3("termdb/singlecellData", { body });
+  }
+  /** May provide active plots to the request and return plot data when
+   * checkPlotAvailability is false. When checkPlotAvailability is true,
+   * only returns which plots are available but not the actual data. */
+  getDataRequestOpts(_plots = [], checkPlotAvailability = true) {
+    const state = this.app.getState();
+    const singleCellTermdbConfig = state.termdbConfig?.queries?.singleCell;
+    if (!singleCellTermdbConfig?.data) throw new Error("No singleCell.data defined in termdbConfig.queries");
+    const config = state.plots.find((p) => p.id === this.id);
+    if (!config.settings.sc.item) return;
+    const plots = _plots?.length ? _plots : singleCellTermdbConfig.data.plots.map((p) => p.name);
+    return {
+      genome: this.state.vocab.genome,
+      dslabel: this.state.vocab.dslabel,
+      // if true, only return available plot names, but not actual plot data
+      checkPlotAvailability,
+      plots,
+      sample: {
+        eID: config.settings.sc.item.eID,
+        sID: config.settings.sc.item.sID
+      }
+    };
+  }
+  /** Essentially for the GDC. Maybe applied to other ds in the future. */
+  async getCategories(_plots) {
+    const body = this.getDataRequestOpts(_plots, false);
+    if (!body) return;
+    let res;
+    try {
+      res = await dofetch3("termdb/singlecellData", { body });
+    } catch (e) {
+      if (e instanceof Error) console.error(`${e.message || e}`);
+    }
+    return this.formatCategories(res);
+  }
+  formatCategories(res) {
+    const plot = structuredClone(res.plots[0]);
+    plot.cells = [...plot.noExpCells, ...plot.expCells];
+    const clusters = new Set(plot.cells.map((c) => c.category));
+    const sortedClusters = Array.from(clusters).sort((a, b) => {
+      const num1 = parseInt(a.split(" ")[1]);
+      const num2 = parseInt(b.split(" ")[1]);
+      return num1 - num2;
+    });
+    return sortedClusters;
+  }
+};
+
+// plots/sc/viewModel/SCViewModel.ts
+var SCViewModel = class {
+  constructor(app, config, _items, sampleColumns) {
+    this.app = app;
+    this.state = this.app.getState();
+    const items = _items.sort((a, b) => b.isMetaResult === a.isMetaResult ? 0 : b.isMetaResult ? 1 : -1);
+    const [rows, columns, sampleColIdx] = this.getTabelData(config, items, sampleColumns);
+    const selectedRows = [];
+    const sID = config.settings.sc.item?.sID;
+    const i = sID ? items.findIndex((item) => item.sample === sID || item.experiments?.some((e) => e.sampleName === sID)) : -1;
+    if (i != -1) selectedRows.push(i);
+    this.tableData = {
+      rows,
+      columns,
+      selectedRows,
+      sampleColIdx
+    };
+  }
+  getTabelData(plotConfig, items, sampleColumns) {
+    const rows = [];
+    const hasExperiments = items.some((i) => i.experiments);
+    let sampleColIdx = -1;
+    const columns = [{ label: plotConfig.settings.sc.columns.sample, sortable: true }];
+    if (hasExperiments) {
+      columns.push({ label: "Sample", sortable: true });
+      sampleColIdx = 1;
+    } else sampleColIdx = 0;
+    columns.push({ label: "Shown plots" });
+    for (const col of sampleColumns || []) {
+      columns.push({
+        label: col.label,
+        width: "14vw",
+        sortable: true
+      });
+    }
+    if (hasExperiments) columns.push({ label: "Experiment", sortable: true });
+    for (const item of items) {
+      if (hasExperiments)
+        for (const exp of item.experiments) {
+          const row = [{ value: item.sample, __experimentID: exp.experimentID }];
+          row.push({ value: exp.sampleName });
+          row.push({ value: "" });
+          for (const col of sampleColumns || []) {
+            row.push({ value: item[col.termid] });
+          }
+          if (this.state.vocab.dslabel == "GDC")
+            row.push({ value: exp.experimentID, url: `https://portal.gdc.cancer.gov/files/${exp.experimentID}` });
+          else row.push({ value: exp.experimentID });
+          rows.push(row);
+        }
+      else {
+        const row = item.isMetaResult ? [{ html: item.sample.replace(/_/g, " "), value: item.sample }] : [{ value: item.sample }];
+        row.push({ value: "" });
+        for (const col of sampleColumns || []) {
+          const value = item[col.termid];
+          if (value == null && item.isMetaResult) row.push({ value: "All" });
+          else row.push({ value: item[col.termid] });
+        }
+        rows.push(row);
+      }
+    }
+    return [rows, columns, sampleColIdx];
+  }
+};
+
+// plots/sc/interactions/SCInteractions.ts
+var SCInteractions = class {
+  constructor(sc) {
+    this.app = sc.app;
+    this.dom = sc.dom;
+    this.id = sc.id;
+    this.model = sc.model;
+  }
+  /** Used in the gene search menu shown on click from a plot btn
+   * Add the plot to the state.plots array with .parentId. Adding
+   * .parentId prevents the plot from launching in a new sandbox.
+   * Pass the .parentId to both the plotConfig and the action.
+   * this.getState() in SC.ts will find all the subplots with the parentId==this.id
+   * SC.main() initializes the subplots as components in chartsDiv
+   */
+  async createSubplot(config) {
+    const c = Object.assign({}, config, { parentId: this.id });
+    await this.app.dispatch({
+      type: "plot_create",
+      parentId: this.id,
+      config: c
+    });
+  }
+  /** Updates the item in the plot settings */
+  async updateItem(item) {
+    await this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config: { settings: { sc: { item } } }
+    });
+  }
+  async getDropDownOptions(plot) {
+    return this.model.getCategories(plot);
+  }
+  toggleLoading(on) {
+    if (on) {
+      this.dom.loading.selectAll("*").remove();
+      this.dom.loading.style("display", "block").append("div").style("position", "relative").style("top", "50%").append("span").attr("class", "sjpp-spinner");
+      this.dom.loading.style("display", "");
+    } else {
+      this.dom.loading.selectAll(".sjpp-spinner").remove();
+      this.dom.loading.style("display", "none");
+    }
+  }
+};
+
+// plots/sc/view/SampleTableRenderer.ts
+var SampleTableRenderer = class {
+  constructor(dom, interactions, tableData) {
+    this.sandboxes = /* @__PURE__ */ new Map();
+    this.dom = dom;
+    this.interactions = interactions;
+    this.tableData = tableData;
+    this.renderSamplesTable(tableData);
+  }
+  /** Users select one item at a time to render the plot buttons
+   * to init() plots in the dashboard.*/
+  renderSamplesTable(tableData) {
+    renderTable({
+      rows: tableData.rows,
+      columns: tableData.columns,
+      div: this.dom.tableDiv,
+      singleMode: true,
+      maxWidth: tableData.columns.length > 3 ? "95vw" : "auto",
+      maxHeight: "30vh",
+      header: {
+        allowSort: true,
+        style: { "text-transform": "capitalize" }
+      },
+      striped: true,
+      selectedRows: tableData.selectedRows,
+      afterRender: () => {
+        this.reapplyAllPlotButtons();
+      },
+      noButtonCallback: (index) => {
+        const item = this.buildItemFromRow(tableData, index);
+        this.interactions.updateItem(item);
+        this.dom.plotsBtnsDiv.style("display", "block");
+      }
+    });
+  }
+  /** Builds an item object from a table row, mapping column labels to keys.
+   * Converts 'sample' -> 'sID' and 'experiment' -> 'eID'.
+   * Extracted out from noButtonCallback for testing.  */
+  buildItemFromRow(tableData, index) {
+    const item = {};
+    tableData.rows[index].forEach((r, idx) => {
+      if (!r.value) return;
+      let key = tableData.columns[idx].label.toLowerCase();
+      key = key === "sample" ? "sID" : key === "experiment" ? "eID" : key;
+      item[key] = r.value;
+    });
+    if (!item.sID) throw new Error("Selected item must have sID property");
+    return item;
+  }
+  updateTable(sampleId, sandboxes) {
+    this.sandboxes = sandboxes;
+    this.applyButtonsForSample(sampleId);
+  }
+  /** Called by afterRender to re-apply buttons for all samples with subplots. */
+  reapplyAllPlotButtons() {
+    for (const sampleId of this.sandboxes.keys()) {
+      this.applyButtonsForSample(sampleId);
+    }
+  }
+  /** Applies buttons for a single sample after plot button click */
+  applyButtonsForSample(sampleId) {
+    const sampleIdx = this.tableData.sampleColIdx;
+    if (!this.sandboxes) return;
+    const row = this.tableData.rows.find((r) => r[sampleIdx].value === sampleId);
+    if (!row) return;
+    const cell = row[sampleIdx + 1].__td;
+    cell.selectAll(".sjpp-sc-table-plot-btn").remove();
+    const sampleSandboxes = this.sandboxes.get(sampleId);
+    if (!sampleSandboxes || sampleSandboxes.length === 0) return;
+    for (const { div, plotName } of sampleSandboxes) {
+      this.appendPlotBtn(cell, div, plotName, sampleId);
+    }
+  }
+  appendPlotBtn(cell, sandboxDiv, plotName, sampleId) {
+    const text = plotName.length > 25 ? plotName.slice(0, 12) + "..." : plotName;
+    const label = `Scroll to ${plotName}`;
+    cell.append("button").attr("class", "sjpp-sc-table-plot-btn").attr("data-testid", `sjpp-sc-table-${sampleId}-${plotName}-btn`).style("padding", "2px 5px").style("margin-left", "4px").style("font-size", "0.8em").style("border-radius", "20px").style("border", "0.5px solid black").style("cursor", "pointer").text(text).attr("aria-label", label).attr("title", label).attr("tabindex", 0).on("click", () => {
+      sandboxDiv.node().scrollIntoView({ behavior: "smooth", block: "start" });
+    });
+  }
+};
+
+// plots/sc/view/PlotButtons.ts
+var PlotButtons = class {
+  /** This is the initial state. scctTerms and the termdbConfig are created on
+   * server init and will not change. */
+  constructor(interactions, holder, state) {
+    holder.style("padding", "10px");
+    const promptDiv = holder.append("div").style("padding", "10px 0").text("Select data from");
+    this.plotBtnsDom = {
+      promptDiv,
+      selectPrompt: promptDiv.append("span"),
+      btnsDiv: holder.append("div"),
+      tip: new Menu({ padding: "" })
+    };
+    this.interactions = interactions;
+    this.scctTerms = state.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
+    this.scTermdbConfig = state.termdbConfig.queries.singleCell;
+  }
+  update(settings, data) {
+    const item = settings.sc.item;
+    this.plotBtnsDom.promptDiv.style("display", !item ? "none" : "block");
+    if (!item) return;
+    if (data != null && data.plots) this.data = data;
+    this.availablePlots = new Set(this.data?.plots?.map((p) => p.name));
+    this.settings = settings;
+    this.item = item;
+    const name = item.sID;
+    this.plotBtnsDom.selectPrompt.text(` ${name}:`);
+    this.renderChartBtns();
+  }
+  renderChartBtns() {
+    this.plotBtnsDom.btnsDiv.selectAll("*").remove();
+    const btns = this.getChartBtnOpts();
+    this.plotBtnsDom.btnsDiv.selectAll("button").data(btns.filter((b) => b.isVisible())).enter().append("button").attr("type", "button").attr("data-testid", (b) => `sjpp-sc-plot-btn-${b.label.toLowerCase().replace(/\s/g, "-")}`).style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "transparent").style("background-color", "#CFE2F3").style("margin", "0 10px").style("cursor", "pointer").text((b) => b.label).on("click", async (e, plot) => {
+      if (plot.open) {
+        this.plotBtnsDom.tip.clear().showunder(e.target);
+        plot.open(plot, this);
+      } else {
+        if (!plot.getPlotConfig)
+          throw new Error(`No getPlotConfig function defined for this plot button = ${plot.label}`);
+        const config = await plot.getPlotConfig();
+        await this.interactions.createSubplot(config);
+      }
+    });
+  }
+  getChartBtnOpts() {
+    const btns = [];
+    for (const plot of this.scTermdbConfig?.data?.plots || []) {
+      btns.push({
+        label: plot.name,
+        isVisible: () => this.availablePlots.has(plot.name),
+        getPlotConfig: async () => {
+          return await this.getSingleCellConfig(plot.name);
+        }
+      });
+    }
+    btns.push(
+      {
+        label: "Summary",
+        isVisible: () => true,
+        getPlotConfig: () => {
+          const sample = { ...this.item, plots: Array.from(this.availablePlots) };
+          return {
+            chartType: "dictionary",
+            sample,
+            spawnConfig: {
+              parentId: this.interactions.id,
+              hidePlotFilter: true,
+              headerText: `Sample: ${this.item.sID}`,
+              sample
+            },
+            tree: {
+              usecase: {
+                target: "dictionary",
+                specialCase: {
+                  type: "singleCell",
+                  config: { sample }
+                }
+              }
+            }
+          };
+        }
+      },
+      {
+        label: "Gene expression",
+        isVisible: () => this.scTermdbConfig?.geneExpression,
+        getPlotConfig: () => {
+          const sample = this.item;
+          const headerText = `Sample: ${this.item.sID}`;
+          return {
+            chartType: "GeneExpInput",
+            termType: SINGLECELL_GENE_EXPRESSION,
+            headerText,
+            termProperties: { sample },
+            sample,
+            spawnConfig: {
+              parentId: this.interactions.id,
+              hidePlotFilter: true,
+              headerText
+            }
+          };
+        }
+      },
+      {
+        label: "Differential expression",
+        isVisible: () => this.scTermdbConfig?.DEgenes,
+        open: this.termDropdownMenu,
+        getPlotConfig: (value) => {
+          return {
+            chartType: "differentialAnalysis",
+            termType: SINGLECELL_CELLTYPE,
+            categoryName: `${value}`,
+            headerText: `Sample: ${this.item.sID} ${this.scTermdbConfig.DEgenes.termId} ${value}`,
+            termId: this.scTermdbConfig.DEgenes.termId,
+            sample: this.item
+          };
+        }
+      },
+      {
+        label: this.scTermdbConfig?.images?.label || "Image",
+        isVisible: () => this.scTermdbConfig?.images && this.availablePlots.has(this.scTermdbConfig.images.label || "Image"),
+        getPlotConfig: () => {
+          return {
+            chartType: "imagePlot",
+            sample: this.item,
+            imgDir: this.scTermdbConfig?.images,
+            headerText: `Sample: ${this.item.sID}`,
+            settings: { imagePlot: { width: "", height: 400 } }
+          };
+        }
+      }
+    );
+    return btns;
+  }
+  //********** Btn Menus **********/
+  async termDropdownMenu(plot, self) {
+    const _plot = Array.from(self.availablePlots)[0];
+    const options = await self.interactions.getDropDownOptions([_plot]);
+    if (!options?.length) throw new Error("No options found for this plot. Cannot open dropdown menu.");
+    self.plotBtnsDom.tip.clear();
+    const wrapper = self.plotBtnsDom.tip.d.append("div").style("padding", "10px");
+    wrapper.append("div").style("display", "block").style("width", "300px").text(`View differentially expressed genes of a ${self.scTermdbConfig.DEgenes.termId} versus rest of the cells:`);
+    const select = wrapper.append("select").style("margin", "10px 0").style("width", "auto").style("padding", "5px").on("change", async function() {
+      self.plotBtnsDom.tip.hide();
+      const value = select.node().value;
+      if (value.indexOf("Select") == 0) return;
+      const config = plot.getPlotConfig(value);
+      await self.interactions.createSubplot(config);
+    });
+    const regex = new RegExp(self.scTermdbConfig.DEgenes.termId, "gi");
+    options.unshift(`Select a ${self.scTermdbConfig.DEgenes.termId}...`);
+    for (const cluster of options) {
+      select.append("option").attr("value", cluster.replace(regex, "").trim()).text(cluster);
+    }
+  }
+  //********** Plot Config Helpers **********/
+  async getSingleCellConfig(plotName) {
+    if (!this.item) throw new Error("No item selected");
+    const plot = this.scTermdbConfig.data.plots.find((p) => p.name == plotName);
+    if (!plot) throw new Error(`No plot by name ${plotName} in data.plots.`);
+    const sample = this.item;
+    const config = {
+      chartType: "sampleScatter",
+      name: `Sample: ${this.item.sID}`,
+      sample,
+      singleCellPlot: {
+        name: plotName,
+        sample
+      }
+    };
+    if (plot.colorColumns?.[0]) {
+      config.colorTW = await this.makeScctTW(sample, plot);
+    }
+    return config;
+  }
+  // Quick fix. Eventually use the handler to get the proper term from the termdbConfig
+  async makeScctTW(item, plot) {
+    const colorColName = plot.colorColumns[0].name;
+    const savedTerm = this.scctTerms?.find((t) => t.name == colorColName && t.plot == plot.name);
+    if (!savedTerm)
+      throw new Error(
+        `No term found for colorColumn=${colorColName} in .termType2terms.[TermTypeGroups.SINGLECELL_CELLTYPE] for plot ${plot.name}`
+      );
+    const term = Object.assign(structuredClone(savedTerm), {
+      sample: item
+    });
+    const id = await digestMessage(`${plot.name}-${item.sID}-${item.eID}`);
+    return Object.assign({ $id: id }, { term });
+  }
+};
+
+// plots/sc/view/SectionRenderer.ts
+var SectionRenderer = class {
+  constructor(sectionsDiv, groupBy) {
+    this.sections = {};
+    this.holder = sectionsDiv;
+    this.plotId2Key = /* @__PURE__ */ new Map();
+    this.groupBy = groupBy;
+  }
+  /** Send the sc with the updated state. May not be necessary long term. If not,
+   * remove and put in the constructor. */
+  async update(sc, subplots, groupBy) {
+    if (groupBy !== this.groupBy) {
+      this.groupBy = groupBy;
+      this.regroupSections(sc, subplots);
+      return;
+    }
+    const activeSubplots = new Set(subplots.map((s) => s.id));
+    for (const plotId of Object.keys(sc.components.plots)) {
+      if (!activeSubplots.has(plotId)) {
+        this.removeSandbox(plotId, sc);
+      }
+    }
+    for (const subplot of subplots) {
+      const key = this.getKey(subplot);
+      if (!key) continue;
+      if (!this.sections[key]) this.initSection(key, sc);
+      if (!this.sections[key].sandboxes[subplot.id]) {
+        this.plotId2Key.set(subplot.id, key);
+        await this.initSandbox(sc, subplot, key);
+      }
+    }
+    for (const key of Object.keys(this.sections)) {
+      if (Object.keys(this.sections[key].sandboxes).length === 0) {
+        this.removeSection(key, sc);
+      }
+    }
+  }
+  /** Reparent existing sandboxes into new section containers
+   * without destroying/recreating plot components. */
+  regroupSections(sc, subplots) {
+    const detached = /* @__PURE__ */ new Map();
+    for (const [plotId, key] of this.plotId2Key) {
+      const sandboxNode = this.sections[key]?.sandboxes[plotId];
+      if (sandboxNode) {
+        sandboxNode.remove();
+        detached.set(plotId, sandboxNode);
+      }
+    }
+    this.holder.selectAll("*").remove();
+    this.sections = {};
+    this.plotId2Key = /* @__PURE__ */ new Map();
+    const activeSubplots = new Set(subplots.map((s) => s.id));
+    for (const plotId of Object.keys(sc.components.plots)) {
+      if (!activeSubplots.has(plotId)) {
+        sc.removeComponent(plotId);
+        detached.delete(plotId);
+      }
+    }
+    for (const subplot of subplots) {
+      const key = this.getKey(subplot);
+      if (!key) continue;
+      if (!this.sections[key]) this.initSection(key, sc);
+      this.plotId2Key.set(subplot.id, key);
+      const existing = detached.get(subplot.id);
+      if (existing) {
+        this.sections[key].subplots.node().prepend(existing.node());
+        this.sections[key].sandboxes[subplot.id] = existing;
+      }
+    }
+  }
+  getKey(subplot) {
+    if (this.groupBy === "none") return "none";
+    if (this.groupBy === "sample") return this.getSampleId(subplot);
+    return this.getPlotName(subplot);
+  }
+  /** Extract sID from a subplot's config.
+   * Actual subplots store sample as {sID, eID} at top level or on term.term.sample. */
+  getSampleId(subplot) {
+    return subplot.sample?.sID || subplot.singleCellPlot?.sample?.sID || subplot.term?.term?.sample?.sID;
+  }
+  getPlotName(subplot) {
+    let plotName = subplot?.plotName || subplot?.singleCellPlot?.name;
+    if (!plotName) {
+      if (subplot.chartType === "dictionary") plotName = "Summary";
+      else if (subplot.chartType === "summary") plotName = "Summary";
+      else if (subplot.chartType === "GeneExpInput") plotName = "Gene expression";
+      else if (subplot?.term?.term?.plot) plotName = subplot.term.term.plot;
+    }
+    return plotName;
+  }
+  initSection(key, sc) {
+    const item = this.findSampleMetadata(key, sc);
+    const titleAttrText = this.groupBy == "sample" ? "this sample section" : this.groupBy == "plot" ? "this plot section" : "all plots";
+    const sectionWrapper = this.holder.insert("div", ":first-child").style("padding", "10px").attr("data-testid", `sjpp-sc-section-wrapper-${key}`);
+    sectionWrapper.append("span").attr("data-testid", `sjpp-sc-section-remove-btn-${key}`).style("margin", "0px 5px").style("cursor", "pointer").attr("title", `Remove ${titleAttrText}`).html(
+      `<svg xmlns="http://www.w3.org/2000/svg" width="12" height="12" fill="#000" class="bi bi-x-lg" viewBox="0 0 12 12">
+                <path
+                    stroke="#000"
+                    transform="scale(0.75)"
+                    d="M2.146 2.854a.5.5 0 1 1 .708-.708L8 7.293l5.146-5.147a.5.5 0 0 1 .708.708L8.707 8l5.147 5.146a.5.5 0 0 1-.708.708L8 8.707l-5.146 5.147a.5.5 0 0 1-.708-.708L7.293 8 2.146 2.854Z"/>
+                </svg>`
+    ).on("click", () => {
+      this.removeSection(key, sc);
+    });
+    const titleText = this.makeSectionTitleText(key, item);
+    const titleWrapper = sectionWrapper.append("span").style("font-weight", 600).style("opacity", 0.7).text(titleText);
+    if (titleText.length) {
+      const arrow = titleWrapper.append("span").style("font-size", "0.8em").style("padding-left", "3px").attr("title", `Show/hide plots in ${titleAttrText}`).text("\u25BC");
+      titleWrapper.on("click", () => {
+        const isHidden = this.sections[key].subplots.style("display") === "none";
+        this.sections[key].subplots.style("display", isHidden ? "block" : "none");
+        arrow.text(isHidden ? "\u25BC" : "\u25B2");
+      });
+    }
+    this.sections[key] = {
+      sectionWrapper,
+      title: titleWrapper,
+      subplots: sectionWrapper.append("div").attr("data-testid", `sjpp-sc-subplots-${key}`),
+      sandboxes: {}
+    };
+  }
+  /** Look up sample metadata from the fetched items list.
+   * For experiment datasets, matches sID against experiments[].sampleName.
+   * For non-experiment datasets, matches sID against item.sample. */
+  findSampleMetadata(sampleId, sc) {
+    if (!sc.items) return void 0;
+    return sc.items.find((item) => item.sample === sampleId || item.experiments?.some((e) => e.sampleName === sampleId));
+  }
+  makeSectionTitleText(key, item) {
+    if (this.groupBy === "none") return "All plots";
+    if (this.groupBy === "plot") return key;
+    const caseText = item?.sample && item.sample !== key ? `Case: ${item.sample}` : "";
+    const itemText = `Sample: ${key}`;
+    const projectText = item?.["project id"] ? `Project: ${item["project id"]}` : "";
+    return [itemText, caseText, projectText].filter(Boolean).join(" ");
+  }
+  async initSandbox(sc, subplot, key) {
+    const sandboxHolder = this.sections[key].subplots.insert("div", ":first-child").attr("data-testid", `sjpp-sc-sandbox-${subplot.id}`);
+    const sandbox = newSandboxDiv(sandboxHolder, {
+      close: () => {
+        this.removeSandbox(subplot.id, sc);
+        sc.app.dispatch({
+          type: "plot_delete",
+          id: subplot.id,
+          parentId: sc.id
+        });
+      },
+      plotId: subplot.id
+    });
+    const opts = Object.assign({}, subplot, {
+      app: sc.app,
+      parentId: sc.id,
+      id: subplot.id
+    });
+    if (subplot.chartType == "summary") {
+      opts.holder = sandbox;
+    } else {
+      opts.holder = sandbox.body;
+      opts.header = sandbox.header;
+    }
+    await sc.initPlotComponent(subplot.id, opts);
+    this.sections[key].sandboxes[subplot.id] = sandbox.app_div;
+  }
+  removeSection(key, sc) {
+    const subactions = [];
+    for (const plotId of Object.keys(this.sections[key].sandboxes || {})) {
+      this.removeSandbox(plotId, sc, key);
+      subactions.push({
+        type: "plot_delete",
+        id: plotId,
+        parentId: sc.id
+      });
+    }
+    if (subactions.length > 0) {
+      sc.app.dispatch({
+        type: "app_refresh",
+        subactions
+      });
+    }
+    this.sections[key].sectionWrapper.remove();
+    delete this.sections[key];
+  }
+  removeSandbox(plotId, sc, _key) {
+    sc.removeComponent(plotId);
+    const key = _key || this.plotId2Key.get(plotId);
+    if (!key) return;
+    this.sections[key].sandboxes[plotId].remove();
+    delete this.sections[key].sandboxes[plotId];
+    this.plotId2Key.delete(plotId);
+  }
+  /** Derives a map of sampleId → sandbox info for all active subplots.
+   * Used by SampleTableRenderer to render scroll-to buttons. */
+  getSampleSandboxes(subplots) {
+    const sandboxes = /* @__PURE__ */ new Map();
+    for (const subplot of subplots) {
+      const sampleId = this.getSampleId(subplot);
+      const key = this.plotId2Key.get(subplot.id);
+      if (!sampleId || !key) continue;
+      const div = this.sections[key]?.sandboxes[subplot.id];
+      if (!div) continue;
+      const plotName = this.getPlotName(subplot) || subplot.id;
+      if (!sandboxes.has(sampleId)) sandboxes.set(sampleId, []);
+      sandboxes.get(sampleId).push({ plotId: subplot.id, div, plotName });
+    }
+    return sandboxes;
+  }
+};
+
+// plots/sc/settings/Settings.ts
+var GroupByOptions = ["none", "sample", "plot"];
+
+// plots/sc/view/SCViewRenderer.ts
+var SCViewRenderer = class _SCViewRenderer {
+  static {
+    //On load, show table
+    //Eventually maybe an app dispatch and not a flag
+    this.inUse = true;
+  }
+  constructor(sc, state) {
+    this.sc = sc;
+    this.dom = sc.dom;
+    this.interactions = sc.interactions;
+    this.plotBtns = new PlotButtons(this.interactions, this.dom.plotsBtnsDiv, state);
+    this.sectionRenderer = new SectionRenderer(this.dom.sectionsDiv, state.config.settings.sc.groupBy);
+  }
+  render(tableData, settings) {
+    this.renderSelectBtn();
+    this.renderGroupByOptions(settings);
+    this.sampleTableRenderer = new SampleTableRenderer(this.dom, this.interactions, tableData);
+    this.dom.plotsBtnsDiv.style("display", "none");
+  }
+  /** Renders the select btn at the top of the page that
+   * show/hides the item table and plot buttons */
+  renderSelectBtn() {
+    this.dom.controlsDiv.style("padding", "10px");
+    const btn = this.dom.controlsDiv.append("button").attr("data-testid", "sjpp-sc-item-table-select-btn").attr("title", "Show/hide sample table and plot buttons").style("border-radius", "20px").style("padding", "5px 10px").style("background-color", "transparent").text("Select sample and plots");
+    const arrowSpan = btn.append("span").style("font-size", "0.8em").style("padding-left", "3px").text("\u25BC");
+    btn.on("click", () => {
+      _SCViewRenderer.inUse = !_SCViewRenderer.inUse;
+      arrowSpan.text(_SCViewRenderer.inUse ? "\u25BC" : "\u25B2");
+      this.dom.tableDiv.style("display", _SCViewRenderer.inUse ? "block" : "none");
+      this.dom.plotsBtnsDiv.style("display", _SCViewRenderer.inUse ? "block" : "none");
+    });
+  }
+  renderGroupByOptions(settings) {
+    this.dom.controlsDiv.append("span").style("padding", "3px 0px 3px 20px").style("opacity", 0.7).text("Group plots by:");
+    const optionsDiv = this.dom.controlsDiv.append("span").style("display", "inline-block");
+    const options = GroupByOptions.map((option) => {
+      return {
+        label: `${option.charAt(0).toUpperCase() + option.slice(1)}`,
+        value: option,
+        checked: settings.groupBy === option
+      };
+    });
+    make_radios({
+      holder: optionsDiv,
+      styles: { display: "inline-block" },
+      options,
+      callback: async (value) => {
+        await this.sc.app.dispatch({
+          type: "plot_edit",
+          id: this.sc.id,
+          config: { settings: { sc: { ...settings, groupBy: value } } }
+        });
+      }
+    });
+  }
+  async update(settings, data, subplots) {
+    this.plotBtns.update(settings, data);
+    await this.sectionRenderer.update(this.sc, subplots, settings.sc.groupBy);
+    if (!settings.sc.item?.sID) return;
+    const sandboxes = this.sectionRenderer.getSampleSandboxes(subplots);
+    this.sampleTableRenderer.updateTable(settings.sc.item.sID, sandboxes);
+  }
+};
+
+// plots/sc/settings/defaults.ts
+function getDefaultSCAppSettings(overrides = {}, app) {
+  const defaults = {
+    sc: {
+      columns: {
+        // TODO: Implement ds specific column name
+        sample: "Sample"
+      },
+      item: void 0,
+      groupBy: "sample"
+    },
+    hierCluster: {
+      unit: getGEunit(app.vocabApi),
+      yDendrogramHeight: 0,
+      clusterSamples: false
+    }
+  };
+  return Object.assign(defaults, overrides);
+}
+
+// plots/sc/SC.ts
+var SCViewer = class _SCViewer extends PlotBase {
+  static {
+    this.type = "sc";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _SCViewer.type;
+    this.components = {
+      plots: {}
+    };
+    const div = opts.holder.classed("sjpp-sc-main", true).append("div").style("padding", "5px").style("display", "inline-block").style("vertical-align", "top");
+    this.dom = {
+      div,
+      loading: opts.holder.append("div").attr("class", "sjpp-sc-main-loading").attr("data-testid", "sjpp-sc-main-loading").style("position", "absolute").style("top", "0").style("left", "0").style("width", "100%").style("height", "100%").style("background-color", "rgba(255, 255, 255, 0.95)").style("text-align", "center"),
+      controlsDiv: div.append("div").attr("id", "sjpp-sc-controls-btn"),
+      tableDiv: div.append("div").attr("id", "sjpp-sc-item-table"),
+      plotsBtnsDiv: div.append("div").attr("id", "sjpp-sc-plot-buttons").style("display", "none"),
+      sectionsDiv: div.append("div").attr("id", "sjpp-sc-sections")
+    };
+    if (opts.header) opts.header.html(`SINGLE CELL`).style("font-size", "0.9em");
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw new Error(
+        `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
+      );
+    }
+    return {
+      config,
+      subplots: appState.plots.filter((p) => p.parentId === this.id),
+      termfilter: appState.termfilter,
+      termdbConfig: appState.termdbConfig,
+      vocab: appState.vocab
+    };
+  }
+  async init(appState) {
+    const state = this.getState(appState);
+    const dsScSamples = state.termdbConfig.queries?.singleCell?.samples;
+    this.model = new SCModel(this.app, this.id);
+    try {
+      const response = await this.model.getSampleData();
+      if (response.error || !response.samples || !response.samples.length) {
+        this.app.printError("No samples found for this dataset");
+        return;
+      }
+      this.items = response.samples;
+      this.itemColumns = await this.model.getColumnLabels(dsScSamples);
+    } catch (e) {
+      if (e instanceof Error) console.error(`${e.message || e} [SC init()]`);
+      else if (e.stack) console.log(e.stack);
+      throw new Error(e.message || e);
+    }
+    this.interactions = new SCInteractions(this);
+    this.viewModel = new SCViewModel(this.app, state.config, this.items, this.itemColumns);
+    this.view = new SCViewRenderer(this, state);
+    this.view.render(this.viewModel.tableData, state.config.settings.sc);
+  }
+  async main() {
+    const state = structuredClone(this.state);
+    const config = state.config;
+    if (!this.model) throw new Error(`Model not initialized`);
+    if (!this.viewModel) throw new Error(`ViewModel not initialized`);
+    if (!this.view) throw new Error(`View not initialized`);
+    if (!this.interactions) throw new Error(`Interactions not initialized`);
+    this.interactions.toggleLoading(true);
+    let data = null;
+    if (config.settings.sc.item) {
+      try {
+        data = await this.model.getData();
+        if (data.error || !data.plots || !data.plots.length) {
+          this.interactions.toggleLoading(false);
+          this.app.printError(data.error);
+          return;
+        }
+      } catch (e) {
+        this.interactions.toggleLoading(false);
+        if (e instanceof Error) console.error(`${e.message || e} [SC main()]`);
+        else if (e.stack) console.log(e.stack);
+        throw new Error(e.message || e);
+      }
+    }
+    await this.view.update(config.settings, data, state.subplots);
+    this.interactions.toggleLoading(false);
+  }
+  async initPlotComponent(subplotId, opts) {
+    const { componentInit: componentInit2 } = await importPlot(opts.chartType);
+    this.components.plots[subplotId] = await componentInit2(opts);
+  }
+  removeComponent(subplotId) {
+    this.components.plots[subplotId].destroy();
+    delete this.components.plots[subplotId];
+  }
+};
+var SCInit = getCompInit(SCViewer);
+var componentInit = SCInit;
+function getPlotConfig(opts, app) {
+  const config = {
+    chartType: "sc",
+    hidePlotFilter: true,
+    settings: getDefaultSCAppSettings(opts.overrides, app)
+  };
+  return copyMerge(config, opts);
+}
+export {
+  SCInit,
+  SCViewer,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=SC-M6RGALZM.js.map