@sjcrh/proteinpaint-client 2.205.0 → 2.206.0

package/dist/stattable-RLMYQ4G6.js

@@ -0,0 +1,117 @@
+import {
+  PlotBase
+} from "./chunk-Q5SK3U2T.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-54KC7DAB.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-RPDVFM7E.js";
+import "./chunk-M4XXKTH2.js";
+import "./chunk-5ILEFNXJ.js";
+import "./chunk-IZUYLFOX.js";
+import {
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/stattable.js
+var TdbStatTable = class _TdbStatTable extends PlotBase {
+  static type = "stattable";
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _TdbStatTable.type;
+  }
+  async init() {
+    this.dom = {
+      div: this.opts.holder.append("div").style("margin", "10px")
+    };
+    setRenderers(this);
+  }
+  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)?`;
+    }
+    return {
+      activeCohort: appState.activeCohort,
+      termfilter: appState.termfilter,
+      config: {
+        term: config.term,
+        term0: config.term0,
+        term2: config.term2,
+        settings: {
+          common: config.settings.common,
+          barchart: config.settings.barchart
+        }
+      },
+      filter: appState.termfilter.filter
+    };
+  }
+  async main() {
+    try {
+      this.config = structuredClone(this.state.config);
+      if (this.state.isVisible) {
+        const reqOpts = this.getDataRequestOpts();
+        const data = await this.vocabApi.getNestedChartSeriesData(reqOpts);
+        this.app.vocabApi.syncTermData(this.state.config, data);
+      }
+      if (!this.state.isVisible || !this.data || !this.data.boxplot) {
+        this.dom.div.style("display", "none");
+        return;
+      }
+      this.render(this.data);
+    } catch (e) {
+      throw e;
+    }
+  }
+  // creates an opts object for the vocabApi.getNestedChartsData()
+  getDataRequestOpts() {
+    const c = this.config;
+    const opts = { term: c.term, filter: this.state.termfilter.filter };
+    if (c.term2) opts.term2 = c.term2;
+    if (c.term0) opts.term0 = c.term0;
+    if (this.state.ssid) opts.ssid = this.state.ssid;
+    return opts;
+  }
+};
+function setRenderers(self) {
+  self.render = function(data) {
+    self.dom.div.style("display", "block").selectAll("*").remove();
+    let exposed_data = "";
+    const sd = data.boxplot.sd ? " (" + data.boxplot.sd.toFixed(2) + ") " : "";
+    let rows = "";
+    if (Number.isFinite(data.boxplot.min)) {
+      rows += "<tr><td>Minimum</td><td>" + data.boxplot.min.toFixed(2) + "</td></tr>";
+    }
+    if (Number.isFinite(data.boxplot.max)) {
+      rows += "<tr><td>Maximum</td><td>" + data.boxplot.max.toFixed(2) + "</td></tr>";
+    }
+    rows += "<tr><td>Mean (SD)</td><td>" + data.boxplot.mean.toFixed(2) + sd + "</td></tr>";
+    if ("p50" in data.boxplot) {
+      rows += "<tr><td>Median (IQR)</td><td>" + data.boxplot.p50.toFixed(2) + " (" + data.boxplot.iqr.toFixed(2) + ") </td></tr><tr><td>5th Percentile</td><td>" + data.boxplot.p05.toFixed(2) + "</td></tr><tr><td>25th Percentile</td><td>" + data.boxplot.p25.toFixed(2) + "</td></tr><tr><td>75th Percentile</td><td>" + data.boxplot.p75.toFixed(2) + "</td></tr><tr><td>95th Percentile</td><td>" + data.boxplot.p95.toFixed(2) + "</td></tr>";
+    }
+    self.dom.div.html("<table><tr><th></th><th>Value</th></tr>" + exposed_data + rows + "</table>");
+    self.dom.div.selectAll("td, th, table").style("border", "1px solid black").style("padding", "0").style("border-collapse", "collapse");
+    self.dom.div.selectAll("th, td").style("padding", "2px 10px");
+  };
+}
+var statTableInit = getCompInit(TdbStatTable);
+export {
+  statTableInit
+};
+//# sourceMappingURL=stattable-RLMYQ4G6.js.map

package/dist/studyCatalog-DKB3U7EV.js

@@ -0,0 +1,414 @@
+import {
+  orderBy
+} from "./chunk-RFW5BRIZ.js";
+import "./chunk-ILEXRHF7.js";
+import {
+  PlotBase,
+  addGeneSearchbox,
+  renderTable
+} from "./chunk-Q5SK3U2T.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-54KC7DAB.js";
+import "./chunk-N7DVQTPC.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-RPDVFM7E.js";
+import "./chunk-M4XXKTH2.js";
+import "./chunk-5ILEFNXJ.js";
+import "./chunk-IZUYLFOX.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/studyCatalog.ts
+var DATA_TYPE_FACET = "dataType";
+var DATA_TYPE_CHILD = "proteome";
+var DATA_TYPE_LABEL = "Data type";
+var DATA_TYPE_ORDER = ["Protein", "PTM"];
+function proteomeOrder(organisms) {
+  const out = [];
+  for (const org of Object.values(organisms || {})) {
+    for (const assay in org?.assays || {}) {
+      const label = org.assays[assay].proteomeLabel || assay;
+      if (!out.includes(label)) out.push(label);
+    }
+  }
+  return out;
+}
+var FACET_CHART = {
+  disease: {
+    chartType: "animatedBubbleChart",
+    label: "Bubble Chart",
+    needsGene: false,
+    requires: (q) => !!q?.geneRanking
+  },
+  cellType: {
+    chartType: "cellTypeBubbleHeatmap",
+    label: "Cell-type Bubble Heatmap",
+    needsGene: true,
+    requires: (q) => !!q?.proteome?.cellTypeBubbleHeatmap
+  },
+  brainRegion: {
+    chartType: "brainRegions",
+    label: "Brain Regional Proteome",
+    needsGene: true,
+    requires: (q) => !!q?.proteome?.brainRegions
+  }
+};
+var defaultConfig = {
+  chartType: "studyCatalog"
+};
+var PANEL_GAP = 24;
+var FACET_WIDTH = 210;
+var StudyCatalog = class _StudyCatalog extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    /** active filter values per facet key; empty set (or absent) = no filter on that facet */
+    this.activeFilters = /* @__PURE__ */ new Map();
+    /** derived rows, one per cohort */
+    this.rows = [];
+    /** currently checked rows */
+    this.selected = [];
+    /** stable keys of the checked cohorts, so selection survives a table re-render */
+    this.selectedKeys = /* @__PURE__ */ new Set();
+    /** number of cohorts currently passing the filters (shown when nothing is selected) */
+    this.filteredCount = 0;
+    this.type = _StudyCatalog.type;
+  }
+  static {
+    this.type = "studyCatalog";
+  }
+  async init() {
+    const holder = this.opts.holder.append("div").style("padding", "10px");
+    const body = holder.append("div");
+    this.dom = {
+      holder,
+      body,
+      facetsDiv: void 0,
+      rightDiv: void 0,
+      actionBtn: void 0,
+      countSpan: void 0,
+      tableDiv: void 0,
+      tip: new Menu({ padding: "" }),
+      header: this.opts.header
+    };
+    if (this.dom.header) this.dom.header.html("Studies");
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw `No plot with id='${this.id}' found`;
+    return { config };
+  }
+  async main() {
+    const proteome = this.app.vocabApi.termdbConfig?.queries?.proteome;
+    const ui = proteome?.studyCatalog;
+    this.dom.body.selectAll("*").remove();
+    if (!ui || !proteome?.organisms) {
+      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text("No study catalog is configured.");
+      return;
+    }
+    this.rows = this.deriveRows(proteome.organisms);
+    if (!this.rows.length) {
+      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text("No cohorts found.");
+      return;
+    }
+    const topBar = this.dom.body.append("div").style("display", "flex").style("align-items", "center").style("gap", "12px").style("margin-bottom", "8px").style("padding-left", `${FACET_WIDTH + PANEL_GAP}px`);
+    this.dom.actionBtn = topBar.append("button").property("disabled", true).text("Analyze Cohort").on("click", () => this.onAction());
+    this.dom.countSpan = topBar.append("span").style("font-size", "0.85em").style("color", "#555");
+    const layout = this.dom.body.append("div").style("display", "flex").style("gap", `${PANEL_GAP}px`);
+    this.dom.facetsDiv = layout.append("div").style("flex", `0 0 ${FACET_WIDTH}px`).style("box-sizing", "border-box").style("max-height", "60vh").style("overflow-y", "auto").style("border-right", "1px solid #eee").style("padding-right", "12px");
+    this.dom.rightDiv = layout.append("div").style("flex", "1 1 auto").style("min-width", "0");
+    this.dom.tableDiv = this.dom.rightDiv.append("div");
+    this.renderFacets(ui);
+    this.renderTable(ui);
+  }
+  /** one row per organism→assay→cohort. `species` and `proteome` are derived from the query
+   *  structure (organism key + the assay's proteomeLabel); every other display field comes from
+   *  the cohort's `catalog` object in the dataset. A `catalog` key can still override either. */
+  deriveRows(organisms) {
+    const rows = [];
+    for (const organism in organisms) {
+      const species = organism.charAt(0).toUpperCase() + organism.slice(1);
+      const assays = organisms[organism].assays || {};
+      for (const assay in assays) {
+        const proteome = assays[assay].proteomeLabel || assay;
+        const cohorts = assays[assay].cohorts || {};
+        for (const cohort in cohorts) {
+          const dataType = assays[assay].PTMType ? "PTM" : "Protein";
+          rows.push({
+            species,
+            proteome,
+            dataType,
+            ...cohorts[cohort].catalog || {},
+            organism,
+            assay,
+            cohort
+          });
+        }
+      }
+    }
+    return rows;
+  }
+  /** rows passing every active filter, optionally excluding one facet (for that facet's own counts) */
+  filteredRows(excludeFacet) {
+    const excluded = new Set(Array.isArray(excludeFacet) ? excludeFacet : excludeFacet ? [excludeFacet] : []);
+    return this.rows.filter((row) => {
+      for (const [facet, values] of this.activeFilters) {
+        if (excluded.has(facet)) continue;
+        if (values.size === 0) continue;
+        if (!values.has(row[facet] || "")) return false;
+      }
+      return true;
+    });
+  }
+  facetLabel(ui, key) {
+    if (key === DATA_TYPE_FACET) return DATA_TYPE_LABEL;
+    return ui.columns.find((c) => c.key === key)?.label || key;
+  }
+  /** facet order to render: the proteome facet is replaced by its Data type parent,
+   *  which renders the proteome values nested under the active radio option */
+  effectiveFacets(ui) {
+    return ui.facets.map((f) => f === DATA_TYPE_CHILD ? DATA_TYPE_FACET : f);
+  }
+  sortValues(facet, values) {
+    const fixed = facet === DATA_TYPE_FACET ? DATA_TYPE_ORDER : facet === DATA_TYPE_CHILD ? proteomeOrder(this.app.vocabApi.termdbConfig?.queries?.proteome?.organisms) : null;
+    if (fixed)
+      return orderBy(
+        [...values].sort((a, b) => a.localeCompare(b)),
+        fixed
+      );
+    return [...values].sort((a, b) => a.localeCompare(b, void 0, { numeric: true }));
+  }
+  /** filters to ignore when computing a facet's own value counts: itself, plus — for the
+   *  Data type parent — its nested proteome filter, so that ticking e.g. "Insoluble" under
+   *  Protein never makes the PTM option disappear (it must stay clickable to switch class) */
+  facetScopeExclusions(facet) {
+    return facet === DATA_TYPE_FACET ? [DATA_TYPE_FACET, DATA_TYPE_CHILD] : [facet];
+  }
+  /** counts of one facet's values under all OTHER active filters (standard faceted behavior) */
+  facetCounts(facet) {
+    const counts = /* @__PURE__ */ new Map();
+    for (const row of this.filteredRows(this.facetScopeExclusions(facet))) {
+      const v = row[facet] || "";
+      if (!v) continue;
+      counts.set(v, (counts.get(v) || 0) + 1);
+    }
+    return counts;
+  }
+  /** one radio/checkbox line of a facet */
+  appendFacetOption(ui, group, facet, value, count, single, checked, indentPx = 0) {
+    const line = group.append("label").style("display", "flex").style("align-items", "center").style("gap", "6px").style("font-size", "0.85em").style("cursor", "pointer").style("padding", "1px 0").style("margin-left", indentPx ? `${indentPx}px` : null);
+    line.append("input").attr("type", single ? "radio" : "checkbox").attr("name", single ? `sjpp-studyCatalog-facet-${this.id}-${facet}` : null).property("checked", checked).on("change", (event) => {
+      if (single) {
+        this.activeFilters.set(facet, /* @__PURE__ */ new Set([value]));
+        if (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD);
+      } else {
+        const set = this.activeFilters.get(facet) || /* @__PURE__ */ new Set();
+        if (event.target.checked) set.add(value);
+        else set.delete(value);
+        if (set.size) this.activeFilters.set(facet, set);
+        else this.activeFilters.delete(facet);
+      }
+      this.renderFacets(ui);
+      this.renderTable(ui);
+    });
+    line.append("span").style("flex", "1 1 auto").text(value);
+    line.append("span").style("color", "#999").text(count);
+  }
+  renderFacets(ui) {
+    const div = this.dom.facetsDiv;
+    div.selectAll("*").remove();
+    const queries = this.app.vocabApi.termdbConfig?.queries;
+    const facets = this.effectiveFacets(ui);
+    const singleSelect = new Set(ui.singleSelectFacets || []);
+    if (facets.includes(DATA_TYPE_FACET)) singleSelect.add(DATA_TYPE_FACET);
+    for (const facet of singleSelect) {
+      if (!facets.includes(facet)) continue;
+      const scope = this.filteredRows(this.facetScopeExclusions(facet));
+      const values = this.sortValues(facet, [...new Set(scope.map((r) => r[facet]).filter(Boolean))]);
+      if (!values.length) {
+        this.activeFilters.delete(facet);
+        if (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD);
+        continue;
+      }
+      const active = this.activeFilters.get(facet);
+      const activeValue = active && active.size === 1 ? [...active][0] : null;
+      if (activeValue && values.includes(activeValue)) continue;
+      this.activeFilters.set(facet, /* @__PURE__ */ new Set([values[0]]));
+      if (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD);
+    }
+    const header = div.append("div").style("display", "flex").style("align-items", "center").style("margin-bottom", "8px");
+    header.append("span").style("font-weight", "bold").text("Filter by");
+    const anyActive = [...this.activeFilters.entries()].some(([f, s]) => !singleSelect.has(f) && s.size > 0);
+    header.append("span").style("margin-left", "auto").style("font-size", "0.8em").style("color", anyActive ? "#0a5" : "#aaa").style("cursor", anyActive ? "pointer" : "default").text("clear all").on("click", () => {
+      if (!anyActive) return;
+      this.activeFilters.clear();
+      this.renderFacets(ui);
+      this.renderTable(ui);
+    });
+    for (const facet of facets) {
+      const counts = this.facetCounts(facet);
+      if (counts.size === 0) continue;
+      const group = div.append("div").style("margin-bottom", "12px");
+      const titleRow = group.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px").style("margin-bottom", "4px");
+      titleRow.append("span").style("font-weight", "600").style("font-size", "0.9em").text(this.facetLabel(ui, facet));
+      const chart = FACET_CHART[facet];
+      if (chart && chart.requires(queries)) {
+        titleRow.append("button").attr("class", "sja_menuoption sja_sharp_border").style("font-size", "0.72em").style("padding", "1px 5px").style("cursor", "pointer").attr("title", `Open ${chart.label}`).text("\u{1F4CA}").on("click", (event) => this.openChartMenu(chart, event));
+      }
+      const single = singleSelect.has(facet);
+      const active = this.activeFilters.get(facet) || /* @__PURE__ */ new Set();
+      for (const value of this.sortValues(facet, [...counts.keys()])) {
+        this.appendFacetOption(ui, group, facet, value, counts.get(value), single, active.has(value));
+        if (facet === DATA_TYPE_FACET && active.has(value)) {
+          const childCounts = this.facetCounts(DATA_TYPE_CHILD);
+          const childActive = this.activeFilters.get(DATA_TYPE_CHILD) || /* @__PURE__ */ new Set();
+          for (const cv of this.sortValues(DATA_TYPE_CHILD, [...childCounts.keys()])) {
+            this.appendFacetOption(ui, group, DATA_TYPE_CHILD, cv, childCounts.get(cv), false, childActive.has(cv), 22);
+          }
+        }
+      }
+    }
+  }
+  renderTable(ui) {
+    const rows = this.filteredRows();
+    this.filteredCount = rows.length;
+    this.dom.tableDiv.selectAll("*").remove();
+    this.dom.tableDiv.style("font-size", "13px");
+    const selectedRows = [];
+    rows.forEach((r, i) => {
+      if (this.selectedKeys.has(this.cohortKey(r))) selectedRows.push(i);
+    });
+    this.selected = selectedRows.map((i) => rows[i]);
+    this.selectedKeys = new Set(this.selected.map((r) => this.cohortKey(r)));
+    this.updateActionBtn();
+    const singleSelect = new Set(ui.singleSelectFacets || []);
+    const visibleColumns = rows.length ? ui.columns.filter((c) => !singleSelect.has(c.key) && rows.some((row) => row[c.key] != null && row[c.key] !== "")) : ui.columns;
+    const columns = visibleColumns.map((c) => ({ label: c.label, sortable: true }));
+    const tableRows = rows.map(
+      (row) => visibleColumns.map((c) => {
+        const value = row[c.key] ?? "";
+        return c.urlBase && value ? { value, url: c.urlBase + value } : { value };
+      })
+    );
+    renderTable({
+      columns,
+      rows: tableRows,
+      div: this.dom.tableDiv,
+      showLines: true,
+      striped: true,
+      maxHeight: "60vh",
+      maxWidth: "72vw",
+      resize: true,
+      selectedRows,
+      header: { allowSort: true, style: { "font-weight": "bold", color: "#000" } },
+      buttons: [
+        {
+          text: "select",
+          callback: () => {
+          },
+          onChange: (idxs, button) => {
+            button.style.display = "none";
+            this.selected = idxs.map((i) => rows[i]);
+            this.selectedKeys = new Set(this.selected.map((r) => this.cohortKey(r)));
+            this.updateActionBtn();
+          }
+        }
+      ]
+    });
+  }
+  /** stable identity of a cohort row, used to keep the selection across re-renders */
+  cohortKey(row) {
+    return `${row.organism}|${row.assay}|${row.cohort}`;
+  }
+  /** update the action button + count text from the current selection.
+   *  count: nothing selected → total filtered cohorts; 1 selected → hidden; ≥2 → selected count */
+  updateActionBtn() {
+    const btn = this.dom.actionBtn;
+    if (!btn) return;
+    const n = this.selected.length;
+    btn.property("disabled", n === 0).text(n >= 2 ? "Compare cohorts" : "Analyze Cohort");
+    const cs = this.dom.countSpan;
+    if (n === 1) cs.style("display", "none");
+    else if (n >= 2) cs.style("display", "").text(`${n} cohorts`);
+    else cs.style("display", "").text(`${this.filteredCount} cohort${this.filteredCount === 1 ? "" : "s"}`);
+  }
+  /** run the action for the current selection: 1 cohort → Analyze; ≥2 → Compare */
+  onAction() {
+    const sel = this.selected;
+    if (sel.length === 1) this.openAnalyticsTools(sel[0]);
+    else if (sel.length >= 2) this.openCompare(sel);
+  }
+  /** launch a facet's chart. Charts that don't need a gene open directly; gene-centric ones
+   *  prompt for a gene first. Dispatches exactly chart.chartType (no importPlot indirection). */
+  openChartMenu(chart, event) {
+    if (!chart.needsGene) {
+      this.app.dispatch({ type: "plot_create", config: { chartType: chart.chartType } });
+      return;
+    }
+    this.dom.tip.clear().show(event.clientX, event.clientY);
+    const row = this.dom.tip.d.append("div").style("padding", "5px");
+    row.append("span").style("font-weight", "bold").text("Enter a gene name:");
+    const geneSearch = addGeneSearchbox({
+      row,
+      genome: this.app.opts.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: () => {
+        if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
+        this.dom.tip.hide();
+        this.app.dispatch({ type: "plot_create", config: { chartType: chart.chartType, gene: geneSearch.geneSymbol } });
+      }
+    });
+  }
+  /** open the ProteomeInput "Analytics Tools" panel for a cohort, mirroring the
+   *  Sample Selection (proteomeAbundance) chart's "Analytics Tools" button */
+  openAnalyticsTools(row) {
+    this.app.dispatch({
+      type: "plot_create",
+      config: {
+        chartType: "ProteomeInput",
+        proteomeDetails: { organism: row.organism, assay: row.assay, cohort: row.cohort },
+        hidePlotFilter: true
+      }
+    });
+  }
+  /** open the cross-cohort log2FC-z comparison for the selected cohorts */
+  openCompare(selected) {
+    this.app.dispatch({
+      type: "plot_create",
+      config: {
+        chartType: "proteomeCohortCompare",
+        cohorts: selected.map((r) => ({ organism: r.organism, assay: r.assay, cohort: r.cohort, label: r.cohort }))
+      }
+    });
+  }
+};
+var componentInit = getCompInit(StudyCatalog);
+async function getPlotConfig(opts) {
+  const config = structuredClone(defaultConfig);
+  return copyMerge(config, opts);
+}
+export {
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=studyCatalog-DKB3U7EV.js.map

package/dist/studyCatalog-DKB3U7EV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/studyCatalog.ts"],
+  "sourcesContent": ["import type { MassState, BasePlotConfig } from '#mass/types/mass'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport { PlotBase } from './PlotBase'\nimport { Menu, renderTable, addGeneSearchbox } from '#dom'\nimport type { TableColumn, TableRow } from '#dom'\nimport { orderBy } from './proteinView.tiles'\n\n/** The Proteome facet is nested under a derived single-select \"Data type\" facet\n *  (Protein \u2192 protein-level assays; PTM \u2192 assays marked PTMType in the dataset config).\n *  PTM layers are kept separate from protein-level layers because PTM z is site-level\n *  collapsed to gene, so the two aren't directly comparable in a scatter/heatmap: the\n *  radio keeps them apart structurally and the Proteome checkboxes only ever list the\n *  active class \u2014 no rows need to be greyed out after the fact. Proteome values sort\n *  in the order their assays appear in the dataset config. */\nconst DATA_TYPE_FACET = 'dataType'\nconst DATA_TYPE_CHILD = 'proteome'\nconst DATA_TYPE_LABEL = 'Data type'\nconst DATA_TYPE_ORDER = ['Protein', 'PTM']\n\n/** proteome labels in dataset order (first appearance across organisms/assays) */\nfunction proteomeOrder(organisms: any): string[] {\n\tconst out: string[] = []\n\tfor (const org of Object.values(organisms || {}) as any[]) {\n\t\tfor (const assay in org?.assays || {}) {\n\t\t\tconst label = org.assays[assay].proteomeLabel || assay\n\t\t\tif (!out.includes(label)) out.push(label)\n\t\t}\n\t}\n\treturn out\n}\n\n/** facets that get a \"launch chart\" button. needsGene=false charts launch directly (no gene\n *  picker); gene-centric charts prompt for a gene first. `requires(queries)` gates the button on\n *  the dataset config that chart needs, so it only shows where the chart can actually run. */\nconst FACET_CHART: Record<\n\tstring,\n\t{ chartType: string; label: string; needsGene: boolean; requires: (q: any) => boolean }\n> = {\n\tdisease: {\n\t\tchartType: 'animatedBubbleChart',\n\t\tlabel: 'Bubble Chart',\n\t\tneedsGene: false,\n\t\trequires: q => !!q?.geneRanking\n\t},\n\tcellType: {\n\t\tchartType: 'cellTypeBubbleHeatmap',\n\t\tlabel: 'Cell-type Bubble Heatmap',\n\t\tneedsGene: true,\n\t\trequires: q => !!q?.proteome?.cellTypeBubbleHeatmap\n\t},\n\tbrainRegion: {\n\t\tchartType: 'brainRegions',\n\t\tlabel: 'Brain Regional Proteome',\n\t\tneedsGene: true,\n\t\trequires: q => !!q?.proteome?.brainRegions\n\t}\n}\n\nconst defaultConfig = {\n\tchartType: 'studyCatalog'\n}\n\n/** urlBase renders the cell as a link to urlBase+value (e.g. a PubMed ID column) */\ntype CatalogColumn = { key: string; label: string; urlBase?: string }\ntype CatalogUiConfig = {\n\tcolumns: CatalogColumn[]\n\tfacets: string[]\n\t/** facets rendered as radio buttons instead of checkboxes: exactly one value is active at\n\t *  all times (defaults to the first value), so rows of different values never mix in the table */\n\tsingleSelectFacets?: string[]\n}\ntype CatalogRow = { [key: string]: string } & { organism: string; assay: string; cohort: string }\n\nconst PANEL_GAP = 24\nconst FACET_WIDTH = 210\n\nclass StudyCatalog extends PlotBase implements RxComponent {\n\tstatic type = 'studyCatalog'\n\ttype: string\n\tdom!: {\n\t\tholder: any\n\t\tbody: any\n\t\tfacetsDiv: any\n\t\trightDiv: any\n\t\tactionBtn: any\n\t\tcountSpan: any\n\t\ttableDiv: any\n\t\ttip: Menu\n\t\theader?: any\n\t}\n\t/** active filter values per facet key; empty set (or absent) = no filter on that facet */\n\tactiveFilters: Map<string, Set<string>> = new Map()\n\t/** derived rows, one per cohort */\n\trows: CatalogRow[] = []\n\t/** currently checked rows */\n\tselected: CatalogRow[] = []\n\t/** stable keys of the checked cohorts, so selection survives a table re-render */\n\tselectedKeys: Set<string> = new Set()\n\t/** number of cohorts currently passing the filters (shown when nothing is selected) */\n\tfilteredCount = 0\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = StudyCatalog.type\n\t}\n\n\tasync init() {\n\t\tconst holder = this.opts.holder.append('div').style('padding', '10px')\n\t\tconst body = holder.append('div')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tbody,\n\t\t\tfacetsDiv: undefined,\n\t\t\trightDiv: undefined,\n\t\t\tactionBtn: undefined,\n\t\t\tcountSpan: undefined,\n\t\t\ttableDiv: undefined,\n\t\t\ttip: new Menu({ padding: '' }),\n\t\t\theader: this.opts.header\n\t\t}\n\t\tif (this.dom.header) this.dom.header.html('Studies')\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config: any = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn { config }\n\t}\n\n\tasync main() {\n\t\tconst proteome = this.app.vocabApi.termdbConfig?.queries?.proteome\n\t\tconst ui: CatalogUiConfig | undefined = proteome?.studyCatalog\n\t\tthis.dom.body.selectAll('*').remove()\n\t\tif (!ui || !proteome?.organisms) {\n\t\t\tthis.dom.body\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '20px')\n\t\t\t\t.style('color', '#666')\n\t\t\t\t.text('No study catalog is configured.')\n\t\t\treturn\n\t\t}\n\n\t\tthis.rows = this.deriveRows(proteome.organisms)\n\t\tif (!this.rows.length) {\n\t\t\tthis.dom.body.append('div').style('padding', '20px').style('color', '#666').text('No cohorts found.')\n\t\t\treturn\n\t\t}\n\n\t\t// top bar (above facets + table): action button + count, indented so they line up with\n\t\t// the table's left edge (its line-number column), not with the filter rail\n\t\tconst topBar = this.dom.body\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '12px')\n\t\t\t.style('margin-bottom', '8px')\n\t\t\t.style('padding-left', `${FACET_WIDTH + PANEL_GAP}px`)\n\t\tthis.dom.actionBtn = topBar\n\t\t\t.append('button')\n\t\t\t.property('disabled', true)\n\t\t\t.text('Analyze Cohort')\n\t\t\t.on('click', () => this.onAction())\n\t\tthis.dom.countSpan = topBar.append('span').style('font-size', '0.85em').style('color', '#555')\n\n\t\tconst layout = this.dom.body.append('div').style('display', 'flex').style('gap', `${PANEL_GAP}px`)\n\n\t\t// left rail \u2014 filters; border-box so its total width is exactly FACET_WIDTH (keeps the\n\t\t// button/table alignment above), capped to the table's height so the two line up\n\t\tthis.dom.facetsDiv = layout\n\t\t\t.append('div')\n\t\t\t.style('flex', `0 0 ${FACET_WIDTH}px`)\n\t\t\t.style('box-sizing', 'border-box')\n\t\t\t.style('max-height', '60vh')\n\t\t\t.style('overflow-y', 'auto')\n\t\t\t.style('border-right', '1px solid #eee')\n\t\t\t.style('padding-right', '12px')\n\n\t\t// right \u2014 table\n\t\tthis.dom.rightDiv = layout.append('div').style('flex', '1 1 auto').style('min-width', '0')\n\t\tthis.dom.tableDiv = this.dom.rightDiv.append('div')\n\n\t\tthis.renderFacets(ui)\n\t\tthis.renderTable(ui)\n\t}\n\n\t/** one row per organism\u2192assay\u2192cohort. `species` and `proteome` are derived from the query\n\t *  structure (organism key + the assay's proteomeLabel); every other display field comes from\n\t *  the cohort's `catalog` object in the dataset. A `catalog` key can still override either. */\n\tderiveRows(organisms: any): CatalogRow[] {\n\t\tconst rows: CatalogRow[] = []\n\t\tfor (const organism in organisms) {\n\t\t\tconst species = organism.charAt(0).toUpperCase() + organism.slice(1)\n\t\t\tconst assays = organisms[organism].assays || {}\n\t\t\tfor (const assay in assays) {\n\t\t\t\tconst proteome = assays[assay].proteomeLabel || assay\n\t\t\t\tconst cohorts = assays[assay].cohorts || {}\n\t\t\t\tfor (const cohort in cohorts) {\n\t\t\t\t\t// species/proteome first so catalog may override them; identity keys last so it can't\n\t\t\t\t\tconst dataType = assays[assay].PTMType ? 'PTM' : 'Protein'\n\t\t\t\t\trows.push({\n\t\t\t\t\t\tspecies,\n\t\t\t\t\t\tproteome,\n\t\t\t\t\t\tdataType,\n\t\t\t\t\t\t...(cohorts[cohort].catalog || {}),\n\t\t\t\t\t\torganism,\n\t\t\t\t\t\tassay,\n\t\t\t\t\t\tcohort\n\t\t\t\t\t} as CatalogRow)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn rows\n\t}\n\n\t/** rows passing every active filter, optionally excluding one facet (for that facet's own counts) */\n\tfilteredRows(excludeFacet?: string | string[]): CatalogRow[] {\n\t\tconst excluded = new Set(Array.isArray(excludeFacet) ? excludeFacet : excludeFacet ? [excludeFacet] : [])\n\t\treturn this.rows.filter(row => {\n\t\t\tfor (const [facet, values] of this.activeFilters) {\n\t\t\t\tif (excluded.has(facet)) continue\n\t\t\t\tif (values.size === 0) continue\n\t\t\t\tif (!values.has(row[facet] || '')) return false\n\t\t\t}\n\t\t\treturn true\n\t\t})\n\t}\n\n\tfacetLabel(ui: CatalogUiConfig, key: string): string {\n\t\tif (key === DATA_TYPE_FACET) return DATA_TYPE_LABEL\n\t\treturn ui.columns.find(c => c.key === key)?.label || key\n\t}\n\n\t/** facet order to render: the proteome facet is replaced by its Data type parent,\n\t *  which renders the proteome values nested under the active radio option */\n\teffectiveFacets(ui: CatalogUiConfig): string[] {\n\t\treturn ui.facets.map(f => (f === DATA_TYPE_CHILD ? DATA_TYPE_FACET : f))\n\t}\n\n\tsortValues(facet: string, values: string[]): string[] {\n\t\tconst fixed =\n\t\t\tfacet === DATA_TYPE_FACET\n\t\t\t\t? DATA_TYPE_ORDER\n\t\t\t\t: facet === DATA_TYPE_CHILD\n\t\t\t\t? proteomeOrder(this.app.vocabApi.termdbConfig?.queries?.proteome?.organisms)\n\t\t\t\t: null\n\t\tif (fixed)\n\t\t\treturn orderBy(\n\t\t\t\t[...values].sort((a, b) => a.localeCompare(b)),\n\t\t\t\tfixed\n\t\t\t)\n\t\treturn [...values].sort((a, b) => a.localeCompare(b, undefined, { numeric: true }))\n\t}\n\n\t/** filters to ignore when computing a facet's own value counts: itself, plus \u2014 for the\n\t *  Data type parent \u2014 its nested proteome filter, so that ticking e.g. \"Insoluble\" under\n\t *  Protein never makes the PTM option disappear (it must stay clickable to switch class) */\n\tfacetScopeExclusions(facet: string): string[] {\n\t\treturn facet === DATA_TYPE_FACET ? [DATA_TYPE_FACET, DATA_TYPE_CHILD] : [facet]\n\t}\n\n\t/** counts of one facet's values under all OTHER active filters (standard faceted behavior) */\n\tfacetCounts(facet: string): Map<string, number> {\n\t\tconst counts = new Map<string, number>()\n\t\tfor (const row of this.filteredRows(this.facetScopeExclusions(facet))) {\n\t\t\tconst v = row[facet] || ''\n\t\t\tif (!v) continue\n\t\t\tcounts.set(v, (counts.get(v) || 0) + 1)\n\t\t}\n\t\treturn counts\n\t}\n\n\t/** one radio/checkbox line of a facet */\n\tappendFacetOption(\n\t\tui: CatalogUiConfig,\n\t\tgroup: any,\n\t\tfacet: string,\n\t\tvalue: string,\n\t\tcount: number,\n\t\tsingle: boolean,\n\t\tchecked: boolean,\n\t\tindentPx = 0\n\t) {\n\t\tconst line = group\n\t\t\t.append('label')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('gap', '6px')\n\t\t\t.style('font-size', '0.85em')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.style('padding', '1px 0')\n\t\t\t.style('margin-left', indentPx ? `${indentPx}px` : null)\n\t\tline\n\t\t\t.append('input')\n\t\t\t.attr('type', single ? 'radio' : 'checkbox')\n\t\t\t.attr('name', single ? `sjpp-studyCatalog-facet-${this.id}-${facet}` : null)\n\t\t\t.property('checked', checked)\n\t\t\t.on('change', (event: any) => {\n\t\t\t\tif (single) {\n\t\t\t\t\t// radio: picking a value replaces the facet's single active value\n\t\t\t\t\tthis.activeFilters.set(facet, new Set([value]))\n\t\t\t\t\t// the nested proteome values belong to the previous class; drop them\n\t\t\t\t\tif (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD)\n\t\t\t\t} else {\n\t\t\t\t\tconst set = this.activeFilters.get(facet) || new Set<string>()\n\t\t\t\t\tif (event.target.checked) set.add(value)\n\t\t\t\t\telse set.delete(value)\n\t\t\t\t\tif (set.size) this.activeFilters.set(facet, set)\n\t\t\t\t\telse this.activeFilters.delete(facet)\n\t\t\t\t}\n\t\t\t\tthis.renderFacets(ui)\n\t\t\t\tthis.renderTable(ui)\n\t\t\t})\n\t\tline.append('span').style('flex', '1 1 auto').text(value)\n\t\tline.append('span').style('color', '#999').text(count)\n\t}\n\n\trenderFacets(ui: CatalogUiConfig) {\n\t\tconst div = this.dom.facetsDiv\n\t\tdiv.selectAll('*').remove()\n\n\t\t// dataset query config, used to gate each facet's chart button on what the chart needs\n\t\tconst queries = this.app.vocabApi.termdbConfig?.queries\n\n\t\t// single-select facets always have exactly one active value; default to the first available value\n\t\t// under the other active filters (also reapplied after \"clear all\"), so the table never mixes e.g. species\n\t\tconst facets = this.effectiveFacets(ui)\n\t\tconst singleSelect = new Set(ui.singleSelectFacets || [])\n\t\tif (facets.includes(DATA_TYPE_FACET)) singleSelect.add(DATA_TYPE_FACET)\n\t\tfor (const facet of singleSelect) {\n\t\t\tif (!facets.includes(facet)) continue\n\t\t\t// available values given the other active filters (exclude this facet itself)\n\t\t\tconst scope = this.filteredRows(this.facetScopeExclusions(facet))\n\t\t\tconst values = this.sortValues(facet, [...new Set(scope.map(r => r[facet]).filter(Boolean))])\n\t\t\tif (!values.length) {\n\t\t\t\tthis.activeFilters.delete(facet)\n\t\t\t\tif (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tconst active = this.activeFilters.get(facet)\n\t\t\tconst activeValue = active && active.size === 1 ? [...active][0] : null\n\t\t\tif (activeValue && values.includes(activeValue)) continue\n\t\t\tthis.activeFilters.set(facet, new Set([values[0]]))\n\t\t\t// the class changed under the user: its nested proteome values belong to the old\n\t\t\t// class and would otherwise filter invisibly (nothing checked, empty table)\n\t\t\tif (facet === DATA_TYPE_FACET) this.activeFilters.delete(DATA_TYPE_CHILD)\n\t\t}\n\n\t\tconst header = div\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('margin-bottom', '8px')\n\t\theader.append('span').style('font-weight', 'bold').text('Filter by')\n\t\t// single-select facets are always active by design, so they don't count towards \"clear all\"\n\t\tconst anyActive = [...this.activeFilters.entries()].some(([f, s]) => !singleSelect.has(f) && s.size > 0)\n\t\theader\n\t\t\t.append('span')\n\t\t\t.style('margin-left', 'auto')\n\t\t\t.style('font-size', '0.8em')\n\t\t\t.style('color', anyActive ? '#0a5' : '#aaa')\n\t\t\t.style('cursor', anyActive ? 'pointer' : 'default')\n\t\t\t.text('clear all')\n\t\t\t.on('click', () => {\n\t\t\t\tif (!anyActive) return\n\t\t\t\tthis.activeFilters.clear()\n\t\t\t\tthis.renderFacets(ui)\n\t\t\t\tthis.renderTable(ui)\n\t\t\t})\n\n\t\tfor (const facet of facets) {\n\t\t\tconst counts = this.facetCounts(facet)\n\t\t\tif (counts.size === 0) continue\n\n\t\t\tconst group = div.append('div').style('margin-bottom', '12px')\n\t\t\tconst titleRow = group\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('align-items', 'center')\n\t\t\t\t.style('gap', '6px')\n\t\t\t\t.style('margin-bottom', '4px')\n\t\t\ttitleRow.append('span').style('font-weight', '600').style('font-size', '0.9em').text(this.facetLabel(ui, facet))\n\t\t\t// some facets get a button that launches a related chart \u2014 only if the dataset supports it\n\t\t\tconst chart = FACET_CHART[facet]\n\t\t\tif (chart && chart.requires(queries)) {\n\t\t\t\ttitleRow\n\t\t\t\t\t.append('button')\n\t\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t\t.style('font-size', '0.72em')\n\t\t\t\t\t.style('padding', '1px 5px')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.attr('title', `Open ${chart.label}`)\n\t\t\t\t\t.text('\uD83D\uDCCA')\n\t\t\t\t\t.on('click', (event: any) => this.openChartMenu(chart, event))\n\t\t\t}\n\n\t\t\tconst single = singleSelect.has(facet)\n\t\t\tconst active = this.activeFilters.get(facet) || new Set<string>()\n\t\t\tfor (const value of this.sortValues(facet, [...counts.keys()])) {\n\t\t\t\tthis.appendFacetOption(ui, group, facet, value, counts.get(value)!, single, active.has(value))\n\t\t\t\t// nested proteome checkboxes under the active Data type option\n\t\t\t\tif (facet === DATA_TYPE_FACET && active.has(value)) {\n\t\t\t\t\tconst childCounts = this.facetCounts(DATA_TYPE_CHILD)\n\t\t\t\t\tconst childActive = this.activeFilters.get(DATA_TYPE_CHILD) || new Set<string>()\n\t\t\t\t\tfor (const cv of this.sortValues(DATA_TYPE_CHILD, [...childCounts.keys()])) {\n\t\t\t\t\t\tthis.appendFacetOption(ui, group, DATA_TYPE_CHILD, cv, childCounts.get(cv)!, false, childActive.has(cv), 22)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\trenderTable(ui: CatalogUiConfig) {\n\t\tconst rows = this.filteredRows()\n\t\tthis.filteredCount = rows.length\n\t\tthis.dom.tableDiv.selectAll('*').remove()\n\t\tthis.dom.tableDiv.style('font-size', '13px')\n\n\t\t// preserve selection across re-renders (rx main() rebuilds the table): preselect the\n\t\t// still-visible rows whose cohort is selected, and prune keys that got filtered out\n\t\tconst selectedRows: number[] = []\n\t\trows.forEach((r, i) => {\n\t\t\tif (this.selectedKeys.has(this.cohortKey(r))) selectedRows.push(i)\n\t\t})\n\t\tthis.selected = selectedRows.map(i => rows[i])\n\t\tthis.selectedKeys = new Set(this.selected.map(r => this.cohortKey(r)))\n\t\tthis.updateActionBtn()\n\n\t\t// Columns are data-driven: a column that is empty for every row under the\n\t\t// current facet selection is dropped, so a single-species selection shows\n\t\t// only that species' attributes (e.g. brain region for human; model, cell\n\t\t// type and age group for mouse) instead of a fixed column set. With no rows\n\t\t// at all, keep every column so the empty table still has a header.\n\t\t// Single-select facets (e.g. Species) are dropped too: their radio always\n\t\t// states the one active value, so the column would just repeat it.\n\t\tconst singleSelect = new Set(ui.singleSelectFacets || [])\n\t\tconst visibleColumns = rows.length\n\t\t\t? ui.columns.filter(c => !singleSelect.has(c.key) && rows.some(row => row[c.key] != null && row[c.key] !== ''))\n\t\t\t: ui.columns\n\t\tconst columns: TableColumn[] = visibleColumns.map(c => ({ label: c.label, sortable: true }))\n\t\tconst tableRows: TableRow[] = rows.map(\n\t\t\trow =>\n\t\t\t\tvisibleColumns.map(c => {\n\t\t\t\t\tconst value = row[c.key] ?? ''\n\t\t\t\t\treturn c.urlBase && value ? { value, url: c.urlBase + value } : { value }\n\t\t\t\t}) as TableRow\n\t\t)\n\n\t\trenderTable({\n\t\t\tcolumns,\n\t\t\trows: tableRows,\n\t\t\tdiv: this.dom.tableDiv,\n\t\t\tshowLines: true,\n\t\t\tstriped: true,\n\t\t\tmaxHeight: '60vh',\n\t\t\tmaxWidth: '72vw',\n\t\t\tresize: true,\n\t\t\tselectedRows,\n\t\t\theader: { allowSort: true, style: { 'font-weight': 'bold', color: '#000' } },\n\t\t\tbuttons: [\n\t\t\t\t{\n\t\t\t\t\ttext: 'select',\n\t\t\t\t\tcallback: () => {},\n\t\t\t\t\tonChange: (idxs: number[], button: any) => {\n\t\t\t\t\t\tbutton.style.display = 'none'\n\t\t\t\t\t\t// the Data type radio already keeps PTM and protein-level cohorts apart,\n\t\t\t\t\t\t// so any combination of visible rows is a valid selection\n\t\t\t\t\t\tthis.selected = idxs.map(i => rows[i])\n\t\t\t\t\t\tthis.selectedKeys = new Set(this.selected.map(r => this.cohortKey(r)))\n\t\t\t\t\t\tthis.updateActionBtn()\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t}\n\n\t/** stable identity of a cohort row, used to keep the selection across re-renders */\n\tcohortKey(row: CatalogRow): string {\n\t\treturn `${row.organism}|${row.assay}|${row.cohort}`\n\t}\n\n\t/** update the action button + count text from the current selection.\n\t *  count: nothing selected \u2192 total filtered cohorts; 1 selected \u2192 hidden; \u22652 \u2192 selected count */\n\tupdateActionBtn() {\n\t\tconst btn = this.dom.actionBtn\n\t\tif (!btn) return\n\t\tconst n = this.selected.length\n\t\tbtn.property('disabled', n === 0).text(n >= 2 ? 'Compare cohorts' : 'Analyze Cohort')\n\t\tconst cs = this.dom.countSpan\n\t\tif (n === 1) cs.style('display', 'none')\n\t\telse if (n >= 2) cs.style('display', '').text(`${n} cohorts`)\n\t\telse cs.style('display', '').text(`${this.filteredCount} cohort${this.filteredCount === 1 ? '' : 's'}`)\n\t}\n\n\t/** run the action for the current selection: 1 cohort \u2192 Analyze; \u22652 \u2192 Compare */\n\tonAction() {\n\t\tconst sel = this.selected\n\t\tif (sel.length === 1) this.openAnalyticsTools(sel[0])\n\t\telse if (sel.length >= 2) this.openCompare(sel)\n\t}\n\n\t/** launch a facet's chart. Charts that don't need a gene open directly; gene-centric ones\n\t *  prompt for a gene first. Dispatches exactly chart.chartType (no importPlot indirection). */\n\topenChartMenu(chart: { chartType: string; needsGene: boolean }, event: any) {\n\t\tif (!chart.needsGene) {\n\t\t\tthis.app.dispatch({ type: 'plot_create', config: { chartType: chart.chartType } })\n\t\t\treturn\n\t\t}\n\t\tthis.dom.tip.clear().show(event.clientX, event.clientY)\n\t\tconst row = this.dom.tip.d.append('div').style('padding', '5px')\n\t\trow.append('span').style('font-weight', 'bold').text('Enter a gene name:')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\trow,\n\t\t\tgenome: this.app.opts.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: () => {\n\t\t\t\tif (!geneSearch.geneSymbol) throw new Error('A valid gene selection is required')\n\t\t\t\tthis.dom.tip.hide()\n\t\t\t\tthis.app.dispatch({ type: 'plot_create', config: { chartType: chart.chartType, gene: geneSearch.geneSymbol } })\n\t\t\t}\n\t\t})\n\t}\n\n\t/** open the ProteomeInput \"Analytics Tools\" panel for a cohort, mirroring the\n\t *  Sample Selection (proteomeAbundance) chart's \"Analytics Tools\" button */\n\topenAnalyticsTools(row: CatalogRow) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'ProteomeInput',\n\t\t\t\tproteomeDetails: { organism: row.organism, assay: row.assay, cohort: row.cohort },\n\t\t\t\thidePlotFilter: true\n\t\t\t}\n\t\t})\n\t}\n\n\t/** open the cross-cohort log2FC-z comparison for the selected cohorts */\n\topenCompare(selected: CatalogRow[]) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tconfig: {\n\t\t\t\tchartType: 'proteomeCohortCompare',\n\t\t\t\tcohorts: selected.map(r => ({ organism: r.organism, assay: r.assay, cohort: r.cohort, label: r.cohort }))\n\t\t\t}\n\t\t})\n\t}\n}\n\nexport const componentInit = getCompInit(StudyCatalog)\n\nexport async function getPlotConfig(opts: any) {\n\tconst config = structuredClone(defaultConfig)\n\treturn copyMerge(config, opts)\n}\n"],
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