@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/studyCatalog-O3VGIKDM.js

@@ -0,0 +1,358 @@
+import {
+  PlotBase,
+  addGeneSearchbox,
+  renderTable
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/studyCatalog.ts
+var PTM_PROTEOMES = /* @__PURE__ */ new Set(["Phospho", "Ubiquitin"]);
+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("Sample Sets");
+  }
+  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").attr("class", "sjpp_apply_btn sja_sharp_border").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) {
+          rows.push({ species, proteome, ...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) {
+    return this.rows.filter((row) => {
+      for (const [facet, values] of this.activeFilters) {
+        if (facet === excludeFacet) continue;
+        if (values.size === 0) continue;
+        if (!values.has(row[facet] || "")) return false;
+      }
+      return true;
+    });
+  }
+  facetLabel(ui, key) {
+    return ui.columns.find((c) => c.key === key)?.label || key;
+  }
+  renderFacets(ui) {
+    const div = this.dom.facetsDiv;
+    div.selectAll("*").remove();
+    const queries = this.app.vocabApi.termdbConfig?.queries;
+    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.values()].some((s) => 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 ui.facets) {
+      const scope = this.filteredRows(facet);
+      const counts = /* @__PURE__ */ new Map();
+      for (const row of scope) {
+        const v = row[facet] || "";
+        if (!v) continue;
+        counts.set(v, (counts.get(v) || 0) + 1);
+      }
+      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 active = this.activeFilters.get(facet) || /* @__PURE__ */ new Set();
+      const values = [...counts.keys()].sort((a, b) => a.localeCompare(b, void 0, { numeric: true }));
+      for (const value of values) {
+        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");
+        line.append("input").attr("type", "checkbox").property("checked", active.has(value)).on("change", (event) => {
+          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(counts.get(value));
+      }
+    }
+  }
+  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 columns = ui.columns.map((c) => ({ label: c.label, sortable: true }));
+    const tableRows = rows.map((row) => ui.columns.map((c) => ({ value: row[c.key] ?? "" })));
+    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";
+            let sel = idxs.map((i) => rows[i]);
+            if (sel.length > 1) {
+              const cls = this.proteomeClass(sel[0]);
+              const offIdx = new Set(idxs.filter((i) => this.proteomeClass(rows[i]) !== cls));
+              if (offIdx.size) {
+                sel = idxs.filter((i) => !offIdx.has(i)).map((i) => rows[i]);
+                const nodes = this.dom.tableDiv.selectAll('tbody input[type="checkbox"]').nodes();
+                for (const node of nodes) if (offIdx.has(Number(node.getAttribute("value")))) node.checked = false;
+              }
+            }
+            this.selected = sel;
+            this.selectedKeys = new Set(sel.map((r) => this.cohortKey(r)));
+            this.updateActionBtn();
+            this.applyClassLock(rows);
+          }
+        }
+      ]
+    });
+  }
+  /** stable identity of a cohort row, used to keep the selection across re-renders */
+  cohortKey(row) {
+    return `${row.organism}|${row.assay}|${row.cohort}`;
+  }
+  /** PTM (site-level) vs non-PTM (protein-level) class of a cohort row */
+  proteomeClass(row) {
+    return PTM_PROTEOMES.has(row.proteome) ? "ptm" : "nonptm";
+  }
+  /** PTM/non-PTM lock: once a cohort is selected, disable + dim checkboxes
+   *  for cohorts of the OTHER class. */
+  applyClassLock(rows) {
+    const locked = this.selected.length ? this.proteomeClass(this.selected[0]) : null;
+    const nodes = this.dom.tableDiv.selectAll('tbody input[type="checkbox"]').nodes();
+    for (const input of nodes) {
+      const vAttr = input.getAttribute("value");
+      if (vAttr === null) continue;
+      const idx = Number(vAttr);
+      if (!Number.isInteger(idx) || idx < 0 || idx >= rows.length) continue;
+      const disable = locked !== null && !input.checked && this.proteomeClass(rows[idx]) !== locked;
+      input.disabled = disable;
+      const tr = input.closest("tr");
+      if (tr) tr.style.opacity = disable ? "0.4" : "";
+    }
+  }
+  /** 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 })),
+        crossSpecies: false
+      }
+    });
+  }
+};
+var componentInit = getCompInit(StudyCatalog);
+async function getPlotConfig(opts) {
+  const config = structuredClone(defaultConfig);
+  return copyMerge(config, opts);
+}
+export {
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=studyCatalog-O3VGIKDM.js.map

package/dist/studyCatalog-O3VGIKDM.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 } from '#rx'\nimport { PlotBase } from './PlotBase'\nimport { Menu, renderTable, addGeneSearchbox } from '#dom'\nimport type { TableColumn, TableRow } from '#dom'\n\n/** PTM proteome layers \u2014 kept separate from protein-level (Whole/Insoluble) layers because\n *  PTM z is site-level collapsed to gene, so the two aren't directly comparable in a scatter/heatmap */\nconst PTM_PROTEOMES = new Set(['Phospho', 'Ubiquitin'])\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\ntype CatalogColumn = { key: string; label: string }\ntype CatalogUiConfig = {\n\tcolumns: CatalogColumn[]\n\tfacets: 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) {\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('Sample Sets')\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.attr('class', 'sjpp_apply_btn sja_sharp_border')\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\trows.push({ species, proteome, ...(cohorts[cohort].catalog || {}), organism, assay, cohort } 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): CatalogRow[] {\n\t\treturn this.rows.filter(row => {\n\t\t\tfor (const [facet, values] of this.activeFilters) {\n\t\t\t\tif (facet === excludeFacet) 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\treturn ui.columns.find(c => c.key === key)?.label || key\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\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\tconst anyActive = [...this.activeFilters.values()].some(s => 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 ui.facets) {\n\t\t\t// counts reflect all OTHER active filters (standard faceted behavior)\n\t\t\tconst scope = this.filteredRows(facet)\n\t\t\tconst counts = new Map<string, number>()\n\t\t\tfor (const row of scope) {\n\t\t\t\tconst v = row[facet] || ''\n\t\t\t\tif (!v) continue\n\t\t\t\tcounts.set(v, (counts.get(v) || 0) + 1)\n\t\t\t}\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 active = this.activeFilters.get(facet) || new Set<string>()\n\t\t\tconst values = [...counts.keys()].sort((a, b) => a.localeCompare(b, undefined, { numeric: true }))\n\t\t\tfor (const value of values) {\n\t\t\t\tconst line = group\n\t\t\t\t\t.append('label')\n\t\t\t\t\t.style('display', 'flex')\n\t\t\t\t\t.style('align-items', 'center')\n\t\t\t\t\t.style('gap', '6px')\n\t\t\t\t\t.style('font-size', '0.85em')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.style('padding', '1px 0')\n\t\t\t\tline\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t\t.property('checked', active.has(value))\n\t\t\t\t\t.on('change', (event: any) => {\n\t\t\t\t\t\tconst set = this.activeFilters.get(facet) || new Set<string>()\n\t\t\t\t\t\tif (event.target.checked) set.add(value)\n\t\t\t\t\t\telse set.delete(value)\n\t\t\t\t\t\tif (set.size) this.activeFilters.set(facet, set)\n\t\t\t\t\t\telse this.activeFilters.delete(facet)\n\t\t\t\t\t\tthis.renderFacets(ui)\n\t\t\t\t\t\tthis.renderTable(ui)\n\t\t\t\t\t})\n\t\t\t\tline.append('span').style('flex', '1 1 auto').text(value)\n\t\t\t\tline.append('span').style('color', '#999').text(counts.get(value)!)\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\tconst columns: TableColumn[] = ui.columns.map(c => ({ label: c.label, sortable: true }))\n\t\tconst tableRows: TableRow[] = rows.map(row => ui.columns.map(c => ({ value: row[c.key] ?? '' })) as TableRow)\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\tlet sel = idxs.map(i => rows[i])\n\t\t\t\t\t\tif (sel.length > 1) {\n\t\t\t\t\t\t\tconst cls = this.proteomeClass(sel[0])\n\t\t\t\t\t\t\tconst offIdx = new Set(idxs.filter(i => this.proteomeClass(rows[i]) !== cls))\n\t\t\t\t\t\t\tif (offIdx.size) {\n\t\t\t\t\t\t\t\tsel = idxs.filter(i => !offIdx.has(i)).map(i => rows[i])\n\t\t\t\t\t\t\t\tconst nodes = this.dom.tableDiv.selectAll('tbody input[type=\"checkbox\"]').nodes() as HTMLInputElement[]\n\t\t\t\t\t\t\t\tfor (const node of nodes) if (offIdx.has(Number(node.getAttribute('value')))) node.checked = false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.selected = sel\n\t\t\t\t\t\tthis.selectedKeys = new Set(sel.map(r => this.cohortKey(r)))\n\t\t\t\t\t\tthis.updateActionBtn()\n\t\t\t\t\t\tthis.applyClassLock(rows)\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/** PTM (site-level) vs non-PTM (protein-level) class of a cohort row */\n\tproteomeClass(row: CatalogRow): 'ptm' | 'nonptm' {\n\t\treturn PTM_PROTEOMES.has(row.proteome) ? 'ptm' : 'nonptm'\n\t}\n\n\t/** PTM/non-PTM lock: once a cohort is selected, disable + dim checkboxes\n\t *  for cohorts of the OTHER class. */\n\tapplyClassLock(rows: CatalogRow[]) {\n\t\tconst locked = this.selected.length ? this.proteomeClass(this.selected[0]) : null\n\t\tconst nodes = this.dom.tableDiv.selectAll('tbody input[type=\"checkbox\"]').nodes() as HTMLInputElement[]\n\t\tfor (const input of nodes) {\n\t\t\tconst vAttr = input.getAttribute('value')\n\t\t\tif (vAttr === null) continue\n\t\t\tconst idx = Number(vAttr)\n\t\t\tif (!Number.isInteger(idx) || idx < 0 || idx >= rows.length) continue\n\t\t\tconst disable = locked !== null && !input.checked && this.proteomeClass(rows[idx]) !== locked\n\t\t\tinput.disabled = disable\n\t\t\tconst tr = input.closest('tr') as HTMLElement | null\n\t\t\tif (tr) tr.style.opacity = disable ? '0.4' : ''\n\t\t}\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\tcrossSpecies: false\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"],
+  "mappings": 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+  "names": []
+}

package/dist/summarizeCnvGeneexp-55DNXHXA.js

@@ -0,0 +1,163 @@
+import {
+  launchPlot
+} from "./chunk-W76X6W73.js";
+import {
+  addGeneSearchbox,
+  fillTermWrapper,
+  make_one_checkbox,
+  table2col
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import {
+  dtcnv
+} from "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/summarizeCnvGeneexp.ts
+var tip = new Menu({ padding: "0px" });
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let expTw, cnvTw, cnvGeneSameAsExp = true, expSearchPrompt, cnvTableRow;
+  make_one_checkbox({
+    holder: holder.append("div").style("margin", "20px 10px 5px 15px"),
+    labeltext: "Use Same Gene For CNV",
+    checked: true,
+    testid: "sjpp-summarizeCnvGeneexp-useSameGeneCheckbox",
+    callback: async (checked) => {
+      cnvGeneSameAsExp = checked;
+      await updateUi();
+    }
+  });
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Search Gene For Expression");
+    const searchDiv = td2.append("div");
+    expSearchPrompt = td2.append("div").style("font-size", ".7em");
+    const result = addGeneSearchbox({
+      row: searchDiv,
+      tip,
+      searchOnly: "gene",
+      testid: "sjpp-summarizeCnvGeneexp-genesearch-exp",
+      genome: chartsInstance.app.opts.genome,
+      callback: async () => {
+        expSearchPrompt.text("LOADING ...");
+        try {
+          expTw = { term: { gene: result.geneSymbol, type: "geneExpression" }, q: {} };
+          await updateUi();
+          if (cnvGeneSameAsExp) launch();
+          expSearchPrompt.text("");
+        } catch (e) {
+          expSearchPrompt.text("Error: " + (e.message || e));
+          console.log(e.stack);
+        }
+      }
+    });
+  }
+  {
+    const [td1, td2] = table.addRow();
+    cnvTableRow = select_default(td1.node().parentNode);
+    td1.text("Search Gene for CNV");
+    const searchDiv = td2.append("div");
+    const cnvSearchPrompt = td2.append("div").style("font-size", ".7em");
+    const result = addGeneSearchbox({
+      row: searchDiv,
+      tip,
+      searchOnly: "gene",
+      testid: "sjpp-summarizeCnvGeneexp-genesearch-cnv",
+      genome: chartsInstance.app.opts.genome,
+      callback: async () => {
+        cnvSearchPrompt.text("LOADING ...");
+        try {
+          cnvTw = await fillGvTw(result.geneSymbol, dtcnv);
+          await updateUi();
+          cnvSearchPrompt.text("");
+        } catch (e) {
+          cnvSearchPrompt.text("Error: " + (e.message || e));
+          if (e.stack) console.log(e.stack);
+        }
+      }
+    });
+  }
+  const submitBtn = holder.append("button").attr("data-testid", "sjpp-summarizeCnvGeneexp-submitBtn").text("Launch Plot").style("margin", "0px 15px 15px 15px").property("disabled", true).on("click", launch);
+  async function updateUi() {
+    if (cnvGeneSameAsExp) {
+      if (expTw) {
+        cnvTw = await fillGvTw(expTw.term.gene, dtcnv);
+      }
+    }
+    cnvTableRow.style("display", cnvGeneSameAsExp ? "none" : "");
+    expSearchPrompt.text(cnvGeneSameAsExp ? "Hit ENTER to launch plot." : "");
+    submitBtn.style("display", cnvGeneSameAsExp ? "none" : "").property("disabled", !expTw || !cnvTw);
+  }
+  updateUi();
+  async function fillGvTw(geneSymbol, dt) {
+    const name = geneSymbol;
+    const tw = {
+      term: {
+        id: name,
+        name,
+        genes: [
+          {
+            kind: "gene",
+            id: name,
+            gene: name,
+            name,
+            type: "geneVariant"
+          }
+        ],
+        type: "geneVariant"
+      },
+      q: { type: "predefined-groupset", dtLst: [dt] }
+    };
+    await fillTermWrapper(tw, chartsInstance.app.vocabApi);
+    return tw;
+  }
+  function launch() {
+    if (!expTw || !cnvTw) throw "either tw is missing";
+    launchPlot({
+      tw1: expTw,
+      tw2: cnvTw,
+      chartsInstance,
+      holder
+    });
+  }
+}
+export {
+  makeChartBtnMenu
+};
+//# sourceMappingURL=summarizeCnvGeneexp-55DNXHXA.js.map