@sjcrh/proteinpaint-client 2.195.0 → 2.196.0

package/dist/geneRanking-6AXL5ZJS.js

@@ -0,0 +1,553 @@
+import {
+  PlotBase,
+  renderTable,
+  sayerror
+} from "./chunk-WY2PGUVX.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-MBUQ34CF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import {
+  icons
+} from "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OVSKJROY.js";
+import "./chunk-A3URBFXN.js";
+import {
+  dofetch3
+} from "./chunk-LYVLF6HO.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-NNFAUP2I.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import {
+  linear
+} from "./chunk-SOTB4FRE.js";
+import {
+  roundValueAuto
+} from "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/geneRanking.ts
+var Integrative_rank_COLUMN = "Integrative rank";
+var MISSING_COLOR = "#d9d9d9";
+var SEQ_COLOR_LOW = "#08306b";
+var SEQ_COLOR_HIGH = "#f7fbff";
+var GeneRanking = class _GeneRanking extends PlotBase {
+  constructor(opts) {
+    super(opts);
+    this.sortIdx = -1;
+    this.sortAsc = true;
+    this.pageSize = 10;
+    this.currentPage = 1;
+    this.searchQuery = "";
+    this.heatmapOrder = "clustered";
+    this.minAssays = 3;
+    /** identity-tag of the data the current heatmap was rendered for; used to abort stale responses */
+    this.heatmapRenderKey = "";
+    this.type = _GeneRanking.type;
+    const main = opts.holder.append("div").style("padding", "12px").style("max-width", "95vw");
+    this.errDiv = main.append("div").style("color", "red").style("display", "none").style("padding", "8px");
+    this.loadingDiv = main.append("div").style("padding", "8px").text("Loading...");
+    this.toolbarDiv = main.append("div").style("display", "none").style("align-items", "center").style("justify-content", "space-between").style("flex-wrap", "wrap").style("gap", "8px").style("margin-bottom", "6px").style("font-size", "12px");
+    const leftBar = this.toolbarDiv.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px");
+    const dlBtn = leftBar.append("button").style("display", "inline-flex").style("align-items", "center").style("gap", "6px").style("padding", "4px 10px").style("cursor", "pointer").on("click", () => this.downloadAll());
+    icons["download"](dlBtn.append("span").style("display", "inline-flex").style("align-items", "center"), {
+      width: 14,
+      height: 14,
+      title: "Download data as TSV"
+    });
+    dlBtn.append("span").text("Download data");
+    const rightBar = this.toolbarDiv.append("div");
+    rightBar.append("span").text("Search: ").style("margin-right", "4px");
+    this.searchInput = rightBar.append("input").attr("type", "search").attr("placeholder", "gene name").style("padding", "3px 6px").on("input", (event) => {
+      this.searchQuery = (event.target.value || "").trim().toLowerCase();
+      this.currentPage = 1;
+      this.renderTable();
+    });
+    this.noteDiv = main.append("div").style("display", "none").style("font-size", "0.85em").style("color", "#555").style("margin-bottom", "10px").style("line-height", "1.4").style("white-space", "normal").style("word-break", "normal").style("overflow-wrap", "break-word");
+    this.tableDiv = main.append("div").attr("data-testid", "sjpp-geneRanking-table").style("font-size", "12px");
+    this.heatmapSection = main.append("div").style("display", "none").style("margin-top", "24px").attr("data-testid", "sjpp-geneRanking-heatmap");
+    const hmHeader = this.heatmapSection.append("div").style("display", "flex").style("align-items", "center").style("gap", "12px").style("margin-bottom", "8px");
+    hmHeader.append("div").style("font-weight", "bold").text("Heatmap of the current page");
+    this.heatmapControls = hmHeader.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px");
+    this.heatmapControls.append("span").style("font-size", "0.85em").style("color", "#555").text("Row order:");
+    const orderSelect = this.heatmapControls.append("select").style("padding", "2px 4px").on("change", (event) => {
+      this.heatmapOrder = event.target.value;
+      this.renderHeatmap();
+    });
+    orderSelect.append("option").attr("value", "clustered").text("Clustered").property("selected", true);
+    orderSelect.append("option").attr("value", "rank").text("Ranking score");
+    const minAssaysWrap = this.heatmapControls.append("span").attr("class", "sjpp-mr-min-assays-wrap").style("display", "inline-flex").style("align-items", "center").style("gap", "6px");
+    minAssaysWrap.append("span").style("font-size", "0.85em").style("color", "#555").text("Min assays:");
+    this.minAssaysSelect = minAssaysWrap.append("select").style("padding", "2px 4px").on("change", (event) => {
+      this.minAssays = Number(event.target.value);
+      this.renderHeatmap();
+    });
+    this.heatmapStatus = this.heatmapSection.append("div").style("font-size", "0.85em").style("color", "#777").style("margin-bottom", "6px");
+    this.heatmapDiv = this.heatmapSection.append("div").style("overflow-x", "auto");
+    this.dom = {
+      holder: main,
+      header: opts.header,
+      errDiv: this.errDiv,
+      loadingDiv: this.loadingDiv,
+      toolbarDiv: this.toolbarDiv,
+      noteDiv: this.noteDiv,
+      tableDiv: this.tableDiv
+    };
+  }
+  static {
+    this.type = "geneRanking";
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw `No plot with id='${this.id}' found`;
+    return { config, vocab: appState.vocab, termdbConfig: appState.termdbConfig };
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("plot_")) return action.id === this.id;
+    return false;
+  }
+  async main() {
+    this.config = structuredClone(this.state.config);
+    const key = this.config.rankingKey;
+    if (!key) {
+      this.loadingDiv.style("display", "none");
+      this.errDiv.style("display", "block").text("No ranking key selected");
+      return;
+    }
+    if (this.dom.header)
+      this.dom.header.html(`${key} <span style="font-size:.8em;opacity:.7">MULTIOMIC RANKINGS</span>`);
+    if (this.dataKey !== key) {
+      this.loadingDiv.style("display", "block");
+      this.tableDiv.selectAll("*").remove();
+      try {
+        const resp = await dofetch3("termdb/geneRanking", {
+          body: {
+            genome: this.state.vocab.genome,
+            dslabel: this.state.vocab.dslabel,
+            key
+          }
+        });
+        if (resp.error) throw resp.error;
+        this.cachedData = { columns: resp.columns, rows: resp.rows };
+        this.dataKey = key;
+        const integrativeRankIdx = resp.columns.indexOf(Integrative_rank_COLUMN);
+        this.sortIdx = integrativeRankIdx >= 0 ? integrativeRankIdx : -1;
+        this.sortAsc = true;
+        this.currentPage = 1;
+        this.searchQuery = "";
+        if (this.searchInput) this.searchInput.node().value = "";
+      } catch (e) {
+        this.loadingDiv.style("display", "none");
+        sayerror(this.errDiv.style("display", "block"), e.message || e);
+        return;
+      }
+      this.loadingDiv.style("display", "none");
+    }
+    this.toolbarDiv.style("display", "flex");
+    const desc = this.state.termdbConfig?.queries?.geneRanking?.description;
+    this.noteDiv.style("display", desc ? "block" : "none").text(desc || "");
+    this.renderTable();
+  }
+  downloadAll() {
+    if (!this.cachedData) return;
+    const { columns, rows } = this.cachedData;
+    const filtered = this.searchQuery ? rows.filter((r) => {
+      const gene = r[0];
+      return typeof gene === "string" && gene.toLowerCase().includes(this.searchQuery);
+    }) : rows;
+    const sorted = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered;
+    const lines = [columns.join("	")];
+    for (const row of sorted) {
+      lines.push(row.map((v) => v == null ? "NA" : String(v)).join("	"));
+    }
+    const blob = new Blob([lines.join("\n")], { type: "text/tab-separated-values" });
+    const url = URL.createObjectURL(blob);
+    const a = document.createElement("a");
+    const slug = (this.dataKey || "geneRanking").replace(/[^A-Za-z0-9_-]+/g, "_");
+    a.href = url;
+    a.download = `${slug}.tsv`;
+    document.body.appendChild(a);
+    a.click();
+    document.body.removeChild(a);
+    URL.revokeObjectURL(url);
+  }
+  renderTable() {
+    if (!this.cachedData) return;
+    const { columns, rows } = this.cachedData;
+    const filtered = this.searchQuery ? rows.filter((r) => {
+      const gene = r[0];
+      return typeof gene === "string" && gene.toLowerCase().includes(this.searchQuery);
+    }) : rows;
+    const sortedRows = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered;
+    const cols = columns.map((label, i) => ({
+      label,
+      sortable: true,
+      align: i === 0 ? "left" : "right",
+      nowrap: i === 0
+    }));
+    const tableRows = sortedRows.map(
+      (row) => row.map((v) => {
+        if (v === null || v === void 0) return { value: "" };
+        if (typeof v === "number") return { value: roundValueAuto(v) };
+        return { value: v };
+      })
+    );
+    this.tableDiv.selectAll("*").remove();
+    renderTable({
+      columns: cols,
+      rows: tableRows,
+      div: this.tableDiv,
+      showLines: true,
+      striped: true,
+      showHeader: true,
+      header: { allowSort: false },
+      maxWidth: "95vw",
+      maxHeight: "70vh",
+      pagination: {
+        pageSize: this.pageSize,
+        pageSizeOptions: [10, 25, 50, 100],
+        currentPage: this.currentPage,
+        onChange: ({ currentPage, pageSize }) => {
+          this.currentPage = currentPage;
+          this.pageSize = pageSize;
+          this.renderHeatmap();
+        }
+      }
+    });
+    const ths = this.tableDiv.selectAll("thead th");
+    ths.each((_d, i, nodes) => {
+      const th = nodes[i];
+      th.style.cursor = "pointer";
+      th.style.userSelect = "none";
+      th.style.whiteSpace = "nowrap";
+      th.style.color = "#000";
+      th.style.fontWeight = "bold";
+      th.style.opacity = "1";
+      const colIdx = i;
+      const label = columns[colIdx];
+      if (!label) return;
+      const active = this.sortIdx === colIdx;
+      const upColor = active && this.sortAsc ? "#000" : "#ccc";
+      const downColor = active && !this.sortAsc ? "#000" : "#ccc";
+      th.innerHTML = `<span>${escapeHtml(label)}</span><span style="display:inline-flex;flex-direction:column;line-height:0.6em;margin-left:4px;vertical-align:middle;font-size:0.7em;"><span style="color:${upColor}">\u25B2</span><span style="color:${downColor}">\u25BC</span></span>`;
+      th.onclick = () => {
+        if (this.sortIdx === colIdx) this.sortAsc = !this.sortAsc;
+        else {
+          this.sortIdx = colIdx;
+          this.sortAsc = true;
+        }
+        this.currentPage = 1;
+        this.renderTable();
+      };
+    });
+    requestAnimationFrame(() => {
+      const wrapper = this.tableDiv.select(":scope > div").node();
+      const measured = wrapper || this.tableDiv.select("table").node();
+      if (!measured) return;
+      const w = measured.getBoundingClientRect().width;
+      if (w > 0) {
+        const px = `${Math.ceil(w)}px`;
+        this.toolbarDiv.style("width", px).style("box-sizing", "border-box");
+        this.noteDiv.style("width", px).style("box-sizing", "border-box");
+      }
+    });
+    this.renderHeatmap();
+  }
+  /** rows displayed on the current page after filter + sort + pagination */
+  getVisibleRows() {
+    if (!this.cachedData) return [];
+    const { rows } = this.cachedData;
+    const filtered = this.searchQuery ? rows.filter((r) => {
+      const gene = r[0];
+      return typeof gene === "string" && gene.toLowerCase().includes(this.searchQuery);
+    }) : rows;
+    const sorted = this.sortIdx >= 0 ? sortRows(filtered, this.sortIdx, this.sortAsc) : filtered;
+    const start = (this.currentPage - 1) * this.pageSize;
+    return sorted.slice(start, start + this.pageSize);
+  }
+  async renderHeatmap() {
+    if (!this.cachedData) {
+      this.heatmapSection.style("display", "none");
+      return;
+    }
+    const { columns } = this.cachedData;
+    const colNameToIdx = new Map(columns.map((c, i) => [c, i]));
+    const modalities = this.state.termdbConfig?.queries?.geneRanking?.modalities || [];
+    const usedCols = modalities.filter((m) => colNameToIdx.has(m));
+    if (usedCols.length < 2) {
+      this.heatmapSection.style("display", "none");
+      return;
+    }
+    this.heatmapSection.style("display", "block");
+    if (this.minAssays > usedCols.length) this.minAssays = usedCols.length;
+    if (this.minAssays < 2) this.minAssays = 2;
+    const optionVals = this.minAssaysSelect.selectAll("option").nodes().map((o) => Number(o.value));
+    const want = Array.from({ length: usedCols.length - 1 }, (_, i) => i + 2);
+    if (optionVals.length !== want.length || optionVals.some((v, i) => v !== want[i])) {
+      this.minAssaysSelect.selectAll("option").remove();
+      for (const n of want) {
+        this.minAssaysSelect.append("option").attr("value", n).text(String(n)).property("selected", n === this.minAssays);
+      }
+    }
+    const visible = this.getVisibleRows();
+    const geneNames = visible.map((r) => String(r[0]));
+    const matrix = visible.map(
+      (r) => usedCols.map((c) => {
+        const v = r[colNameToIdx.get(c)];
+        return typeof v === "number" && Number.isFinite(v) ? v : null;
+      })
+    );
+    const fullStats = computeColStats(
+      this.cachedData.rows,
+      usedCols.map((c) => colNameToIdx.get(c))
+    );
+    const toPct = (val, c) => {
+      if (val === null || !Number.isFinite(val)) return null;
+      const lo = fullStats.min[c];
+      const hi = fullStats.max[c];
+      if (!Number.isFinite(lo) || !Number.isFinite(hi) || hi === lo) return 0;
+      return (val - lo) / (hi - lo);
+    };
+    const buildPct = (raw) => raw.map((row) => row.map((v, c) => toPct(v, c)));
+    const renderKey = `${this.dataKey}|${this.heatmapOrder}|${this.minAssays}|${this.currentPage}|${this.pageSize}|${this.searchQuery}|${this.sortIdx}|${this.sortAsc}|${geneNames.join(",")}`;
+    this.heatmapRenderKey = renderKey;
+    this.heatmapDiv.selectAll("*").remove();
+    this.heatmapStatus.text("Computing heatmap\u2026");
+    this.heatmapControls.select(".sjpp-mr-min-assays-wrap").style("display", this.heatmapOrder === "clustered" ? "inline-flex" : "none");
+    if (this.heatmapOrder === "rank") {
+      if (geneNames.length < 1) {
+        this.heatmapStatus.text("No rows to display.");
+        return;
+      }
+      this.heatmapStatus.text(
+        `${geneNames.length} rows in current page order. Missing values shown in gray; cells colored by rank within the full dataset per column (lower = better).`
+      );
+      this.drawHeatmap({
+        rowNames: geneNames,
+        colNames: usedCols,
+        matrix: buildPct(matrix),
+        rankMatrix: matrix,
+        totals: fullStats.n,
+        dendrogram: null
+      });
+      return;
+    }
+    try {
+      const resp = await dofetch3("termdb/geneRanking", {
+        body: {
+          for: "cluster",
+          matrix,
+          row_names: geneNames,
+          col_names: usedCols,
+          minAssays: this.minAssays
+        }
+      });
+      if (renderKey !== this.heatmapRenderKey) return;
+      if (resp.error) throw resp.error;
+      const keptCount = resp.usedRowNames?.length ?? 0;
+      this.heatmapStatus.text(
+        `${keptCount} of ${visible.length} rows shown (proteins with \u2265${this.minAssays} assays). Missing values shown in gray; cells colored by rank within the full dataset per column (lower = better).`
+      );
+      const nameToIdx = new Map(geneNames.map((n, i) => [n, i]));
+      const keptRawMatrix = resp.usedRowNames.map((n) => matrix[nameToIdx.get(n)]);
+      const keptNameToIdx = new Map(resp.usedRowNames.map((n, i) => [n, i]));
+      const orderedRowNames = resp.row.order.map((o) => o.name);
+      const orderedRank = orderedRowNames.map((name) => keptRawMatrix[keptNameToIdx.get(name)]);
+      const orderedPct = buildPct(orderedRank);
+      this.drawHeatmap({
+        rowNames: orderedRowNames,
+        colNames: resp.usedColNames,
+        matrix: orderedPct,
+        rankMatrix: orderedRank,
+        totals: fullStats.n,
+        dendrogram: resp.row
+      });
+    } catch (e) {
+      if (renderKey !== this.heatmapRenderKey) return;
+      this.heatmapStatus.text(`Heatmap error: ${e?.message || e}`);
+    }
+  }
+  drawHeatmap(opts) {
+    const { rowNames, colNames, matrix, rankMatrix, totals, dendrogram } = opts;
+    const cellW = 44;
+    const cellH = 22;
+    const dendroW = dendrogram ? 110 : 0;
+    const dendroPad = dendrogram ? 8 : 0;
+    const colLabelH = 110;
+    const rowLabelW = 130;
+    const legendBlockW = 110;
+    const gridW = colNames.length * cellW;
+    const gridH = rowNames.length * cellH;
+    const legendGradH = Math.max(120, Math.min(gridH, 240));
+    const missingSwatchExtra = 18 + 12;
+    const totalW = dendroW + dendroPad + gridW + 8 + rowLabelW + legendBlockW;
+    const totalH = colLabelH + Math.max(gridH, legendGradH + missingSwatchExtra) + 16;
+    this.heatmapDiv.selectAll("*").remove();
+    const svg = this.heatmapDiv.append("svg").attr("width", totalW).attr("height", totalH).attr("font-family", "sans-serif");
+    const seq = linear().domain([0, 1]).range([SEQ_COLOR_LOW, SEQ_COLOR_HIGH]).clamp(true);
+    const color = (v) => seq(v);
+    if (dendrogram) {
+      const g = svg.append("g").attr("transform", `translate(0,${colLabelH})`);
+      drawRowDendrogram(g, dendrogram, dendroW, gridH, cellH);
+    }
+    const gridX = dendroW + dendroPad;
+    const labelsG = svg.append("g").attr("transform", `translate(${gridX},${colLabelH - 4})`);
+    labelsG.selectAll("text").data(colNames).enter().append("text").attr("x", (_d, i) => i * cellW + cellW / 2).attr("y", 0).attr("transform", (_d, i) => `rotate(-45,${i * cellW + cellW / 2},0)`).attr("text-anchor", "start").attr("font-size", "13px").attr("fill", "#000").text((d) => d);
+    const cellsG = svg.append("g").attr("transform", `translate(${gridX},${colLabelH})`);
+    const cellData = [];
+    for (let r = 0; r < matrix.length; r++) {
+      for (let c = 0; c < matrix[r].length; c++) {
+        cellData.push({ x: c * cellW, y: r * cellH, v: matrix[r][c], row: r, col: c });
+      }
+    }
+    cellsG.selectAll("rect").data(cellData).enter().append("rect").attr("x", (d) => d.x).attr("y", (d) => d.y).attr("width", cellW).attr("height", cellH).attr("fill", (d) => d.v === null || !Number.isFinite(d.v) ? MISSING_COLOR : color(d.v)).attr("stroke", "#fff").attr("stroke-width", 0.5).append("title").text((d) => {
+      if (d.v === null || !Number.isFinite(d.v)) return `${rowNames[d.row]} \u2014 ${colNames[d.col]}
+missing`;
+      const r = rankMatrix[d.row][d.col];
+      const n = totals[d.col];
+      const rStr = Number.isInteger(r) ? String(r) : r.toFixed(1);
+      return `${rowNames[d.row]} \u2014 ${colNames[d.col]}
+rank: ${rStr} of ${n}
+scaled rank: ${d.v.toFixed(
+        3
+      )}`;
+    });
+    cellsG.selectAll("text.sjpp-mr-rank").data(cellData.filter((d) => d.v !== null && Number.isFinite(d.v))).enter().append("text").attr("class", "sjpp-mr-rank").attr("x", (d) => d.x + cellW / 2).attr("y", (d) => d.y + cellH / 2 + 3).attr("text-anchor", "middle").attr("font-size", "9px").attr("font-weight", 300).attr("pointer-events", "none").attr("fill", (d) => d.v < 0.5 ? "rgba(255,255,255,0.85)" : "rgba(40,40,40,0.7)").text((d) => {
+      const r = rankMatrix[d.row][d.col];
+      return Number.isInteger(r) ? String(r) : r.toFixed(1);
+    });
+    const rowLabelsG = svg.append("g").attr("transform", `translate(${gridX + gridW + 6},${colLabelH})`);
+    rowLabelsG.selectAll("text").data(rowNames).enter().append("text").attr("x", 0).attr("y", (_d, i) => i * cellH + cellH / 2 + 4).attr("font-size", "13px").attr("fill", "#000").text((d) => d);
+    const legendGradW = 16;
+    const legendX = gridX + gridW + 8 + rowLabelW + 8;
+    const legendY = colLabelH;
+    const legendG = svg.append("g").attr("transform", `translate(${legendX},${legendY})`);
+    legendG.append("text").attr("transform", `translate(-6,${legendGradH / 2}) rotate(-90)`).attr("text-anchor", "middle").attr("font-size", "11px").attr("fill", "#555").text("scaled rank (per column)");
+    const stops = 32;
+    for (let i = 0; i < stops; i++) {
+      const v = i / (stops - 1);
+      legendG.append("rect").attr("x", 0).attr("y", i * legendGradH / stops).attr("width", legendGradW).attr("height", legendGradH / stops + 0.5).attr("fill", color(v));
+    }
+    legendG.append("rect").attr("x", 0).attr("y", 0).attr("width", legendGradW).attr("height", legendGradH).attr("fill", "none").attr("stroke", "#999").attr("stroke-width", 0.5);
+    const maxRank = totals.reduce((m, t) => Number.isFinite(t) && t > m ? t : m, 0);
+    const midRank = Math.round((1 + maxRank) / 2);
+    legendG.append("text").attr("x", legendGradW + 6).attr("y", 4).attr("font-size", "11px").text("1 (top)");
+    legendG.append("text").attr("x", legendGradW + 6).attr("y", legendGradH / 2 + 4).attr("font-size", "11px").text(String(midRank));
+    legendG.append("text").attr("x", legendGradW + 6).attr("y", legendGradH).attr("font-size", "11px").text(`${maxRank} (bottom)`);
+    const missingG = svg.append("g").attr("transform", `translate(${legendX},${legendY + legendGradH + 18})`);
+    missingG.append("rect").attr("width", legendGradW).attr("height", 12).attr("fill", MISSING_COLOR).attr("stroke", "#999").attr("stroke-width", 0.5);
+    missingG.append("text").attr("x", legendGradW + 6).attr("y", 10).attr("font-size", "11px").attr("fill", "#555").text("missing");
+  }
+};
+function escapeHtml(s) {
+  return s.replace(/[&<>"']/g, (c) => ({ "&": "&amp;", "<": "&lt;", ">": "&gt;", '"': "&quot;", "'": "&#39;" })[c]);
+}
+function sortRows(rows, idx, asc) {
+  const sign = asc ? 1 : -1;
+  return rows.map((r, i) => ({ r, i })).sort((a, b) => {
+    const va = a.r[idx];
+    const vb = b.r[idx];
+    if (va == null && vb == null) return a.i - b.i;
+    if (va == null) return 1;
+    if (vb == null) return -1;
+    if (typeof va === "number" && typeof vb === "number") return (va - vb) * sign;
+    return String(va).localeCompare(String(vb)) * sign;
+  }).map((x) => x.r);
+}
+function computeColStats(allRows, colIdxs) {
+  const min = colIdxs.map(() => Infinity);
+  const max = colIdxs.map(() => -Infinity);
+  const n = colIdxs.map(() => 0);
+  for (const row of allRows) {
+    for (let i = 0; i < colIdxs.length; i++) {
+      const v = row[colIdxs[i]];
+      if (typeof v === "number" && Number.isFinite(v)) {
+        if (v < min[i]) min[i] = v;
+        if (v > max[i]) max[i] = v;
+        n[i]++;
+      }
+    }
+  }
+  return { min, max, n };
+}
+function drawRowDendrogram(g, dend, width, gridH, cellH) {
+  const heights = dend.height.map((h) => h.height);
+  const maxH = Math.max(...heights, 1e-9);
+  const hToX = linear().domain([0, maxH]).range([width, 0]);
+  const leafYByName = /* @__PURE__ */ new Map();
+  dend.order.forEach((leaf, i) => {
+    leafYByName.set(leaf.name, i * cellH + cellH / 2);
+  });
+  const merged = /* @__PURE__ */ new Map();
+  for (let i = 0; i < dend.merge.length; i++) {
+    const { n1, n2 } = dend.merge[i];
+    const pos = (n) => {
+      if (n < 0) {
+        const name = dend.inputOrder[-n - 1];
+        return { x: width, y: leafYByName.get(name) ?? 0 };
+      }
+      return merged.get(n) || { x: width, y: 0 };
+    };
+    const a = pos(n1);
+    const b = pos(n2);
+    const x = hToX(heights[i]);
+    const y = (a.y + b.y) / 2;
+    g.append("line").attr("x1", a.x).attr("x2", x).attr("y1", a.y).attr("y2", a.y).attr("stroke", "#000").attr("stroke-width", 1);
+    g.append("line").attr("x1", b.x).attr("x2", x).attr("y1", b.y).attr("y2", b.y).attr("stroke", "#000").attr("stroke-width", 1);
+    g.append("line").attr("x1", x).attr("x2", x).attr("y1", a.y).attr("y2", b.y).attr("stroke", "#000").attr("stroke-width", 1);
+    merged.set(i + 1, { x, y });
+  }
+}
+async function getPlotConfig(opts) {
+  const config = {
+    chartType: GeneRanking.type,
+    rankingKey: opts.rankingKey || ""
+  };
+  return copyMerge(config, opts);
+}
+var componentInit = getCompInit(GeneRanking);
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.dom.tip.clear();
+  const cfg = chartsInstance.state.termdbConfig?.queries?.geneRanking;
+  const rankings = cfg?.rankings;
+  if (!rankings || !Object.keys(rankings).length) {
+    holder.append("div").style("padding", "8px").style("color", "#888").text("No multiomic rankings available for this dataset.");
+    return;
+  }
+  for (const key of Object.keys(rankings)) {
+    holder.append("div").attr("class", "sja_menuoption sja_sharp_border").text(key).on("click", () => {
+      chartsInstance.dom.tip.hide();
+      chartsInstance.prepPlot({
+        config: {
+          chartType: "geneRanking",
+          rankingKey: key
+        }
+      });
+    });
+  }
+}
+export {
+  componentInit,
+  getPlotConfig,
+  makeChartBtnMenu
+};
+//# sourceMappingURL=geneRanking-6AXL5ZJS.js.map

package/dist/geneVariant-RZFDP5J5.js

@@ -0,0 +1,41 @@
+import {
+  SearchHandler,
+  addParentTerm,
+  getChildTerms
+} from "./chunk-WY2PGUVX.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-MBUQ34CF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OVSKJROY.js";
+import "./chunk-A3URBFXN.js";
+import "./chunk-LYVLF6HO.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-NNFAUP2I.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.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";
+export {
+  SearchHandler,
+  addParentTerm,
+  getChildTerms
+};
+//# sourceMappingURL=geneVariant-RZFDP5J5.js.map

package/dist/geneVariant-UIBZ5UIQ.js

@@ -0,0 +1,39 @@
+import {
+  getDtsFromGroups,
+  getHandler
+} from "./chunk-WY2PGUVX.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-MBUQ34CF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OVSKJROY.js";
+import "./chunk-A3URBFXN.js";
+import "./chunk-LYVLF6HO.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-NNFAUP2I.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.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";
+export {
+  getDtsFromGroups,
+  getHandler
+};
+//# sourceMappingURL=geneVariant-UIBZ5UIQ.js.map