@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

package/dist/proteinView-WVI3OVDD.js

@@ -1,1352 +0,0 @@
-import {
-  closeTilePanes,
-  getLog2Ratio,
-  getTileConfig,
-  launchViolinPlot,
-  makeTileGrid,
-  prepareTileData,
-  renderCoverageLine,
-  renderOverviewVolcanoCard,
-  renderPTMSummaryCard,
-  renderPlaceholderTiles,
-  renderStudyTiles
-} from "./chunk-R3UYQXJL.js";
-import "./chunk-ILEXRHF7.js";
-import {
-  DataPointInteractions,
-  LegendCircleReference,
-  PlotBase,
-  addGeneSearchbox,
-  axisstyle,
-  make_radios,
-  shapeSelector,
-  shapes,
-  table2col,
-  to_svg
-} from "./chunk-FIFNXVTS.js";
-import {
-  aa2gmcoord
-} from "./chunk-HJ6L54YS.js";
-import "./chunk-N2FCAFJH.js";
-import "./chunk-OH33WT6Q.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-EEB5VE2A.js";
-import {
-  icons
-} from "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-5MHE7AIV.js";
-import "./chunk-6WYKPBZI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-DBOJ3TMI.js";
-import {
-  TermTypes,
-  axisBottom,
-  axisLeft,
-  getColors,
-  mclass
-} from "./chunk-EZFO5UYD.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import {
-  roundValue
-} from "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  creator_default,
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/proteinView.ts
-var defaultConfig = {
-  chartType: "proteinView"
-};
-var COHORT_VOLCANO_HIT_RADIUS_PADDING_PX = 3;
-var COHORT_VOLCANO_HIT_BUFFER_PX = 2;
-var COHORT_VOLCANO_HOVER_RING_SIZE_SCALE = 1.15;
-var COHORT_VOLCANO_HOVER_RING_STROKE_PX = 1.5;
-var COHORT_VOLCANO_HOVER_MAX_COHORTS = 5;
-var ProteinView = class _ProteinView extends PlotBase {
-  static {
-    this.type = "proteinView";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _ProteinView.type;
-    this.components = {};
-  }
-  async init() {
-    const holder = this.opts.holder.append("div").style("padding", "10px");
-    this.dom = {
-      holder,
-      body: holder.append("div"),
-      tip: new Menu({ padding: "" }),
-      header: this.opts.header
-    };
-    if (this.dom.header) this.dom.header.html("Protein View");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config };
-  }
-  maySetSandboxHeader() {
-    if (!this.dom.header) return;
-    const term = this.state.config?.tw?.term;
-    const header = `Protein View: ${term?.name}`;
-    this.dom.header.text(header);
-  }
-  async main() {
-    const term = this.state.config?.tw?.term;
-    if (!term?.name) throw new Error("proteinView: selected protein term is missing");
-    const body = {
-      genome: this.app.opts.state.vocab.genome,
-      dslabel: this.app.opts.state.vocab.dslabel,
-      term: this.state.config.tw,
-      filter: this.state.config.filter,
-      filter0: this.state.config.filter0
-    };
-    this.maySetSandboxHeader();
-    closeTilePanes(this);
-    const data = await dofetch3("termdb/proteome", { body });
-    if (data.error) throw data.error;
-    this.dom.body.selectAll("*").remove();
-    const tileData = prepareTileData(data, this);
-    renderCoverageLine(this.dom.body, tileData);
-    const grid = makeTileGrid(this.dom.body);
-    renderOverviewVolcanoCard(grid, data, this, {
-      onExpandRender: (holder) => {
-        renderCohortVolcano(holder, data, this, tileData.ptmSiteCount);
-      }
-    });
-    const { missing: missingTiles } = renderStudyTiles(grid, tileData, this);
-    const ptmDataByOrganism = /* @__PURE__ */ new Map();
-    for (const cohortData of data.cohorts || []) {
-      if (!cohortData.PTMType) continue;
-      const organism = cohortData.organism;
-      const isoform = cohortData.isoform;
-      const ptmDataByIsoform = ptmDataByOrganism.get(organism) || /* @__PURE__ */ new Map();
-      ptmDataByOrganism.set(organism, ptmDataByIsoform);
-      const existingCohorts = ptmDataByIsoform.get(isoform);
-      if (!existingCohorts) {
-        ptmDataByIsoform.set(isoform, [cohortData]);
-      } else {
-        existingCohorts.push(cohortData);
-      }
-    }
-    const sections = [];
-    for (const [organism, byIso] of ptmDataByOrganism) {
-      for (const [isoform, cohorts] of byIso) {
-        sections.push({ organism, isoform, cohorts, genomeName: cohorts[0].genomeName });
-      }
-    }
-    let allGenomes = null;
-    const baseGenome = this.app.opts.genome;
-    const getGenome = async (genomeName) => {
-      if (genomeName === baseGenome.name) return baseGenome;
-      if (!allGenomes) {
-        const result = await dofetch3("genomes");
-        allGenomes = result.genomes || {};
-        for (const g2 of Object.values(allGenomes)) {
-          if (g2.chrlookup || g2.name == baseGenome.name) continue;
-          g2.chrlookup = {};
-          for (const chr in g2.majorchr) {
-            g2.chrlookup[chr.toUpperCase()] = { name: chr, len: g2.majorchr[chr], major: true };
-          }
-          for (const chr in g2.minorchr || {}) {
-            g2.chrlookup[chr.toUpperCase()] = { name: chr, len: g2.minorchr[chr] };
-          }
-        }
-      }
-      const g = allGenomes[genomeName];
-      if (!g) throw `genome ${genomeName} not supported`;
-      return g;
-    };
-    const renderPTMSectionsInto = async (holder) => {
-      if (sections.length === 1) {
-        const s = sections[0];
-        const genome = await getGenome(s.genomeName);
-        await renderPTMLollipop(holder.append("div"), s.cohorts, this, s.isoform, genome);
-        return;
-      }
-      const keyOf = (s) => `${s.organism}
${s.isoform}`;
-      const selectedKeys = /* @__PURE__ */ new Set([keyOf(sections[0])]);
-      let compareMode = false;
-      const layoutDiv = holder.append("div").style("display", "flex").style("gap", "16px").style("margin-top", "10px").style("margin-left", "70px").style("align-items", "flex-start");
-      const sidebar = layoutDiv.append("div").style("flex", "0 0 220px").style("border", "1px solid #e5e7eb").style("border-radius", "4px").style("padding", "8px").style("font-size", ".85em").style("position", "sticky").style("top", "8px").style("margin-top", "20px").style("max-height", "85vh").style("overflow", "auto");
-      const rightPane = layoutDiv.append("div").style("flex", "1 1 auto").style("min-width", "0");
-      const sidebarHeader = sidebar.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "6px").style("margin-bottom", "8px");
-      sidebarHeader.append("span").style("font-weight", "600").style("font-size", "1.5em").style("text-transform", "uppercase").text("Isoforms");
-      const modeToggle = sidebarHeader.append("div").style("display", "inline-flex").style("align-items", "center").style("gap", "6px");
-      modeToggle.append("span").style("color", "#6b7280").text("Mode:");
-      make_radios({
-        holder: modeToggle.append("div").attr("aria-label", "Isoform view mode"),
-        options: [
-          { label: "Single", value: "single", checked: true },
-          { label: "Compare", value: "compare" }
-        ],
-        styles: { display: "inline-block" },
-        callback: (value) => {
-          const asCompare = value === "compare";
-          if (asCompare === compareMode) return;
-          compareMode = asCompare;
-          if (!compareMode && selectedKeys.size > 1) {
-            const first = selectedKeys.values().next().value;
-            selectedKeys.clear();
-            selectedKeys.add(first);
-          }
-          renderSidebar();
-          void renderRight();
-        }
-      });
-      const sidebarList = sidebar.append("div");
-      const sectionsByOrganism = /* @__PURE__ */ new Map();
-      for (const s of sections) {
-        const arr = sectionsByOrganism.get(s.organism) || [];
-        arr.push(s);
-        sectionsByOrganism.set(s.organism, arr);
-      }
-      const showOrganismHeading = sectionsByOrganism.size > 1;
-      const renderSidebar = () => {
-        sidebarList.selectAll("*").remove();
-        for (const [organism, items] of sectionsByOrganism) {
-          if (showOrganismHeading) {
-            sidebarList.append("div").text(organism).style("font-weight", "600").style("color", "#374151").style("margin", "6px 0 4px 0");
-          }
-          for (const s of items) {
-            const key = keyOf(s);
-            const isSelected = selectedKeys.has(key);
-            const isSoleSelection = isSelected && selectedKeys.size === 1;
-            const toggleSelection = () => {
-              if (compareMode) {
-                if (selectedKeys.has(key)) {
-                  if (selectedKeys.size > 1) selectedKeys.delete(key);
-                  else return;
-                } else selectedKeys.add(key);
-              } else {
-                if (selectedKeys.has(key) && selectedKeys.size === 1) return;
-                selectedKeys.clear();
-                selectedKeys.add(key);
-              }
-              renderSidebar();
-              void renderRight();
-            };
-            const row = sidebarList.append("div").attr("role", compareMode ? "checkbox" : "radio").attr("aria-checked", String(isSelected)).attr("aria-label", `${s.organism} ${s.isoform}`).attr("tabindex", "0").style("display", "flex").style("align-items", "center").style("gap", "6px").style("padding", "3px 4px").style("border-radius", "3px").style("background", isSelected ? "#eff6ff" : "transparent").style("cursor", "pointer").on("click", toggleSelection).on("keydown", (event) => {
-              if (event.key === "Enter" || event.key === " ") {
-                event.preventDefault();
-                toggleSelection();
-              }
-            });
-            if (compareMode) {
-              row.append("input").attr("type", "checkbox").attr("tabindex", "-1").attr("aria-hidden", "true").property("checked", isSelected).property("disabled", isSoleSelection).style("margin", "0").style("cursor", isSoleSelection ? "not-allowed" : "pointer").on("click", (event) => {
-                event.stopPropagation();
-                toggleSelection();
-              });
-            }
-            row.append("span").text(s.isoform);
-            row.append("span").style("color", "#6b7280").style("margin-left", "auto").text(String(s.cohorts.length));
-          }
-        }
-      };
-      const renderRight = async () => {
-        rightPane.selectAll("*").remove();
-        const selected = sections.filter((s) => selectedKeys.has(keyOf(s)));
-        if (!selected.length) return;
-        const cols = rightPane.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "16px");
-        for (const s of selected) {
-          const col = cols.append("div").style("min-width", "0");
-          try {
-            const genome = await getGenome(s.genomeName);
-            await renderPTMLollipop(col, s.cohorts, this, s.isoform, genome);
-          } catch (err) {
-            col.append("div").style("color", "#b91c1c").style("padding", "6px").text(`Failed to render ${s.organism} \xB7 ${s.isoform}: ${err?.message || err}`);
-          }
-        }
-      };
-      renderSidebar();
-      await renderRight();
-    };
-    if (sections.length) {
-      renderPTMSummaryCard(
-        grid,
-        (data.cohorts || []).filter((c) => c.PTMType),
-        this,
-        { onExpandRender: renderPTMSectionsInto }
-      );
-    }
-    const ptmCfg = getTileConfig(this, "ptm");
-    const placeholders = missingTiles.map((t) => ({ title: t.title }));
-    if (!sections.length && ptmCfg && ptmAssaysConfigured(this)) placeholders.push({ title: ptmCfg.title });
-    renderPlaceholderTiles(grid, placeholders);
-  }
-  /** rx calls this when the plot is deleted: expanded-tile panes live on document.body
-   *  and would otherwise outlive the plot with handlers bound to a dead instance */
-  destroy() {
-    closeTilePanes(this);
-  }
-};
-function ptmAssaysConfigured(self) {
-  const organisms = self.app.vocabApi.termdbConfig?.queries?.proteome?.organisms || {};
-  for (const org of Object.values(organisms)) {
-    for (const assay of Object.values(org?.assays || {})) if (assay?.PTMType) return true;
-  }
-  return false;
-}
-function renderCohortVolcano(holder, data, self, ptmSiteCount = 0) {
-  const dots = [];
-  const sampleRegionById = data?.sampleRegions || {};
-  for (const cohortData of data?.cohorts || []) {
-    if (cohortData.PTMType) continue;
-    const log2fc = getLog2Ratio(cohortData.foldChange);
-    const fdr = Number(cohortData.fdr);
-    const testedN = Number(cohortData.testedN);
-    const controlN = Number(cohortData.controlN);
-    if (log2fc === null || !Number.isFinite(fdr) || fdr <= 0) continue;
-    dots.push({
-      organismName: cohortData.organism,
-      disease: cohortData.disease,
-      assayName: cohortData.assayName,
-      cohortName: cohortData.cohortName,
-      proteinAccession: cohortData.proteinAccession,
-      uniqueIdentifier: cohortData.uniqueIdentifier,
-      log2fc,
-      fdr,
-      score: -Math.log10(Math.max(fdr, 1e-300)),
-      testedN: Number.isFinite(testedN) ? testedN : 0,
-      controlN: Number.isFinite(controlN) ? controlN : 0,
-      // per-dot sample identity (case + control); each sample's region comes from the
-      // response-level sampleRegions map and is listed in the dot's tooltip
-      sampleIds: Array.isArray(cohortData.sampleIds) ? cohortData.sampleIds : []
-    });
-  }
-  const panel = holder.append("div").style("margin-bottom", "14px");
-  const header = panel.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px").style("margin-bottom", "6px");
-  const downloadBtn = header.append("div").style("display", "inline-block");
-  if (ptmSiteCount) {
-    header.append("div").style("font-size", ".75em").style("color", "#6b7280").text(
-      `${ptmSiteCount} site-level PTM measurement${ptmSiteCount === 1 ? "" : "s"} excluded \u2014 see the PTM track below.`
-    );
-  }
-  if (!dots.length) {
-    downloadBtn.style("display", "none");
-    panel.append("div").style("font-size", ".85em").style("color", "#666").text("No cohorts with valid fold-change and FDR to plot.");
-    return;
-  }
-  const width = 500;
-  const height = 480;
-  const margin = { top: 20, right: 30, bottom: 60, left: 70 };
-  const innerW = width - margin.left - margin.right;
-  const innerH = height - margin.top - margin.bottom;
-  let minX = Number.POSITIVE_INFINITY;
-  let maxX = Number.NEGATIVE_INFINITY;
-  let maxY = 0;
-  let maxTestedN = 0;
-  let minTestedN = Number.POSITIVE_INFINITY;
-  for (const p of dots) {
-    minX = Math.min(minX, p.log2fc);
-    maxX = Math.max(maxX, p.log2fc);
-    maxY = Math.max(maxY, p.score);
-    maxTestedN = Math.max(maxTestedN, p.testedN);
-    if (p.testedN > 0) minTestedN = Math.min(minTestedN, p.testedN);
-  }
-  if (maxY < 1) maxY = 1;
-  if (!Number.isFinite(minTestedN)) minTestedN = 1;
-  const xSpan = Math.max(0.05, maxX - minX);
-  const xPad = Math.max(0.01, xSpan * 0.1);
-  const xMin = Math.min(0, minX - xPad);
-  const xMax = Math.max(0, maxX + xPad);
-  const yMax = maxY * 1.15;
-  const xScale = linear().domain([xMin, xMax]).range([0, innerW]);
-  const yScale = linear().domain([0, yMax]).range([innerH, 0]);
-  const radiusRange = [4, 12];
-  const radiusScale = linear().domain([minTestedN, Math.max(minTestedN + 1, maxTestedN)]).range(radiusRange);
-  let scaleDotSize = true;
-  const getDotRadius = (d) => scaleDotSize ? radiusScale(Math.max(minTestedN, d.testedN || minTestedN)) : (radiusRange[0] + radiusRange[1]) / 2;
-  const organismNames = [...new Set(dots.map((d) => d.organismName).filter(Boolean))].sort();
-  const assayNames = [...new Set(dots.map((d) => d.assayName))].sort();
-  const cohortNames = [...new Set(dots.map((d) => d.cohortName))].sort();
-  const proteinAccessions = [...new Set(dots.map((d) => d.proteinAccession))].sort();
-  const organismColorScale = getColors(organismNames.length).domain(organismNames);
-  const assayColorScale = getColors(assayNames.length).domain(assayNames);
-  const cohortColorScale = getColors(cohortNames.length).domain(cohortNames);
-  const proteinColorScale = getColors(proteinAccessions.length).domain(proteinAccessions);
-  const organismColors = new Map(
-    organismNames.map((name) => [name, rgb(organismColorScale(name)).formatHex()])
-  );
-  const assayColors = new Map(assayNames.map((name) => [name, rgb(assayColorScale(name)).formatHex()]));
-  const cohortColors = new Map(cohortNames.map((name) => [name, rgb(cohortColorScale(name)).formatHex()]));
-  const proteinColors = new Map(
-    proteinAccessions.map((acc) => [acc, rgb(proteinColorScale(acc)).formatHex()])
-  );
-  const prioritizedShapesArray = (() => {
-    const entries = Object.entries(shapes);
-    const sorted = [
-      ...entries.filter(([, s]) => s.isFilled === true),
-      ...entries.filter(([, s]) => s.isFilled === false),
-      ...entries.filter(([, s]) => !("isFilled" in s))
-    ];
-    return sorted.map(([, s]) => s.path);
-  })();
-  const makeShapeMap = (items) => new Map(items.map((item, i) => [item, i % prioritizedShapesArray.length]));
-  const organismShapes = makeShapeMap(organismNames);
-  const assayShapes = makeShapeMap(assayNames);
-  const cohortShapes = makeShapeMap(cohortNames);
-  const proteinShapes = makeShapeMap(proteinAccessions);
-  let colorMode = "assayType";
-  let shapeMode = "organism";
-  const customGroupPrefix = "__custom_group__:";
-  const makeCustomGroupKey = (name) => `${customGroupPrefix}${name}`;
-  const isCustomGroupKey = (value) => value.startsWith(customGroupPrefix);
-  const getCustomGroupNameFromKey = (value) => value.slice(customGroupPrefix.length);
-  const customShapeGroupPrefix = "__custom_shape_group__:";
-  const makeCustomShapeGroupKey = (name) => `${customShapeGroupPrefix}${name}`;
-  const isCustomShapeGroupKey = (value) => value.startsWith(customShapeGroupPrefix);
-  const getCustomShapeGroupNameFromKey = (value) => value.slice(customShapeGroupPrefix.length);
-  const customColorDomain = Array.from({ length: 64 }, (_, i) => `custom-${i}`);
-  const customColorScale = getColors(customColorDomain.length).domain(customColorDomain);
-  const colorModesWithGroups = ["organism", "assayType", "cohort", "proteinAccession"];
-  const shapeModesWithGroups = ["organism", "assayType", "cohort", "proteinAccession"];
-  const createModeMap = (factory) => ({
-    organism: factory(),
-    assayType: factory(),
-    cohort: factory(),
-    proteinAccession: factory()
-  });
-  const customGroupsByMode = createModeMap(() => /* @__PURE__ */ new Map());
-  const customGroupColorsByMode = createModeMap(() => /* @__PURE__ */ new Map());
-  const customShapeGroupsByMode = createModeMap(() => /* @__PURE__ */ new Map());
-  const customShapeIndicesByMode = createModeMap(() => /* @__PURE__ */ new Map());
-  const checkedItemsByMode = createModeMap(() => /* @__PURE__ */ new Set());
-  const checkedShapeItemsByMode = createModeMap(() => /* @__PURE__ */ new Set());
-  const groupingModeActive = /* @__PURE__ */ new Set();
-  const shapeGroupingModeActive = /* @__PURE__ */ new Set();
-  let customColorSeed = 0;
-  const getBaseColorValue = (d, mode) => {
-    switch (mode) {
-      case "organism":
-        return d.organismName;
-      case "assayType":
-        return d.assayName;
-      case "cohort":
-        return d.cohortName;
-      case "proteinAccession":
-        return d.proteinAccession;
-      default:
-        return "";
-    }
-  };
-  const getCustomGroupOfValue = (mode, value) => {
-    for (const [group, members] of customGroupsByMode[mode]) {
-      if (members.has(value)) return group;
-    }
-    return null;
-  };
-  const getCustomGroupOfDot = (d, mode) => {
-    return getCustomGroupOfValue(mode, getBaseColorValue(d, mode));
-  };
-  const getCustomShapeGroupOfValue = (mode, value) => {
-    for (const [group, members] of customShapeGroupsByMode[mode]) {
-      if (members.has(value)) return group;
-    }
-    return null;
-  };
-  const getCustomShapeGroupOfDot = (d, mode) => {
-    return getCustomShapeGroupOfValue(mode, getBaseColorValue(d, mode));
-  };
-  const getNextCustomColor = () => {
-    const color = rgb(customColorScale(customColorDomain[customColorSeed % customColorDomain.length])).formatHex();
-    customColorSeed++;
-    return color;
-  };
-  const addOrUpdateCustomGroup = (mode, name, baseValues) => {
-    if (!name || !baseValues.length) return;
-    for (const members of customGroupsByMode[mode].values()) {
-      for (const val of baseValues) members.delete(val);
-    }
-    const existing = customGroupsByMode[mode].get(name) || /* @__PURE__ */ new Set();
-    for (const val of baseValues) existing.add(val);
-    customGroupsByMode[mode].set(name, existing);
-    if (!customGroupColorsByMode[mode].has(name)) customGroupColorsByMode[mode].set(name, getNextCustomColor());
-  };
-  const removeCustomGroup = (mode, name) => {
-    customGroupsByMode[mode].delete(name);
-    customGroupColorsByMode[mode].delete(name);
-    hiddenColor[mode].delete(makeCustomGroupKey(name));
-  };
-  const addOrUpdateCustomShapeGroup = (mode, name, baseValues) => {
-    if (!name || !baseValues.length) return;
-    for (const members of customShapeGroupsByMode[mode].values()) {
-      for (const val of baseValues) members.delete(val);
-    }
-    const existing = customShapeGroupsByMode[mode].get(name) || /* @__PURE__ */ new Set();
-    for (const val of baseValues) existing.add(val);
-    customShapeGroupsByMode[mode].set(name, existing);
-    if (!customShapeIndicesByMode[mode].has(name)) {
-      const idx = customShapeIndicesByMode[mode].size % prioritizedShapesArray.length;
-      customShapeIndicesByMode[mode].set(name, idx);
-    }
-  };
-  const removeCustomShapeGroup = (mode, name) => {
-    customShapeGroupsByMode[mode].delete(name);
-    customShapeIndicesByMode[mode].delete(name);
-    hiddenShape[mode].delete(makeCustomShapeGroupKey(name));
-  };
-  const getCustomGroupItems = (mode) => {
-    return [...customGroupsByMode[mode].keys()].sort().map((name) => makeCustomGroupKey(name));
-  };
-  const getCustomShapeGroupItems = (mode) => {
-    return [...customShapeGroupsByMode[mode].keys()].sort().map((name) => makeCustomShapeGroupKey(name));
-  };
-  const getLegendItemSampleCount = (mode, item, dotsToCount = dots) => {
-    let matched;
-    if (isCustomGroupKey(item)) {
-      const groupName = getCustomGroupNameFromKey(item);
-      matched = dotsToCount.filter(
-        (d) => getCustomGroupOfValue(mode, getBaseColorValue(d, mode)) === groupName
-      );
-    } else if (isCustomShapeGroupKey(item)) {
-      const groupName = getCustomShapeGroupNameFromKey(item);
-      matched = dotsToCount.filter(
-        (d) => getCustomShapeGroupOfValue(mode, getBaseColorValue(d, mode)) === groupName
-      );
-    } else {
-      matched = dotsToCount.filter((d) => getBaseColorValue(d, mode) === item);
-    }
-    return new Set(matched.map((d) => `${d.organismName}|${d.assayName}|${d.cohortName}`)).size;
-  };
-  const getColor = (d) => {
-    const customGroup = getCustomGroupOfDot(d, colorMode);
-    switch (colorMode) {
-      case "organism":
-        if (customGroup) return customGroupColorsByMode[colorMode].get(customGroup) ?? "#888";
-        return organismColors.get(d.organismName) ?? "#888";
-      case "assayType":
-        if (customGroup) return customGroupColorsByMode[colorMode].get(customGroup) ?? "#888";
-        return assayColors.get(d.assayName) ?? "#888";
-      case "cohort":
-        if (customGroup) return customGroupColorsByMode[colorMode].get(customGroup) ?? "#888";
-        return cohortColors.get(d.cohortName) ?? "#888";
-      case "proteinAccession":
-        if (customGroup) return customGroupColorsByMode[colorMode].get(customGroup) ?? "#888";
-        return proteinColors.get(d.proteinAccession) ?? "#888";
-      default:
-        return "#888";
-    }
-  };
-  const getShapeIndex = (d) => {
-    const customShapeGroup = getCustomShapeGroupOfDot(d, shapeMode);
-    if (customShapeGroup) {
-      return customShapeIndicesByMode[shapeMode].get(customShapeGroup) ?? 0;
-    }
-    switch (shapeMode) {
-      case "organism":
-        return organismShapes.get(d.organismName) ?? 0;
-      case "assayType":
-        return assayShapes.get(d.assayName) ?? 0;
-      case "cohort":
-        return cohortShapes.get(d.cohortName) ?? 0;
-      case "proteinAccession":
-        return proteinShapes.get(d.proteinAccession) ?? 0;
-      default:
-        return 0;
-    }
-  };
-  const getShapePath = (d) => {
-    const index = getShapeIndex(d) % prioritizedShapesArray.length;
-    return prioritizedShapesArray[index];
-  };
-  const getShapeTransform = (d, sizeScale = 1) => {
-    const r = getDotRadius(d) * sizeScale;
-    const scale = r / 8;
-    const x = xScale(d.log2fc) - 8 * scale;
-    const y = yScale(d.score) - 8 * scale;
-    return `translate(${x},${y}) scale(${scale})`;
-  };
-  const colorGroupingModes = [
-    { key: "organism", label: "Organism" },
-    { key: "assayType", label: "Assay" },
-    { key: "cohort", label: "Sample Set" },
-    { key: "proteinAccession", label: "Isoform" }
-  ];
-  const shapeGroupingModes = [
-    { key: "organism", label: "Organism" },
-    { key: "assayType", label: "Assay" },
-    { key: "cohort", label: "Sample Set" },
-    { key: "proteinAccession", label: "Isoform" }
-  ];
-  const makeHiddenState = () => ({
-    organism: /* @__PURE__ */ new Set(),
-    assayType: /* @__PURE__ */ new Set(),
-    cohort: /* @__PURE__ */ new Set(),
-    proteinAccession: /* @__PURE__ */ new Set()
-  });
-  const hiddenColor = makeHiddenState();
-  const hiddenShape = makeHiddenState();
-  const getColorValueByMode = (d, mode) => {
-    switch (mode) {
-      case "organism":
-        return getCustomGroupOfDot(d, mode) ? makeCustomGroupKey(getCustomGroupOfDot(d, mode)) : d.organismName;
-      case "assayType":
-        return getCustomGroupOfDot(d, mode) ? makeCustomGroupKey(getCustomGroupOfDot(d, mode)) : d.assayName;
-      case "cohort":
-        return getCustomGroupOfDot(d, mode) ? makeCustomGroupKey(getCustomGroupOfDot(d, mode)) : d.cohortName;
-      case "proteinAccession":
-        return getCustomGroupOfDot(d, mode) ? makeCustomGroupKey(getCustomGroupOfDot(d, mode)) : d.proteinAccession;
-      default:
-        return "";
-    }
-  };
-  const getShapeValueByMode = (d, mode) => {
-    switch (mode) {
-      case "organism":
-        return getCustomShapeGroupOfDot(d, mode) ? makeCustomShapeGroupKey(getCustomShapeGroupOfDot(d, mode)) : d.organismName;
-      case "assayType":
-        return getCustomShapeGroupOfDot(d, mode) ? makeCustomShapeGroupKey(getCustomShapeGroupOfDot(d, mode)) : d.assayName;
-      case "cohort":
-        return getCustomShapeGroupOfDot(d, mode) ? makeCustomShapeGroupKey(getCustomShapeGroupOfDot(d, mode)) : d.cohortName;
-      case "proteinAccession":
-        return getCustomShapeGroupOfDot(d, mode) ? makeCustomShapeGroupKey(getCustomShapeGroupOfDot(d, mode)) : d.proteinAccession;
-      default:
-        return "";
-    }
-  };
-  const isDotHidden = (d) => {
-    const colorValue = getColorValueByMode(d, colorMode);
-    const shapeValue = getShapeValueByMode(d, shapeMode);
-    return hiddenColor[colorMode].has(colorValue) || hiddenShape[shapeMode].has(shapeValue);
-  };
-  const getDotDistancePx = (d1, d2) => {
-    const x = xScale(d1.log2fc) - xScale(d2.log2fc);
-    const y = yScale(d1.score) - yScale(d2.score);
-    return Math.sqrt(x * x + y * y);
-  };
-  const getVisibleDots = () => dots.filter((d) => !isDotHidden(d));
-  const getVisibleTestedNStats = () => {
-    const visibleDots = getVisibleDots();
-    if (!visibleDots.length) {
-      return { domainMin: 1, domainMax: 2, minLabel: 0, maxLabel: 0 };
-    }
-    let visibleMax = 0;
-    let visibleMin = Number.POSITIVE_INFINITY;
-    for (const d of visibleDots) {
-      visibleMax = Math.max(visibleMax, d.testedN);
-      if (d.testedN > 0) visibleMin = Math.min(visibleMin, d.testedN);
-    }
-    if (!Number.isFinite(visibleMin)) visibleMin = 1;
-    const domainMax = Math.max(visibleMin + 1, visibleMax);
-    return { domainMin: visibleMin, domainMax, minLabel: visibleMin, maxLabel: visibleMax || visibleMin };
-  };
-  const updateRadiusScaleForVisibleDots = () => {
-    const stats = getVisibleTestedNStats();
-    radiusScale.domain([stats.domainMin, stats.domainMax]).range(radiusRange);
-    return stats;
-  };
-  const getClusterDots = (seed) => {
-    const thresholdPx = 5;
-    return dots.filter((d) => !isDotHidden(d) && getDotDistancePx(d, seed) < thresholdPx).sort((a, b) => getDotDistancePx(a, seed) - getDotDistancePx(b, seed));
-  };
-  const buildClusterTableData = (clusterDots) => {
-    const columns = [
-      { label: "Organism" },
-      { label: "Assay" },
-      { label: "Sample Set" },
-      { label: "Isoform" },
-      { label: "log\u2082(FC)", sortable: true },
-      { label: "FDR", sortable: true }
-    ];
-    const rows = clusterDots.map((d) => [
-      { value: d.organismName || "" },
-      { value: d.assayName || "" },
-      { value: d.cohortName || "" },
-      { value: d.uniqueIdentifier || "" },
-      { value: roundValue(d.log2fc, 3) },
-      { value: d.fdr.toExponential(2) }
-    ]);
-    return { columns, rows };
-  };
-  const updateDots = () => {
-    cohortDots.attr("fill", (d) => getColor(d)).attr("stroke", (d) => getColor(d)).attr("stroke-width", 1).attr("d", (d) => getShapePath(d)).attr("transform", (d) => getShapeTransform(d)).style("opacity", (d) => isDotHidden(d) ? 0 : 1).style("pointer-events", (d) => isDotHidden(d) ? "none" : "auto");
-  };
-  const getShapeMapInUse = () => {
-    switch (shapeMode) {
-      case "organism":
-        return organismShapes;
-      case "assayType":
-        return assayShapes;
-      case "cohort":
-        return cohortShapes;
-      case "proteinAccession":
-        return proteinShapes;
-      default:
-        return assayShapes;
-    }
-  };
-  const plotAndLegend = panel.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "4px").style("flex-wrap", "wrap");
-  const svg = plotAndLegend.append("svg").attr("width", width).attr("height", height).style("display", "block").style("max-width", "100%").style("height", "auto");
-  const g = svg.append("g").attr("transform", `translate(${margin.left},${margin.top})`);
-  const xAxis = g.append("g").attr("transform", `translate(0,${innerH})`).call(axisBottom(xScale));
-  axisstyle({ axis: xAxis, color: "black", showline: true });
-  const yAxis = g.append("g").call(axisLeft(yScale));
-  axisstyle({ axis: yAxis, color: "black", showline: true });
-  const x0 = xScale(0);
-  const pThreshold = -Math.log10(0.05);
-  const thresholdY = yScale(Math.min(yMax, pThreshold));
-  g.append("line").attr("x1", x0).attr("x2", x0).attr("y1", 0).attr("y2", innerH).attr("stroke", "black").attr("stroke-dasharray", "5 4").attr("stroke-opacity", 0.4);
-  g.append("line").attr("x1", 0).attr("x2", innerW).attr("y1", thresholdY).attr("y2", thresholdY).attr("stroke", "black").attr("stroke-dasharray", "5 4").attr("stroke-opacity", 0.4);
-  g.append("text").attr("x", innerW / 2).attr("y", innerH + 44).attr("text-anchor", "middle").style("font-weight", 600).text("log2 fold change");
-  g.append("text").attr("transform", `translate(${-50},${innerH / 2}) rotate(-90)`).attr("text-anchor", "middle").style("font-weight", 600).text("-log10(FDR)");
-  const cohortDots = g.selectAll("path.cohort-dot").data(dots).enter().append("path").attr("class", "cohort-dot").attr("transform", (d) => getShapeTransform(d, 0.9)).attr("d", (d) => getShapePath(d)).attr("fill", (d) => getColor(d)).attr("fill-opacity", 0.5).attr("stroke", (d) => getColor(d)).attr("stroke-width", 1).attr("vector-effect", "non-scaling-stroke");
-  cohortDots.transition().duration(350).attr("d", (d) => getShapePath(d)).attr("transform", (d) => getShapeTransform(d, 1));
-  const hoverLayer = g.append("g").attr("class", "cohort-volcano-hover").style("pointer-events", "none");
-  const cover = g.append("rect").attr("class", "cohort-volcano-cover").attr("x", 0).attr("y", 0).attr("width", innerW).attr("height", innerH).attr("fill", "transparent").style("pointer-events", "all").style("cursor", "default");
-  updateDots();
-  const renderDotInfoTable = (d, container) => {
-    const tbl = table2col({ holder: container.append("table") });
-    tbl.addRow("Organism", d.organismName);
-    tbl.addRow("Disease", d.disease);
-    tbl.addRow("Assay", d.assayName);
-    tbl.addRow("Sample Set", d.cohortName);
-    const dotRegions = [
-      ...new Set((d.sampleIds || []).map((sid) => sampleRegionById[sid]).filter(Boolean))
-    ];
-    if (dotRegions.length) {
-      const regionNames = self.app.vocabApi.termdbConfig?.queries?.proteome?.brainRegions?.regions || {};
-      tbl.addRow(
-        "Brain Region",
-        dotRegions.sort().map((c) => regionNames[c] ? `${regionNames[c]} (${c})` : c).join(", ")
-      );
-    }
-    tbl.addRow("Protein Accession", d.proteinAccession);
-    tbl.addRow("Isoform", d.uniqueIdentifier);
-    tbl.addRow("log2 fold change", roundValue(d.log2fc, 3));
-    tbl.addRow("FDR", d.fdr.toExponential(2));
-    tbl.addRow("-log10(FDR)", roundValue(d.score, 3));
-    tbl.addRow("Case samples", d.testedN);
-    tbl.addRow("Control samples", d.controlN);
-  };
-  const interactions = new DataPointInteractions({
-    cover,
-    hoverLayer,
-    hoverTip: self.dom.tip,
-    points: dots,
-    getX: (d) => xScale(d.log2fc),
-    getY: (d) => yScale(d.score),
-    // Function form because the size-legend menu mutates radiusRange at runtime;
-    // caching this once would leave the broad-query stale after dots are enlarged.
-    hitRadius: () => radiusRange[1] + COHORT_VOLCANO_HIT_RADIUS_PADDING_PX,
-    perDotRadius: (d) => getDotRadius(d),
-    perDotBuffer: COHORT_VOLCANO_HIT_BUFFER_PX,
-    isHidden: isDotHidden,
-    getCluster: (seed) => getClusterDots(seed),
-    toHoverSpec: (d) => ({
-      path: getShapePath(d),
-      transform: getShapeTransform(d, COHORT_VOLCANO_HOVER_RING_SIZE_SCALE),
-      stroke: "black",
-      strokeWidth: COHORT_VOLCANO_HOVER_RING_STROKE_PX
-    }),
-    maxTooltipRows: COHORT_VOLCANO_HOVER_MAX_COHORTS,
-    itemNoun: "cohort",
-    renderSingleHoverTooltip: renderDotInfoTable,
-    buildMultiHitTableData: buildClusterTableData,
-    getActions: (d) => [
-      {
-        label: "Violin plot",
-        onClick: () => {
-          launchViolinPlot(self, d.organismName, d.assayName, d.cohortName, d.uniqueIdentifier);
-        }
-      }
-    ],
-    renderSingleHitInfo: renderDotInfoTable,
-    getRowKey: (d) => d.uniqueIdentifier
-  });
-  interactions.attach();
-  const legend = plotAndLegend.append("div").style("margin", "0").style("min-width", "220px").style("font-size", ".75em").style("color", "#374151");
-  function renderSizeLegend() {
-    legendSvg.selectAll("*").remove();
-    const stats = updateRadiusScaleForVisibleDots();
-    new LegendCircleReference({
-      g: legendSvg.append("g").attr("transform", "translate(12, 8)"),
-      inputMax: radiusRange[1],
-      inputMin: radiusRange[0],
-      maxLabel: stats.maxLabel,
-      maxRadius: radiusScale(stats.domainMax),
-      minLabel: stats.minLabel,
-      minRadius: radiusScale(stats.domainMin),
-      title: "",
-      menu: {
-        minMaxLabel: "pixels",
-        callback: async (obj) => {
-          radiusRange[0] = obj.min;
-          radiusRange[1] = obj.max;
-          radiusScale.range([obj.min, obj.max]);
-          updateDots();
-          renderSizeLegend();
-        }
-      }
-    });
-  }
-  const refreshAfterVisibilityChange = () => {
-    updateRadiusScaleForVisibleDots();
-    updateDots();
-    renderColorLegend();
-    renderSizeLegend();
-  };
-  const termName = self.state.config?.tw?.term?.name || "";
-  const svgName = `${termName}.cohort-volcano`;
-  const downloadVolcanoSvg = () => {
-    const plotNode = svg.node();
-    const legendNode = legend.node();
-    if (!plotNode) return;
-    const plotWidth = width;
-    const plotHeight = height;
-    const legendRect = legendNode?.getBoundingClientRect();
-    const legendWidth = Math.max(220, Math.ceil(legendRect?.width || 220));
-    const legendHeight = Math.max(plotHeight, Math.ceil(legendRect?.height || 0));
-    const gap = 14;
-    const combinedSvg = select_default(creator_default("svg").call(document.documentElement)).attr("width", plotWidth + gap + legendWidth).attr("height", legendHeight);
-    combinedSvg.append(() => plotNode.cloneNode(true));
-    combinedSvg.append("foreignObject").attr("x", plotWidth + gap).attr("y", 0).attr("width", legendWidth).attr("height", legendHeight).append(() => {
-      const clone = legendNode.cloneNode(true);
-      clone.style.margin = "0px";
-      clone.style.minWidth = "0px";
-      return clone;
-    });
-    to_svg(combinedSvg.node(), svgName, { apply_dom_styles: true });
-  };
-  icons.download(downloadBtn, { handler: downloadVolcanoSvg, title: "Download" });
-  const colorLegendDiv = legend.append("div").style("margin-bottom", "12px");
-  const shapeLegendDiv = legend.append("div").style("margin-bottom", "12px");
-  const sizeLegendRow = legend.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "6px").style("margin-top", "8px");
-  sizeLegendRow.append("div").style("border-top", "1px solid #e5e7eb").style("margin", "8px 0 8px 0");
-  const sizeModeRow = sizeLegendRow.append("div").style("display", "flex").style("align-items", "center").style("gap", "4px").style("flex-wrap", "wrap");
-  const sizeToggleCheckbox = sizeModeRow.append("input").attr("type", "checkbox").attr("aria-label", "Scale dot size by case sample size").property("checked", scaleDotSize).style("cursor", "pointer").style("margin", "0").on("change", function() {
-    scaleDotSize = this.checked;
-    sizeModeText.style("opacity", scaleDotSize ? 1 : 0.4);
-    legendSvg.style("opacity", scaleDotSize ? 1 : 0.4);
-    updateDots();
-    renderSizeLegend();
-  });
-  void sizeToggleCheckbox;
-  const sizeModeText = sizeModeRow.append("span").style("display", "inline-flex").style("gap", "6px");
-  sizeModeText.append("span").text("Scale by");
-  sizeModeText.append("span").text("Case sample size").style("font-weight", "600").style("text-decoration", "underline").style("color", "#111");
-  sizeModeText.style("opacity", scaleDotSize ? 1 : 0.4);
-  const legendSvg = sizeLegendRow.append("svg").attr("width", 190).attr("height", 110).style("display", "block");
-  legendSvg.style("opacity", scaleDotSize ? 1 : 0.4);
-  function renderColorLegend() {
-    colorLegendDiv.selectAll("*").remove();
-    shapeLegendDiv.selectAll("*").remove();
-    const setCreateButtonState = (container, isActive, inputSelector, buttonSelector, hasCheckedItems) => {
-      if (!isActive) return;
-      const inputNode = container.select(inputSelector).node();
-      const createBtn = container.select(buttonSelector);
-      if (!inputNode || createBtn.empty()) return;
-      const shouldDisable = !inputNode.value.trim() || !hasCheckedItems;
-      createBtn.property("disabled", shouldDisable).style("opacity", shouldDisable ? "0.5" : "1").style("cursor", shouldDisable ? "not-allowed" : "pointer");
-    };
-    const updateColorCreateButtonState = () => {
-      setCreateButtonState(
-        colorLegendDiv,
-        groupingModeActive.has(colorMode),
-        'input[data-role="custom-group-name"]',
-        'button[data-role="create-custom-group-submit"]',
-        checkedItemsByMode[colorMode].size > 0
-      );
-    };
-    const updateShapeCreateButtonState = () => {
-      setCreateButtonState(
-        shapeLegendDiv,
-        shapeGroupingModeActive.has(shapeMode),
-        'input[data-role="custom-shape-group-name"]',
-        'button[data-role="create-custom-shape-group-submit"]',
-        checkedShapeItemsByMode[shapeMode].size > 0
-      );
-    };
-    const modeRow = colorLegendDiv.append("div").style("display", "flex").style("gap", "10px").style("margin-bottom", "6px").style("flex-wrap", "wrap");
-    modeRow.append("span").text("Color by");
-    for (const { key, label } of colorGroupingModes) {
-      modeRow.append("span").text(label).style("cursor", "pointer").style("font-weight", key === colorMode ? "600" : "400").style("text-decoration", key === colorMode ? "underline" : "none").style("color", key === colorMode ? "#111" : "#6b7280").on("click", () => {
-        groupingModeActive.delete(colorMode);
-        checkedItemsByMode[colorMode].clear();
-        colorMode = key;
-        refreshAfterVisibilityChange();
-      });
-    }
-    const makeLegendItems = (items, colorMap) => {
-      const dotsVisibleByShape = dots.filter((d) => !hiddenShape[shapeMode].has(getShapeValueByMode(d, shapeMode)));
-      const openColorMenu = (event, name, swatch) => {
-        const menu = new Menu({ padding: "0px" });
-        const div = menu.d.append("div");
-        const hidden = hiddenColor[colorMode].has(name);
-        const hiddenCount = hiddenColor[colorMode].size;
-        div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(hidden ? "Show" : "Hide").on("click", () => {
-          if (hidden) hiddenColor[colorMode].delete(name);
-          else hiddenColor[colorMode].add(name);
-          refreshAfterVisibilityChange();
-          menu.hide();
-        });
-        div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show only").on("click", () => {
-          hiddenColor[colorMode].clear();
-          for (const item of items) {
-            if (item != name) hiddenColor[colorMode].add(item);
-          }
-          refreshAfterVisibilityChange();
-          menu.hide();
-        });
-        if (hiddenCount > 1)
-          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show all").on("click", () => {
-            hiddenColor[colorMode].clear();
-            refreshAfterVisibilityChange();
-            menu.hide();
-          });
-        const input = div.append("div").attr("class", "sja_sharp_border").style("padding", "0px 10px").text("Color:").append("input").attr("type", "color").attr("value", colorMap.get(name) ?? "#888").on("change", () => {
-          const newColor = input.node().value;
-          if (isCustomGroupKey(name)) {
-            customGroupColorsByMode[colorMode].set(getCustomGroupNameFromKey(name), newColor);
-          } else if (!isCustomGroupKey(name)) {
-            if (colorMode == "organism") organismColors.set(name, newColor);
-            else if (colorMode == "assayType") assayColors.set(name, newColor);
-            else if (colorMode == "cohort") cohortColors.set(name, newColor);
-            else if (colorMode == "proteinAccession") proteinColors.set(name, newColor);
-          }
-          colorMap.set(name, newColor);
-          swatch.style("background", newColor);
-          updateDots();
-          menu.hide();
-        });
-        if (isCustomGroupKey(name))
-          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Remove group").on("click", () => {
-            removeCustomGroup(colorMode, getCustomGroupNameFromKey(name));
-            refreshAfterVisibilityChange();
-            menu.hide();
-          });
-        menu.showunder(event.target);
-      };
-      for (const name of items) {
-        const hidden = hiddenColor[colorMode].has(name);
-        const isGroup = isCustomGroupKey(name);
-        const displayName = isGroup ? getCustomGroupNameFromKey(name) : name;
-        const inGroup = !isGroup ? getCustomGroupOfValue(colorMode, name) : null;
-        const sampleCount = getLegendItemSampleCount(colorMode, name, dotsVisibleByShape);
-        if (sampleCount === 0) continue;
-        const row = colorLegendDiv.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px").style("margin-bottom", "3px");
-        if (!isGroup && groupingModeActive.has(colorMode)) {
-          const cb = row.append("input").attr("type", "checkbox").style("cursor", "pointer").style("flex-shrink", "0");
-          const cbNode = cb.node();
-          cbNode.checked = checkedItemsByMode[colorMode].has(name);
-          cb.on("change", () => {
-            if (cbNode.checked) checkedItemsByMode[colorMode].add(name);
-            else checkedItemsByMode[colorMode].delete(name);
-            updateColorCreateButtonState();
-          });
-        }
-        const swatch = row.append("span").style("display", "inline-block").style("width", "10px").style("height", "10px").style("border-radius", "50%").style("background", colorMap.get(name) ?? "#888").style("opacity", hidden ? 0.35 : 0.8).style("flex-shrink", "0").style("cursor", "pointer");
-        swatch.on("click", (event) => openColorMenu(event, name, swatch));
-        row.append("span").text(`${displayName}, ${sampleCount} sample set${sampleCount === 1 ? "" : "s"}`).style("text-decoration", hidden ? "line-through" : "none").style("cursor", "pointer").on("click", (event) => openColorMenu(event, name, swatch));
-        if (isGroup) {
-          const count = customGroupsByMode[colorMode].get(getCustomGroupNameFromKey(name))?.size || 0;
-          const itemLabel = colorMode === "organism" ? "organisms" : colorMode === "assayType" ? "assays" : colorMode === "cohort" ? "sample sets" : colorMode === "proteinAccession" ? "isoforms" : "items";
-          row.append("span").style("color", "#6b7280").text(`(${count} ${itemLabel})`);
-        } else if (inGroup) {
-          row.append("span").style("color", "#6b7280").style("font-style", "italic").text(`\u2192 ${inGroup}`);
-        }
-      }
-    };
-    const buildModeLegendItems = (baseItems, baseColorMap) => {
-      const visibleBaseItems = baseItems.filter((name) => !getCustomGroupOfValue(colorMode, name));
-      const mergedColorMap = /* @__PURE__ */ new Map();
-      for (const name of visibleBaseItems) mergedColorMap.set(name, baseColorMap.get(name) ?? "#888");
-      for (const name of getCustomGroupItems(colorMode)) {
-        const rawName = getCustomGroupNameFromKey(name);
-        mergedColorMap.set(name, customGroupColorsByMode[colorMode].get(rawName) ?? "#888");
-      }
-      return { items: [...visibleBaseItems, ...getCustomGroupItems(colorMode)], colorMap: mergedColorMap };
-    };
-    const renderCustomGroupControls = () => {
-      if (!colorModesWithGroups.includes(colorMode)) return;
-      if (!groupingModeActive.has(colorMode)) {
-        const createBtn = colorLegendDiv.append("button").attr("type", "button").style("font-size", "1em").style("font-weight", "400").style("margin-top", "6px").style("padding", "0").style("border", "none").style("border-radius", "0").style("background", "transparent").style("color", "#6b7280").style("box-shadow", "none").style("cursor", "pointer").style("transition", "color 120ms ease").text("+ Create custom group").on("click", () => {
-          groupingModeActive.add(colorMode);
-          renderColorLegend();
-        });
-        createBtn.on("mouseover", function() {
-          select_default(this).style("color", "#111827");
-        }).on("mouseout", function() {
-          select_default(this).style("color", "#6b7280");
-        });
-        return;
-      }
-      colorLegendDiv.append("div").style("font-size", "11px").style("color", "#6b7280").style("margin-bottom", "4px").text("Check items to include in the new group:");
-      const controls = colorLegendDiv.append("div").style("display", "flex").style("gap", "6px").style("align-items", "center").style("flex-wrap", "wrap").style("margin-top", "4px");
-      const nameInput = controls.append("input").attr("data-role", "custom-group-name").attr("type", "text").attr("placeholder", "Group name").style("font-size", "12px").style("padding", "2px 4px").style("min-width", "100px").on("input", () => updateColorCreateButtonState());
-      controls.append("button").attr("data-role", "create-custom-group-submit").attr("type", "button").style("font-size", "12px").style("padding", "2px 6px").text("Create").on("click", () => {
-        const groupName = (nameInput.node()?.value || "").trim();
-        if (!groupName || checkedItemsByMode[colorMode].size < 1) return;
-        addOrUpdateCustomGroup(colorMode, groupName, [...checkedItemsByMode[colorMode]]);
-        checkedItemsByMode[colorMode].clear();
-        groupingModeActive.delete(colorMode);
-        refreshAfterVisibilityChange();
-      });
-      updateColorCreateButtonState();
-      controls.append("button").attr("type", "button").style("font-size", "12px").style("padding", "2px 6px").text("Cancel").on("click", () => {
-        checkedItemsByMode[colorMode].clear();
-        groupingModeActive.delete(colorMode);
-        renderColorLegend();
-      });
-    };
-    if (colorMode === "organism") {
-      const { items, colorMap } = buildModeLegendItems(organismNames, organismColors);
-      makeLegendItems(items, colorMap);
-      renderCustomGroupControls();
-    } else if (colorMode === "assayType") {
-      const { items, colorMap } = buildModeLegendItems(assayNames, assayColors);
-      makeLegendItems(items, colorMap);
-      renderCustomGroupControls();
-    } else if (colorMode === "cohort") {
-      const { items, colorMap } = buildModeLegendItems(cohortNames, cohortColors);
-      makeLegendItems(items, colorMap);
-      renderCustomGroupControls();
-    } else if (colorMode === "proteinAccession") {
-      const { items, colorMap } = buildModeLegendItems(proteinAccessions, proteinColors);
-      makeLegendItems(items, colorMap);
-      renderCustomGroupControls();
-    }
-    shapeLegendDiv.append("div").style("border-top", "1px solid #e5e7eb").style("margin", "8px 0 8px 0");
-    const shapeModeRow = shapeLegendDiv.append("div").style("display", "flex").style("gap", "10px").style("margin-bottom", "6px").style("flex-wrap", "wrap");
-    shapeModeRow.append("span").text("Shape by");
-    for (const { key, label } of shapeGroupingModes) {
-      shapeModeRow.append("span").text(label).style("cursor", "pointer").style("font-weight", key === shapeMode ? "600" : "400").style("text-decoration", key === shapeMode ? "underline" : "none").style("color", key === shapeMode ? "#111" : "#6b7280").on("click", () => {
-        shapeGroupingModeActive.delete(shapeMode);
-        checkedShapeItemsByMode[shapeMode].clear();
-        shapeMode = key;
-        refreshAfterVisibilityChange();
-      });
-    }
-    const buildShapeLegendItems = (baseItems) => {
-      const visibleBaseItems = baseItems.filter((name) => !getCustomShapeGroupOfValue(shapeMode, name));
-      return { items: [...visibleBaseItems, ...getCustomShapeGroupItems(shapeMode)] };
-    };
-    const drawShapeLegend = (items, shapeMap) => {
-      const dotsVisibleByColor = dots.filter((d) => !hiddenColor[colorMode].has(getColorValueByMode(d, colorMode)));
-      const openShapeMenu = (event, name) => {
-        const menu = new Menu({ padding: "0px" });
-        const activeShapeMap = isCustomShapeGroupKey(name) ? customShapeIndicesByMode[shapeMode] : getShapeMapInUse();
-        const div = menu.d.append("div");
-        const hidden = hiddenShape[shapeMode].has(name);
-        const hiddenCount = hiddenShape[shapeMode].size;
-        div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(hidden ? "Show" : "Hide").on("click", () => {
-          if (hidden) hiddenShape[shapeMode].delete(name);
-          else hiddenShape[shapeMode].add(name);
-          refreshAfterVisibilityChange();
-          menu.hide();
-        });
-        div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show only").on("click", () => {
-          hiddenShape[shapeMode].clear();
-          for (const item of items) {
-            if (item != name) hiddenShape[shapeMode].add(item);
-          }
-          refreshAfterVisibilityChange();
-          menu.hide();
-        });
-        if (hiddenCount > 1)
-          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show all").on("click", () => {
-            hiddenShape[shapeMode].clear();
-            refreshAfterVisibilityChange();
-            menu.hide();
-          });
-        div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Change shape").on("click", () => {
-          div.selectAll("*").remove();
-          shapeSelector(
-            div,
-            (index) => {
-              const shapeKey = isCustomShapeGroupKey(name) ? getCustomShapeGroupNameFromKey(name) : name;
-              activeShapeMap.set(shapeKey, index);
-              updateDots();
-              renderColorLegend();
-              menu.hide();
-            },
-            prioritizedShapesArray
-          );
-        });
-        if (isCustomShapeGroupKey(name))
-          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Remove group").on("click", () => {
-            removeCustomShapeGroup(shapeMode, getCustomShapeGroupNameFromKey(name));
-            refreshAfterVisibilityChange();
-            menu.hide();
-          });
-        menu.showunder(event.target);
-      };
-      for (const name of items) {
-        const hidden = hiddenShape[shapeMode].has(name);
-        const isGroup = isCustomShapeGroupKey(name);
-        const displayName = isGroup ? getCustomShapeGroupNameFromKey(name) : name;
-        const inGroup = !isGroup ? getCustomShapeGroupOfValue(shapeMode, name) : null;
-        const sampleCount = getLegendItemSampleCount(shapeMode, name, dotsVisibleByColor);
-        if (sampleCount === 0) continue;
-        const row = shapeLegendDiv.append("div").style("display", "flex").style("align-items", "center").style("gap", "6px").style("margin-bottom", "3px");
-        if (!isGroup && shapeGroupingModeActive.has(shapeMode)) {
-          const cb = row.append("input").attr("type", "checkbox").style("cursor", "pointer").style("flex-shrink", "0");
-          const cbNode = cb.node();
-          cbNode.checked = checkedShapeItemsByMode[shapeMode].has(name);
-          cb.on("change", () => {
-            if (cbNode.checked) checkedShapeItemsByMode[shapeMode].add(name);
-            else checkedShapeItemsByMode[shapeMode].delete(name);
-            updateShapeCreateButtonState();
-          });
-        }
-        const icon = row.append("svg").attr("width", 16).attr("height", 16).style("display", "inline-block").style("cursor", "pointer");
-        icon.append("path").attr("transform", "scale(0.8)").attr(
-          "d",
-          prioritizedShapesArray[((isGroup ? customShapeIndicesByMode[shapeMode].get(getCustomShapeGroupNameFromKey(name)) : shapeMap.get(name)) || 0) % prioritizedShapesArray.length]
-        ).attr("fill", "#4b5563").attr("fill-opacity", hidden ? 0.35 : 0.9);
-        icon.on("click", (event) => openShapeMenu(event, name));
-        row.append("span").text(`${displayName}, ${sampleCount} sample set${sampleCount === 1 ? "" : "s"}`).style("text-decoration", hidden ? "line-through" : "none").style("cursor", "pointer").on("click", (event) => openShapeMenu(event, name));
-        if (isGroup) {
-          const count = customShapeGroupsByMode[shapeMode].get(getCustomShapeGroupNameFromKey(name))?.size || 0;
-          const itemLabel = shapeMode === "organism" ? "organisms" : shapeMode === "assayType" ? "assays" : shapeMode === "cohort" ? "sample sets" : shapeMode === "proteinAccession" ? "isoforms" : "items";
-          row.append("span").style("color", "#6b7280").text(`(${count} ${itemLabel})`);
-        } else if (inGroup) {
-          row.append("span").style("color", "#6b7280").style("font-style", "italic").text(`\u2192 ${inGroup}`);
-        }
-      }
-    };
-    const renderShapeCustomGroupControls = () => {
-      if (!shapeModesWithGroups.includes(shapeMode)) return;
-      if (!shapeGroupingModeActive.has(shapeMode)) {
-        const createBtn = shapeLegendDiv.append("button").attr("type", "button").style("font-size", "1em").style("font-weight", "400").style("margin-top", "6px").style("padding", "0").style("border", "none").style("border-radius", "0").style("background", "transparent").style("color", "#6b7280").style("box-shadow", "none").style("cursor", "pointer").style("transition", "color 120ms ease").text("+ Create custom group").on("click", () => {
-          shapeGroupingModeActive.add(shapeMode);
-          renderColorLegend();
-        });
-        createBtn.on("mouseover", function() {
-          select_default(this).style("color", "#111827");
-        }).on("mouseout", function() {
-          select_default(this).style("color", "#6b7280");
-        });
-        return;
-      }
-      shapeLegendDiv.append("div").style("font-size", "11px").style("color", "#6b7280").style("margin-bottom", "4px").text("Check items to include in the new group:");
-      const controls = shapeLegendDiv.append("div").style("display", "flex").style("gap", "6px").style("align-items", "center").style("flex-wrap", "wrap").style("margin-top", "4px");
-      const nameInput = controls.append("input").attr("data-role", "custom-shape-group-name").attr("type", "text").attr("placeholder", "Group name").style("font-size", "12px").style("padding", "2px 4px").style("min-width", "100px").on("input", () => updateShapeCreateButtonState());
-      controls.append("button").attr("data-role", "create-custom-shape-group-submit").attr("type", "button").style("font-size", "12px").style("padding", "2px 6px").text("Create").on("click", () => {
-        const groupName = (nameInput.node()?.value || "").trim();
-        if (!groupName || checkedShapeItemsByMode[shapeMode].size < 1) return;
-        addOrUpdateCustomShapeGroup(shapeMode, groupName, [...checkedShapeItemsByMode[shapeMode]]);
-        checkedShapeItemsByMode[shapeMode].clear();
-        shapeGroupingModeActive.delete(shapeMode);
-        refreshAfterVisibilityChange();
-      });
-      updateShapeCreateButtonState();
-      controls.append("button").attr("type", "button").style("font-size", "12px").style("padding", "2px 6px").text("Cancel").on("click", () => {
-        checkedShapeItemsByMode[shapeMode].clear();
-        shapeGroupingModeActive.delete(shapeMode);
-        renderColorLegend();
-      });
-    };
-    if (shapeMode === "organism") {
-      const { items } = buildShapeLegendItems(organismNames);
-      drawShapeLegend(items, organismShapes);
-      renderShapeCustomGroupControls();
-    } else if (shapeMode === "assayType") {
-      const { items } = buildShapeLegendItems(assayNames);
-      drawShapeLegend(items, assayShapes);
-      renderShapeCustomGroupControls();
-    } else if (shapeMode === "cohort") {
-      const { items } = buildShapeLegendItems(cohortNames);
-      drawShapeLegend(items, cohortShapes);
-      renderShapeCustomGroupControls();
-    } else if (shapeMode === "proteinAccession") {
-      const { items } = buildShapeLegendItems(proteinAccessions);
-      drawShapeLegend(items, proteinShapes);
-      renderShapeCustomGroupControls();
-    }
-  }
-  updateRadiusScaleForVisibleDots();
-  renderColorLegend();
-  renderSizeLegend();
-}
-async function renderPTMLollipop(holder, ptmCohorts, self, isoform, genome) {
-  if (!ptmCohorts?.length) return;
-  const custom_variants = [];
-  const mergedMclassOverride = {};
-  const gm = await getGmForPTM(ptmCohorts[0].geneName, genome.name, isoform);
-  for (const ptm of ptmCohorts) {
-    if (!gm) continue;
-    const logValue = getLog2Ratio(ptm.foldChange);
-    const wholeProteomeLog2 = getLog2Ratio(ptm.proteinFoldChange);
-    const normalizedLog2 = logValue != null && wholeProteomeLog2 != null ? logValue - wholeProteomeLog2 : null;
-    const fdr = Number(ptm.fdr);
-    const testedN = Number(ptm.testedN);
-    const controlN = Number(ptm.controlN);
-    if (ptm.mclassOverride && typeof ptm.mclassOverride == "object") {
-      Object.assign(mergedMclassOverride, ptm.mclassOverride);
-    }
-    const site = parsePTMModSites(ptm.modSites);
-    if (!site) continue;
-    const pos = aa2gmcoord(site, gm);
-    if (!Number.isInteger(pos)) continue;
-    const ptmClass = Object.keys(ptm.mclassOverride || {})[0];
-    custom_variants.push({
-      chr: gm.chr,
-      pos,
-      mname: ptm.modSites,
-      class: ptmClass,
-      dt: 1,
-      logValue,
-      wholeProteomeLog2,
-      normalizedLog2,
-      fdr,
-      testedN: Number.isFinite(testedN) ? testedN : null,
-      controlN: Number.isFinite(controlN) ? controlN : null,
-      organism: ptm.organism || null,
-      assayName: ptm.assayName || null,
-      cohortName: ptm.cohortName || null,
-      proteinAccession: ptm.proteinAccession || null,
-      PTMStr: ptm.uniqueIdentifier || null,
-      htmlSections: [
-        {
-          key: "Action",
-          label: "Launch Violin Plot",
-          callback: () => launchViolinPlot(self, ptm.organism, ptm.assayName, ptm.cohortName, ptm.uniqueIdentifier)
-        }
-      ]
-    });
-  }
-  if (!custom_variants.length) return;
-  const mclassOverride = {
-    className: "PTM",
-    classes: mergedMclassOverride
-  };
-  for (const key in mclassOverride.classes) {
-    if (mclass[key]) Object.assign(mclass[key], mclassOverride.classes[key]);
-  }
-  const tk = {
-    type: "mds3",
-    name: "PTMs",
-    custom_variants,
-    skewerModes: [
-      {
-        type: "numeric",
-        byAttribute: "logValue",
-        label: "Log2FC",
-        tooltipPrintValue: (m) => {
-          const p = Number(m.fdr);
-          return [
-            { k: "Organism", v: m.organism ?? "NA" },
-            { k: "Assay", v: m.assayName ?? "NA" },
-            { k: "Sample set", v: m.cohortName ?? "NA" },
-            { k: "PTM", v: m.PTMStr ?? "NA" },
-            { k: "Log2 fold change", v: Number.isFinite(m.logValue) ? roundValue(m.logValue, 3) : "NA" },
-            {
-              k: "Whole proteome Log2 FC",
-              v: Number.isFinite(m.wholeProteomeLog2) ? roundValue(m.wholeProteomeLog2, 3) : "NA"
-            },
-            {
-              k: "Normalized Log2 FC",
-              v: Number.isFinite(m.normalizedLog2) ? roundValue(m.normalizedLog2, 3) : "NA"
-            },
-            { k: "FDR", v: Number.isFinite(p) && p > 0 ? p.toExponential(2) : "NA" },
-            { k: "Case samples", v: Number.isFinite(m.testedN) ? m.testedN : "NA" },
-            { k: "Control samples", v: Number.isFinite(m.controlN) ? m.controlN : "NA" },
-            { k: "Protein accession", v: m.proteinAccession ?? "NA" }
-          ];
-        },
-        inuse: true,
-        axisheight: 100
-      }
-    ],
-    mclassOverride
-  };
-  const arg = {
-    holder: holder.append("div"),
-    genome,
-    nobox: true,
-    tklst: [tk],
-    mclassOverride,
-    debugmode: self.app.opts.debug,
-    query: gm.isoform,
-    hide_dsHandles: true
-  };
-  const _ = await import("./block.init-CQ76SLCN.js");
-  await _.default(arg);
-}
-function parsePTMModSites(modSites) {
-  if (!modSites) return null;
-  const regex = /([A-Za-z])(\d+)/g;
-  let m;
-  while ((m = regex.exec(modSites)) !== null) {
-    const position = Number(m[2]);
-    if (!Number.isInteger(position) || position < 1) continue;
-    return position;
-  }
-  return null;
-}
-async function getGmForPTM(geneName, genomeName, isoform) {
-  if (!geneName) return null;
-  const d = await dofetch3("genelookup", {
-    body: {
-      deep: 1,
-      genome: genomeName,
-      input: geneName
-    }
-  });
-  if (d.error || !Array.isArray(d.gmlst) || !d.gmlst.length) return null;
-  const normalizedIsoform = isoform?.trim().toUpperCase();
-  const gm = d.gmlst.find((i) => i.isoform && normalizedIsoform && i.isoform.toUpperCase() == normalizedIsoform) || d.gmlst.find((i) => i.isdefault) || d.gmlst[0];
-  return gm;
-}
-async function getPlotConfig(opts) {
-  const config = structuredClone(defaultConfig);
-  if (!opts.tw) throw new Error("proteinView requires opts.tw");
-  return copyMerge(config, opts);
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  const row = holder.append("div").style("padding", "5px");
-  row.append("span").style("font-weight", "bold").text("Enter a gene name:");
-  const geneSearch = addGeneSearchbox({
-    row,
-    genome: chartsInstance.app.opts.genome,
-    tip: new Menu({ padding: "0px" }),
-    searchOnly: "gene",
-    callback: async () => {
-      if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
-      chartsInstance.dom.tip.hide();
-      chartsInstance.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "proteinView",
-          tw: {
-            term: {
-              gene: geneSearch.geneSymbol,
-              name: geneSearch.geneSymbol,
-              type: TermTypes.PROTEOME_ABUNDANCE
-            }
-          }
-        }
-      });
-    }
-  });
-}
-var proteinViewInit = getCompInit(ProteinView);
-var componentInit = proteinViewInit;
-export {
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu,
-  proteinViewInit
-};
-//# sourceMappingURL=proteinView-WVI3OVDD.js.map