@sjcrh/proteinpaint-client 2.205.0 → 2.206.0

package/dist/chunk-IIMTOPH3.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-Q5SK3U2T.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+
+// termdb/handlers/snp.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: opts.holder,
+      searchOnly: "snp",
+      allowVariant: true,
+      callback: () => this.selectSnp(geneSearch)
+    });
+  }
+  async selectSnp(geneSearch) {
+    const { chr, ref, alt, fromWhat } = geneSearch;
+    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
+    let start, stop;
+    if (!geneSearch.start && !geneSearch.stop) {
+      if (geneSearch.pos) {
+        start = geneSearch.pos - 1;
+        stop = geneSearch.pos;
+      } else {
+        throw "missing coordinate of snp";
+      }
+    } else {
+      start = geneSearch.start;
+      stop = geneSearch.stop;
+    }
+    const term = {
+      id: fromWhat,
+      chr,
+      start,
+      stop,
+      name: fromWhat,
+      ref,
+      alt: typeof alt == "string" ? [alt] : alt,
+      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
+      type: "snp"
+    };
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-IIMTOPH3.js.map

package/dist/chunk-ILEXRHF7.js

@@ -0,0 +1,367 @@
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+
+// plots/brainRegions.svg.ts
+var cachedBrainAssets = {};
+async function loadBrainAssets(svgUrl, regionCodes) {
+  if (cachedBrainAssets[svgUrl]) return cachedBrainAssets[svgUrl];
+  const res = await fetch(svgUrl);
+  if (!res.ok) throw new Error(`failed to load ${svgUrl}: ${res.status}`);
+  const text = await res.text();
+  const doc = new DOMParser().parseFromString(text, "image/svg+xml");
+  const svgEl = doc.documentElement;
+  let viewBoxW = 0;
+  let viewBoxH = 0;
+  const vb = svgEl.getAttribute("viewBox");
+  if (vb) {
+    const parts = vb.trim().split(/\s+/).map(Number);
+    if (parts.length === 4 && Number.isFinite(parts[2]) && Number.isFinite(parts[3])) {
+      viewBoxW = parts[2];
+      viewBoxH = parts[3];
+    }
+  }
+  if (!viewBoxW || !viewBoxH) {
+    viewBoxW = Number(svgEl.getAttribute("width")) || 0;
+    viewBoxH = Number(svgEl.getAttribute("height")) || 0;
+  }
+  if (!viewBoxW || !viewBoxH) throw new Error(`could not determine viewBox dimensions from ${svgUrl}`);
+  const paths = {};
+  for (const code of regionCodes) {
+    const el = doc.getElementById(code);
+    const d = el?.getAttribute("d");
+    if (d) paths[code] = { d, transform: el?.getAttribute("transform") ?? null };
+  }
+  const assets = { paths, viewBoxW, viewBoxH };
+  cachedBrainAssets[svgUrl] = assets;
+  return assets;
+}
+function visualCenter(pathEl, gridN = 24, boundarySamples = 160) {
+  const bbox = pathEl.getBBox();
+  const svgRoot = pathEl.ownerSVGElement;
+  if (!svgRoot) {
+    return { x: bbox.x + bbox.width / 2, y: bbox.y + bbox.height / 2 };
+  }
+  const probe = svgRoot.createSVGPoint();
+  const len = pathEl.getTotalLength();
+  const bx = new Array(boundarySamples);
+  const by = new Array(boundarySamples);
+  for (let i = 0; i < boundarySamples; i++) {
+    const p = pathEl.getPointAtLength(i / boundarySamples * len);
+    bx[i] = p.x;
+    by[i] = p.y;
+  }
+  let bestX = bbox.x + bbox.width / 2;
+  let bestY = bbox.y + bbox.height / 2;
+  let bestMinSq = -Infinity;
+  for (let i = 0; i < gridN; i++) {
+    for (let j = 0; j < gridN; j++) {
+      const x = bbox.x + (i + 0.5) / gridN * bbox.width;
+      const y = bbox.y + (j + 0.5) / gridN * bbox.height;
+      probe.x = x;
+      probe.y = y;
+      if (!pathEl.isPointInFill(probe)) continue;
+      let minSq = Infinity;
+      for (let k = 0; k < boundarySamples; k++) {
+        const dx = bx[k] - x;
+        const dy = by[k] - y;
+        const d = dx * dx + dy * dy;
+        if (d < minSq) minSq = d;
+      }
+      if (minSq > bestMinSq) {
+        bestMinSq = minSq;
+        bestX = x;
+        bestY = y;
+      }
+    }
+  }
+  return { x: bestX, y: bestY };
+}
+function isPointInRegion(outerX, outerY, r) {
+  const svg = r.pathEl.ownerSVGElement;
+  if (!svg) return false;
+  const pt = svg.createSVGPoint();
+  pt.x = outerX;
+  pt.y = outerY;
+  const local = r.matrix ? pt.matrixTransform(r.matrix.inverse()) : pt;
+  return r.pathEl.isPointInFill(local);
+}
+function findInlineLabelSpot(r, labelW, labelH, others, gridN = 36) {
+  const localBBox = r.pathEl.getBBox();
+  const svg = r.pathEl.ownerSVGElement;
+  if (!svg) return null;
+  const corners = [
+    { x: localBBox.x, y: localBBox.y },
+    { x: localBBox.x + localBBox.width, y: localBBox.y },
+    { x: localBBox.x, y: localBBox.y + localBBox.height },
+    { x: localBBox.x + localBBox.width, y: localBBox.y + localBBox.height }
+  ];
+  const outerCorners = corners.map((c) => {
+    if (!r.matrix) return c;
+    const p = svg.createSVGPoint();
+    p.x = c.x;
+    p.y = c.y;
+    return p.matrixTransform(r.matrix);
+  });
+  const xs = outerCorners.map((c) => c.x);
+  const ys = outerCorners.map((c) => c.y);
+  const minX = Math.min(...xs);
+  const maxX = Math.max(...xs);
+  const minY = Math.min(...ys);
+  const maxY = Math.max(...ys);
+  let bestX = 0;
+  let bestY = 0;
+  let bestConflicts = Infinity;
+  let bestDistSq = Infinity;
+  let found = false;
+  for (let i = 0; i < gridN; i++) {
+    for (let j = 0; j < gridN; j++) {
+      const x = minX + (i + 0.5) / gridN * (maxX - minX);
+      const y = minY + (j + 0.5) / gridN * (maxY - minY);
+      if (!isPointInRegion(x, y, r)) continue;
+      const probes = [
+        [x, y],
+        [x - labelW / 2, y - labelH / 2],
+        [x + labelW / 2, y - labelH / 2],
+        [x - labelW / 2, y + labelH / 2],
+        [x + labelW / 2, y + labelH / 2]
+      ];
+      let conflicts = 0;
+      for (const [px, py] of probes) {
+        for (const o of others) {
+          if (isPointInRegion(px, py, o)) {
+            conflicts++;
+            break;
+          }
+        }
+      }
+      const dx = x - r.vx;
+      const dy = y - r.vy;
+      const distSq = dx * dx + dy * dy;
+      const better = conflicts < bestConflicts || conflicts === bestConflicts && distSq < bestDistSq;
+      if (better) {
+        bestX = x;
+        bestY = y;
+        bestConflicts = conflicts;
+        bestDistSq = distSq;
+        found = true;
+      }
+    }
+  }
+  return found ? { x: bestX, y: bestY, conflicts: bestConflicts } : null;
+}
+function findClearOffset(vx, vy, offset, labelW, labelH, others, viewBoxCx, viewBoxCy) {
+  const baseAngle = Math.atan2(vy - viewBoxCy, vx - viewBoxCx);
+  const angleDeltasDeg = [0, 30, -30, 60, -60, 90, -90, 120, -120, 150, -150, 180];
+  for (const delta of angleDeltasDeg) {
+    const angle = baseAngle + delta * Math.PI / 180;
+    const dx2 = Math.cos(angle);
+    const dy2 = Math.sin(angle);
+    const lx = vx + dx2 * offset;
+    const ly = vy + dy2 * offset;
+    const probePts = [
+      [lx, ly],
+      [lx - labelW / 2, ly - labelH / 2],
+      [lx + labelW / 2, ly - labelH / 2],
+      [lx - labelW / 2, ly + labelH / 2],
+      [lx + labelW / 2, ly + labelH / 2]
+    ];
+    let overlap = false;
+    for (const other of others) {
+      const svgRoot = other.pathEl.ownerSVGElement;
+      if (!svgRoot) continue;
+      const inv = other.matrix ? other.matrix.inverse() : null;
+      const pt = svgRoot.createSVGPoint();
+      for (const [x, y] of probePts) {
+        pt.x = x;
+        pt.y = y;
+        const localPt = inv ? pt.matrixTransform(inv) : pt;
+        if (other.pathEl.isPointInFill(localPt)) {
+          overlap = true;
+          break;
+        }
+      }
+      if (overlap) break;
+    }
+    if (!overlap) return { x: lx, y: ly, dx: dx2, dy: dy2 };
+  }
+  const dx = Math.cos(baseAngle);
+  const dy = Math.sin(baseAngle);
+  return { x: vx + dx * offset, y: vy + dy * offset, dx, dy };
+}
+var DIMMED_FILL = "#dcdcdc";
+var DIMMED_OPACITY = 0.35;
+function renderBrainSvg(opts) {
+  const {
+    holder,
+    width,
+    templateUrl,
+    assets,
+    regions,
+    fillByRegion,
+    tooltipByRegion,
+    title,
+    tip,
+    onRegionClick,
+    isRegionDimmed
+  } = opts;
+  const { paths: regionPaths, viewBoxW, viewBoxH } = assets;
+  const renderH = Math.round(width * viewBoxH / viewBoxW);
+  const col = holder.append("div");
+  if (title) {
+    col.append("div").style("text-align", "center").style("font-weight", "bold").style("font-size", "16px").style("margin-bottom", "8px").text(title);
+  }
+  const svg = col.append("svg").attr("width", width).attr("height", renderH).attr("viewBox", `0 0 ${viewBoxW} ${viewBoxH}`);
+  svg.append("image").attr("href", templateUrl).attr("x", 0).attr("y", 0).attr("width", viewBoxW).attr("height", viewBoxH).style("filter", "grayscale(1) brightness(1.05)").style("opacity", 0.55);
+  const overlayGroup = svg.append("g");
+  const rendered = [];
+  for (const [code, label] of Object.entries(regions)) {
+    const geom = regionPaths[code];
+    if (!geom) continue;
+    const dimmed = isRegionDimmed?.(code) === true;
+    const fillColor = dimmed ? DIMMED_FILL : fillByRegion(code);
+    const tooltipText = tooltipByRegion(code, label);
+    const displayLabel = label && label.includes("/") ? label : code;
+    const outerG = overlayGroup.append("g").style("cursor", "pointer");
+    const innerG = outerG.append("g");
+    if (geom.transform) innerG.attr("transform", geom.transform);
+    const baseStrokePx = 3;
+    let strokeWidth = baseStrokePx;
+    if (geom.transform) {
+      const m = innerG.node().transform.baseVal.consolidate()?.matrix;
+      if (m) {
+        const scale = (Math.abs(m.a) + Math.abs(m.d)) / 2;
+        if (scale > 0) strokeWidth = baseStrokePx / scale;
+      }
+    }
+    const pathSel = innerG.append("path").attr("d", geom.d).attr("fill", fillColor).attr("stroke", "#333").attr("stroke-width", strokeWidth).attr("opacity", dimmed ? DIMMED_OPACITY : 0.75);
+    const pathEl = pathSel.node();
+    const { x: localX, y: localY } = visualCenter(pathEl);
+    const localBBox = pathEl.getBBox();
+    const innerEl = innerG.node();
+    const matrix = innerEl.transform.baseVal.consolidate()?.matrix ?? null;
+    const ownerSvg = pathEl.ownerSVGElement;
+    const localPt = ownerSvg.createSVGPoint();
+    localPt.x = localX;
+    localPt.y = localY;
+    const outerPt = matrix ? localPt.matrixTransform(matrix) : { x: localX, y: localY };
+    const bboxW = localBBox.width * (matrix ? Math.abs(matrix.a) : 1);
+    const bboxH = localBBox.height * (matrix ? Math.abs(matrix.d) : 1);
+    rendered.push({
+      code,
+      displayLabel,
+      fillColor,
+      d: geom.d,
+      dimmed,
+      outerG,
+      innerG,
+      pathSel,
+      pathEl,
+      matrix,
+      vx: outerPt.x,
+      vy: outerPt.y,
+      bboxW,
+      bboxH
+    });
+    outerG.on("mouseover", (event) => {
+      tip.clear().show(event.clientX, event.clientY);
+      const lines = tooltipText.split("\n");
+      const tipDiv = tip.d.append("div").style("padding", "8px").style("font-size", "13px");
+      tipDiv.append("div").style("font-weight", "bold").style("margin-bottom", "4px").text(lines[0]);
+      for (let i = 1; i < lines.length; i++) {
+        tipDiv.append("div").text(lines[i]);
+      }
+    }).on("mouseout", () => {
+      tip.hide();
+    });
+    if (onRegionClick) {
+      outerG.on("click", (event) => onRegionClick(code, event));
+    }
+  }
+  const fontSize = 46;
+  for (const r of rendered) {
+    const labelW = r.displayLabel.length * fontSize * 0.62;
+    const labelH = fontSize;
+    const labelHalfDiag = Math.hypot(labelW / 2, labelH / 2);
+    const others = rendered.filter((rr) => rr !== r);
+    const regionRoomy = r.bboxW * r.bboxH > labelW * labelH * 1.5;
+    const inlinePoint = regionRoomy ? findInlineLabelSpot(r, labelW, labelH, others) : null;
+    const fitsInside = !!inlinePoint;
+    let labelX = inlinePoint ? inlinePoint.x : r.vx;
+    let labelY = inlinePoint ? inlinePoint.y : r.vy;
+    if (!fitsInside) {
+      if (!r.dimmed) r.pathSel.attr("opacity", 1);
+      r.innerG.insert("path", ":first-child").attr("d", r.d).attr("fill", "#fff").attr("stroke", "#fff").attr("stroke-width", 18).attr("stroke-linejoin", "round");
+      const offset = Math.max(r.bboxW, r.bboxH) / 2 + labelHalfDiag * 1.6;
+      const placed = findClearOffset(r.vx, r.vy, offset, labelW, labelH, others, viewBoxW / 2, viewBoxH / 2);
+      labelX = placed.x;
+      labelY = placed.y;
+      r.outerG.append("line").attr("x1", r.vx).attr("y1", r.vy).attr("x2", labelX - placed.dx * labelHalfDiag * 0.9).attr("y2", labelY - placed.dy * labelHalfDiag * 0.9).attr("stroke", "#333").attr("stroke-width", 2);
+    }
+    r.outerG.append("text").attr("x", labelX).attr("y", labelY).attr("text-anchor", "middle").attr("dominant-baseline", "central").attr("font-size", `${fontSize}px`).attr("font-weight", "bold").attr("fill", "#333").attr("paint-order", "stroke").attr("stroke", "#fff").attr("stroke-width", 6).text(r.displayLabel);
+  }
+  return svg.node();
+}
+function makeDiseaseTabs(holder, diseases, initial, onChange, fontSize = ".8em") {
+  const row = holder.append("div").style("display", "flex").style("gap", "12px").style("margin-bottom", "4px").style("font-size", fontSize);
+  let active = initial;
+  const update = () => {
+    row.selectAll("*").remove();
+    for (const d of diseases) {
+      row.append("span").attr("role", "tab").attr("aria-selected", String(d === active)).text(d).style("cursor", "pointer").style("font-weight", d === active ? "600" : "400").style("text-decoration", d === active ? "underline" : "none").style("color", d === active ? "#111827" : "#6b7280").on("click", () => {
+        if (d === active) return;
+        active = d;
+        update();
+        onChange(d);
+      });
+    }
+  };
+  update();
+}
+var BRAIN_P_THRESHOLD = 0.05;
+var BRAIN_NONSIG_COLOR = "#ccc";
+var BRAIN_NEG_COLOR = "#2166ac";
+var BRAIN_ZERO_COLOR = "#f7f7f7";
+var BRAIN_POS_COLOR = "#b2182b";
+var brainSigValue = (e) => e.p_value ?? e.fdr;
+var isBrainRegionSig = (e) => !!e && brainSigValue(e) < BRAIN_P_THRESHOLD;
+function makeBrainFcScale(regionData) {
+  const sigFCs = [];
+  for (const entry of Object.values(regionData)) if (isBrainRegionSig(entry)) sigFCs.push(entry.fold_change);
+  const maxAbsFC = sigFCs.length ? Math.max(...sigFCs.map((v) => Math.abs(v))) : 1;
+  const colorScale = linear().domain([-maxAbsFC, 0, maxAbsFC]).range([BRAIN_NEG_COLOR, BRAIN_ZERO_COLOR, BRAIN_POS_COLOR]).clamp(true);
+  return { maxAbsFC, colorScale, nSig: sigFCs.length };
+}
+function brainFillByRegion(regionData, colorScale) {
+  return (code) => {
+    const entry = regionData[code];
+    return isBrainRegionSig(entry) ? colorScale(entry.fold_change) : BRAIN_NONSIG_COLOR;
+  };
+}
+function brainTooltipByRegion(regionData) {
+  const fmt = (v) => v >= 1e-4 ? v.toFixed(4) : v.toExponential(3);
+  return (code, label) => {
+    const entry = regionData[code];
+    if (!entry) return `${label} (${code})
+No data`;
+    const p = Number.isFinite(entry.p_value) ? fmt(entry.p_value) : "NA";
+    return `${label} (${code})
+log\u2082 fold change: ${entry.fold_change.toFixed(4)}
+p-value: ${p}
+FDR: ${fmt(
+      entry.fdr
+    )}`;
+  };
+}
+
+export {
+  loadBrainAssets,
+  renderBrainSvg,
+  makeDiseaseTabs,
+  BRAIN_P_THRESHOLD,
+  BRAIN_NONSIG_COLOR,
+  makeBrainFcScale,
+  brainFillByRegion,
+  brainTooltipByRegion
+};
+//# sourceMappingURL=chunk-ILEXRHF7.js.map

package/dist/chunk-ILEXRHF7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/brainRegions.svg.ts"],
+  "sourcesContent": ["import type { Menu } from '#dom'\nimport { scaleLinear } from 'd3'\n\nexport type RegionGeom = { d: string; transform: string | null }\n\nexport type BrainAssets = {\n\tpaths: { [code: string]: RegionGeom }\n\tviewBoxW: number\n\tviewBoxH: number\n}\n\ntype RegionRender = {\n\tcode: string\n\t// Text drawn on the shape: the region code, unless the config label is a merged\n\t// code like \"FG/FC\"\n\tdisplayLabel: string\n\tfillColor: string\n\td: string\n\tdimmed: boolean\n\touterG: any\n\tinnerG: any\n\tpathSel: any\n\tpathEl: SVGPathElement\n\tmatrix: DOMMatrix | null\n\tvx: number\n\tvy: number\n\tbboxW: number\n\tbboxH: number\n}\n\nconst cachedBrainAssets: { [svgUrl: string]: BrainAssets } = {}\n\nexport async function loadBrainAssets(svgUrl: string, regionCodes: string[]): Promise<BrainAssets> {\n\tif (cachedBrainAssets[svgUrl]) return cachedBrainAssets[svgUrl]\n\tconst res = await fetch(svgUrl)\n\tif (!res.ok) throw new Error(`failed to load ${svgUrl}: ${res.status}`)\n\tconst text = await res.text()\n\tconst doc = new DOMParser().parseFromString(text, 'image/svg+xml')\n\n\tconst svgEl = doc.documentElement\n\tlet viewBoxW = 0\n\tlet viewBoxH = 0\n\tconst vb = svgEl.getAttribute('viewBox')\n\tif (vb) {\n\t\tconst parts = vb.trim().split(/\\s+/).map(Number)\n\t\tif (parts.length === 4 && Number.isFinite(parts[2]) && Number.isFinite(parts[3])) {\n\t\t\tviewBoxW = parts[2]\n\t\t\tviewBoxH = parts[3]\n\t\t}\n\t}\n\tif (!viewBoxW || !viewBoxH) {\n\t\tviewBoxW = Number(svgEl.getAttribute('width')) || 0\n\t\tviewBoxH = Number(svgEl.getAttribute('height')) || 0\n\t}\n\tif (!viewBoxW || !viewBoxH) throw new Error(`could not determine viewBox dimensions from ${svgUrl}`)\n\n\tconst paths: { [code: string]: RegionGeom } = {}\n\tfor (const code of regionCodes) {\n\t\tconst el = doc.getElementById(code)\n\t\tconst d = el?.getAttribute('d')\n\t\tif (d) paths[code] = { d, transform: el?.getAttribute('transform') ?? null }\n\t}\n\tconst assets = { paths, viewBoxW, viewBoxH }\n\tcachedBrainAssets[svgUrl] = assets\n\treturn assets\n}\n\n// Find the \"pole of inaccessibility\" \u2014 the point inside the filled shape that\n// is farthest from any boundary point. Bbox center fails for concave shapes\n// (cingulate band, frontal lobe curve); this works for any closed path.\nfunction visualCenter(pathEl: SVGPathElement, gridN = 24, boundarySamples = 160): { x: number; y: number } {\n\tconst bbox = pathEl.getBBox()\n\tconst svgRoot = pathEl.ownerSVGElement\n\tif (!svgRoot) {\n\t\treturn { x: bbox.x + bbox.width / 2, y: bbox.y + bbox.height / 2 }\n\t}\n\tconst probe = svgRoot.createSVGPoint()\n\n\tconst len = pathEl.getTotalLength()\n\tconst bx: number[] = new Array(boundarySamples)\n\tconst by: number[] = new Array(boundarySamples)\n\tfor (let i = 0; i < boundarySamples; i++) {\n\t\tconst p = pathEl.getPointAtLength((i / boundarySamples) * len)\n\t\tbx[i] = p.x\n\t\tby[i] = p.y\n\t}\n\n\tlet bestX = bbox.x + bbox.width / 2\n\tlet bestY = bbox.y + bbox.height / 2\n\tlet bestMinSq = -Infinity\n\tfor (let i = 0; i < gridN; i++) {\n\t\tfor (let j = 0; j < gridN; j++) {\n\t\t\tconst x = bbox.x + ((i + 0.5) / gridN) * bbox.width\n\t\t\tconst y = bbox.y + ((j + 0.5) / gridN) * bbox.height\n\t\t\tprobe.x = x\n\t\t\tprobe.y = y\n\t\t\tif (!pathEl.isPointInFill(probe)) continue\n\t\t\tlet minSq = Infinity\n\t\t\tfor (let k = 0; k < boundarySamples; k++) {\n\t\t\t\tconst dx = bx[k] - x\n\t\t\t\tconst dy = by[k] - y\n\t\t\t\tconst d = dx * dx + dy * dy\n\t\t\t\tif (d < minSq) minSq = d\n\t\t\t}\n\t\t\tif (minSq > bestMinSq) {\n\t\t\t\tbestMinSq = minSq\n\t\t\t\tbestX = x\n\t\t\t\tbestY = y\n\t\t\t}\n\t\t}\n\t}\n\treturn { x: bestX, y: bestY }\n}\n\n// Test if an outer-space point lies inside a region's filled path.\nfunction isPointInRegion(outerX: number, outerY: number, r: RegionRender): boolean {\n\tconst svg = r.pathEl.ownerSVGElement\n\tif (!svg) return false\n\tconst pt = svg.createSVGPoint()\n\tpt.x = outerX\n\tpt.y = outerY\n\tconst local = r.matrix ? pt.matrixTransform(r.matrix.inverse()) : pt\n\treturn r.pathEl.isPointInFill(local)\n}\n\n// Find the best label position INSIDE a region. Returns the candidate inside\n// the region that minimizes label-rectangle probe points falling in any OTHER\n// region's path. Returns null only if no point inside the region exists.\nfunction findInlineLabelSpot(\n\tr: RegionRender,\n\tlabelW: number,\n\tlabelH: number,\n\tothers: RegionRender[],\n\tgridN = 36\n): { x: number; y: number; conflicts: number } | null {\n\tconst localBBox = r.pathEl.getBBox()\n\tconst svg = r.pathEl.ownerSVGElement\n\tif (!svg) return null\n\n\tconst corners = [\n\t\t{ x: localBBox.x, y: localBBox.y },\n\t\t{ x: localBBox.x + localBBox.width, y: localBBox.y },\n\t\t{ x: localBBox.x, y: localBBox.y + localBBox.height },\n\t\t{ x: localBBox.x + localBBox.width, y: localBBox.y + localBBox.height }\n\t]\n\tconst outerCorners = corners.map(c => {\n\t\tif (!r.matrix) return c\n\t\tconst p = svg.createSVGPoint()\n\t\tp.x = c.x\n\t\tp.y = c.y\n\t\treturn p.matrixTransform(r.matrix)\n\t})\n\tconst xs = outerCorners.map(c => c.x)\n\tconst ys = outerCorners.map(c => c.y)\n\tconst minX = Math.min(...xs)\n\tconst maxX = Math.max(...xs)\n\tconst minY = Math.min(...ys)\n\tconst maxY = Math.max(...ys)\n\n\tlet bestX = 0\n\tlet bestY = 0\n\tlet bestConflicts = Infinity\n\tlet bestDistSq = Infinity\n\tlet found = false\n\tfor (let i = 0; i < gridN; i++) {\n\t\tfor (let j = 0; j < gridN; j++) {\n\t\t\tconst x = minX + ((i + 0.5) / gridN) * (maxX - minX)\n\t\t\tconst y = minY + ((j + 0.5) / gridN) * (maxY - minY)\n\t\t\tif (!isPointInRegion(x, y, r)) continue\n\t\t\tconst probes: [number, number][] = [\n\t\t\t\t[x, y],\n\t\t\t\t[x - labelW / 2, y - labelH / 2],\n\t\t\t\t[x + labelW / 2, y - labelH / 2],\n\t\t\t\t[x - labelW / 2, y + labelH / 2],\n\t\t\t\t[x + labelW / 2, y + labelH / 2]\n\t\t\t]\n\t\t\tlet conflicts = 0\n\t\t\tfor (const [px, py] of probes) {\n\t\t\t\tfor (const o of others) {\n\t\t\t\t\tif (isPointInRegion(px, py, o)) {\n\t\t\t\t\t\tconflicts++\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tconst dx = x - r.vx\n\t\t\tconst dy = y - r.vy\n\t\t\tconst distSq = dx * dx + dy * dy\n\t\t\tconst better = conflicts < bestConflicts || (conflicts === bestConflicts && distSq < bestDistSq)\n\t\t\tif (better) {\n\t\t\t\tbestX = x\n\t\t\t\tbestY = y\n\t\t\t\tbestConflicts = conflicts\n\t\t\t\tbestDistSq = distSq\n\t\t\t\tfound = true\n\t\t\t}\n\t\t}\n\t}\n\treturn found ? { x: bestX, y: bestY, conflicts: bestConflicts } : null\n}\n\nfunction findClearOffset(\n\tvx: number,\n\tvy: number,\n\toffset: number,\n\tlabelW: number,\n\tlabelH: number,\n\tothers: RegionRender[],\n\tviewBoxCx: number,\n\tviewBoxCy: number\n): { x: number; y: number; dx: number; dy: number } {\n\tconst baseAngle = Math.atan2(vy - viewBoxCy, vx - viewBoxCx)\n\tconst angleDeltasDeg = [0, 30, -30, 60, -60, 90, -90, 120, -120, 150, -150, 180]\n\tfor (const delta of angleDeltasDeg) {\n\t\tconst angle = baseAngle + (delta * Math.PI) / 180\n\t\tconst dx = Math.cos(angle)\n\t\tconst dy = Math.sin(angle)\n\t\tconst lx = vx + dx * offset\n\t\tconst ly = vy + dy * offset\n\t\tconst probePts: [number, number][] = [\n\t\t\t[lx, ly],\n\t\t\t[lx - labelW / 2, ly - labelH / 2],\n\t\t\t[lx + labelW / 2, ly - labelH / 2],\n\t\t\t[lx - labelW / 2, ly + labelH / 2],\n\t\t\t[lx + labelW / 2, ly + labelH / 2]\n\t\t]\n\t\tlet overlap = false\n\t\tfor (const other of others) {\n\t\t\tconst svgRoot = other.pathEl.ownerSVGElement\n\t\t\tif (!svgRoot) continue\n\t\t\tconst inv = other.matrix ? other.matrix.inverse() : null\n\t\t\tconst pt = svgRoot.createSVGPoint()\n\t\t\tfor (const [x, y] of probePts) {\n\t\t\t\tpt.x = x\n\t\t\t\tpt.y = y\n\t\t\t\tconst localPt = inv ? pt.matrixTransform(inv) : pt\n\t\t\t\tif (other.pathEl.isPointInFill(localPt)) {\n\t\t\t\t\toverlap = true\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (overlap) break\n\t\t}\n\t\tif (!overlap) return { x: lx, y: ly, dx, dy }\n\t}\n\tconst dx = Math.cos(baseAngle)\n\tconst dy = Math.sin(baseAngle)\n\treturn { x: vx + dx * offset, y: vy + dy * offset, dx, dy }\n}\n\nexport type RenderBrainSvgOpts = {\n\tholder: any\n\twidth: number\n\ttemplateUrl: string\n\tassets: BrainAssets\n\tregions: { [code: string]: string }\n\tfillByRegion: (code: string) => string\n\ttooltipByRegion: (code: string, label: string) => string\n\ttitle?: string\n\ttip: Menu\n\t// Optional: invoked when the user clicks a region. Caller decides what to do\n\t// (e.g. open a hide/show menu at the event coordinates).\n\tonRegionClick?: (code: string, event: MouseEvent) => void\n\t// Optional: when true for a code, render that region with the \"no-data\" gray\n\t// fill and reduced opacity to signal it's filtered out.\n\tisRegionDimmed?: (code: string) => boolean\n}\n\nconst DIMMED_FILL = '#dcdcdc'\nconst DIMMED_OPACITY = 0.35\n\n// Render one brain SVG (template image + colored region paths + labels) into\n// `holder`. Returns the created <svg> element.\nexport function renderBrainSvg(opts: RenderBrainSvgOpts): SVGSVGElement {\n\tconst {\n\t\tholder,\n\t\twidth,\n\t\ttemplateUrl,\n\t\tassets,\n\t\tregions,\n\t\tfillByRegion,\n\t\ttooltipByRegion,\n\t\ttitle,\n\t\ttip,\n\t\tonRegionClick,\n\t\tisRegionDimmed\n\t} = opts\n\tconst { paths: regionPaths, viewBoxW, viewBoxH } = assets\n\tconst renderH = Math.round((width * viewBoxH) / viewBoxW)\n\n\tconst col = holder.append('div')\n\tif (title) {\n\t\tcol\n\t\t\t.append('div')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-size', '16px')\n\t\t\t.style('margin-bottom', '8px')\n\t\t\t.text(title)\n\t}\n\n\tconst svg = col\n\t\t.append('svg')\n\t\t.attr('width', width)\n\t\t.attr('height', renderH)\n\t\t.attr('viewBox', `0 0 ${viewBoxW} ${viewBoxH}`)\n\n\tsvg\n\t\t.append('image')\n\t\t.attr('href', templateUrl)\n\t\t.attr('x', 0)\n\t\t.attr('y', 0)\n\t\t.attr('width', viewBoxW)\n\t\t.attr('height', viewBoxH)\n\t\t.style('filter', 'grayscale(1) brightness(1.05)')\n\t\t.style('opacity', 0.55)\n\n\tconst overlayGroup = svg.append('g')\n\n\t// PASS 1: render all paths + capture geometry so PASS 2's collision checks\n\t// (isPointInFill on neighbor paths) work against the final positioned paths.\n\tconst rendered: RegionRender[] = []\n\tfor (const [code, label] of Object.entries(regions)) {\n\t\tconst geom = regionPaths[code]\n\t\tif (!geom) continue\n\n\t\tconst dimmed = isRegionDimmed?.(code) === true\n\t\tconst fillColor = dimmed ? DIMMED_FILL : fillByRegion(code)\n\t\tconst tooltipText = tooltipByRegion(code, label)\n\t\t// A merged label like \"FG/FC\" (contains a slash) is drawn on the shape; all\n\t\t// other regions keep their short code (full names go only in the tooltip).\n\t\tconst displayLabel = label && label.includes('/') ? label : code\n\n\t\tconst outerG = overlayGroup.append('g').style('cursor', 'pointer')\n\t\tconst innerG = outerG.append('g')\n\t\tif (geom.transform) innerG.attr('transform', geom.transform)\n\n\t\t// stroke-width is in path-local coordinates. For paths with a transform\n\t\t// (AM, SN), divide by the matrix scale so the rendered stroke ends up\n\t\t// the same thickness as un-transformed regions.\n\t\tconst baseStrokePx = 3\n\t\tlet strokeWidth = baseStrokePx\n\t\tif (geom.transform) {\n\t\t\tconst m = (innerG.node() as SVGGraphicsElement).transform.baseVal.consolidate()?.matrix\n\t\t\tif (m) {\n\t\t\t\tconst scale = (Math.abs(m.a) + Math.abs(m.d)) / 2\n\t\t\t\tif (scale > 0) strokeWidth = baseStrokePx / scale\n\t\t\t}\n\t\t}\n\n\t\tconst pathSel = innerG\n\t\t\t.append('path')\n\t\t\t.attr('d', geom.d)\n\t\t\t.attr('fill', fillColor)\n\t\t\t.attr('stroke', '#333')\n\t\t\t.attr('stroke-width', strokeWidth)\n\t\t\t.attr('opacity', dimmed ? DIMMED_OPACITY : 0.75)\n\n\t\tconst pathEl = pathSel.node() as SVGPathElement\n\t\tconst { x: localX, y: localY } = visualCenter(pathEl)\n\t\tconst localBBox = pathEl.getBBox()\n\n\t\tconst innerEl = innerG.node() as SVGGraphicsElement\n\t\tconst matrix = innerEl.transform.baseVal.consolidate()?.matrix ?? null\n\t\tconst ownerSvg = pathEl.ownerSVGElement!\n\t\tconst localPt = ownerSvg.createSVGPoint()\n\t\tlocalPt.x = localX\n\t\tlocalPt.y = localY\n\t\tconst outerPt = matrix ? localPt.matrixTransform(matrix) : { x: localX, y: localY }\n\t\tconst bboxW = localBBox.width * (matrix ? Math.abs(matrix.a) : 1)\n\t\tconst bboxH = localBBox.height * (matrix ? Math.abs(matrix.d) : 1)\n\n\t\trendered.push({\n\t\t\tcode,\n\t\t\tdisplayLabel,\n\t\t\tfillColor,\n\t\t\td: geom.d,\n\t\t\tdimmed,\n\t\t\touterG,\n\t\t\tinnerG,\n\t\t\tpathSel,\n\t\t\tpathEl,\n\t\t\tmatrix,\n\t\t\tvx: outerPt.x,\n\t\t\tvy: outerPt.y,\n\t\t\tbboxW,\n\t\t\tbboxH\n\t\t})\n\n\t\touterG\n\t\t\t.on('mouseover', (event: MouseEvent) => {\n\t\t\t\ttip.clear().show(event.clientX, event.clientY)\n\t\t\t\tconst lines = tooltipText.split('\\n')\n\t\t\t\tconst tipDiv = tip.d.append('div').style('padding', '8px').style('font-size', '13px')\n\t\t\t\ttipDiv.append('div').style('font-weight', 'bold').style('margin-bottom', '4px').text(lines[0])\n\t\t\t\tfor (let i = 1; i < lines.length; i++) {\n\t\t\t\t\ttipDiv.append('div').text(lines[i])\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\ttip.hide()\n\t\t\t})\n\t\tif (onRegionClick) {\n\t\t\touterG.on('click', (event: MouseEvent) => onRegionClick(code, event))\n\t\t}\n\t}\n\n\t// PASS 2: place labels. Inline when the region is roomy enough to host the\n\t// full label rect; callout with leader line when not (AM, SN).\n\tconst fontSize = 46\n\tfor (const r of rendered) {\n\t\tconst labelW = r.displayLabel.length * fontSize * 0.62\n\t\tconst labelH = fontSize\n\t\tconst labelHalfDiag = Math.hypot(labelW / 2, labelH / 2)\n\n\t\tconst others = rendered.filter(rr => rr !== r)\n\t\tconst regionRoomy = r.bboxW * r.bboxH > labelW * labelH * 1.5\n\t\tconst inlinePoint = regionRoomy ? findInlineLabelSpot(r, labelW, labelH, others) : null\n\t\tconst fitsInside = !!inlinePoint\n\n\t\tlet labelX = inlinePoint ? inlinePoint.x : r.vx\n\t\tlet labelY = inlinePoint ? inlinePoint.y : r.vy\n\n\t\tif (!fitsInside) {\n\t\t\tif (!r.dimmed) r.pathSel.attr('opacity', 1)\n\t\t\t// White halo behind the colored path, inside the same transformed group\n\t\t\tr.innerG\n\t\t\t\t.insert('path', ':first-child')\n\t\t\t\t.attr('d', r.d)\n\t\t\t\t.attr('fill', '#fff')\n\t\t\t\t.attr('stroke', '#fff')\n\t\t\t\t.attr('stroke-width', 18)\n\t\t\t\t.attr('stroke-linejoin', 'round')\n\n\t\t\tconst offset = Math.max(r.bboxW, r.bboxH) / 2 + labelHalfDiag * 1.6\n\t\t\tconst placed = findClearOffset(r.vx, r.vy, offset, labelW, labelH, others, viewBoxW / 2, viewBoxH / 2)\n\t\t\tlabelX = placed.x\n\t\t\tlabelY = placed.y\n\n\t\t\tr.outerG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('x1', r.vx)\n\t\t\t\t.attr('y1', r.vy)\n\t\t\t\t.attr('x2', labelX - placed.dx * labelHalfDiag * 0.9)\n\t\t\t\t.attr('y2', labelY - placed.dy * labelHalfDiag * 0.9)\n\t\t\t\t.attr('stroke', '#333')\n\t\t\t\t.attr('stroke-width', 2)\n\t\t}\n\n\t\tr.outerG\n\t\t\t.append('text')\n\t\t\t.attr('x', labelX)\n\t\t\t.attr('y', labelY)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('font-size', `${fontSize}px`)\n\t\t\t.attr('font-weight', 'bold')\n\t\t\t.attr('fill', '#333')\n\t\t\t.attr('paint-order', 'stroke')\n\t\t\t.attr('stroke', '#fff')\n\t\t\t.attr('stroke-width', 6)\n\t\t\t.text(r.displayLabel)\n\t}\n\n\treturn svg.node() as SVGSVGElement\n}\n\n// clickable disease tabs (e.g. AD | LBD); active one bold + underlined.\n// Shared by the standalone brainRegions plot and the proteinView tile so\n// disease selection behaves the same in both.\nexport function makeDiseaseTabs(\n\tholder: any,\n\tdiseases: string[],\n\tinitial: string,\n\tonChange: (d: string) => void,\n\tfontSize = '.8em'\n) {\n\tconst row = holder\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('gap', '12px')\n\t\t.style('margin-bottom', '4px')\n\t\t.style('font-size', fontSize)\n\tlet active = initial\n\tconst update = () => {\n\t\trow.selectAll('*').remove()\n\t\tfor (const d of diseases) {\n\t\t\trow\n\t\t\t\t.append('span')\n\t\t\t\t.attr('role', 'tab')\n\t\t\t\t.attr('aria-selected', String(d === active))\n\t\t\t\t.text(d)\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('font-weight', d === active ? '600' : '400')\n\t\t\t\t.style('text-decoration', d === active ? 'underline' : 'none')\n\t\t\t\t.style('color', d === active ? '#111827' : '#6b7280')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tif (d === active) return\n\t\t\t\t\tactive = d\n\t\t\t\t\tupdate()\n\t\t\t\t\tonChange(d)\n\t\t\t\t})\n\t\t}\n\t}\n\tupdate()\n}\n\n/************ region coloring shared by the standalone plot and the proteinView tile ************/\n\n// brain-region DAP files usually carry a nominal p column; the region map is\n// thresholded on that (FDR is too conservative here to color any region). When\n// a file has no p column the server omits p_value and the FDR is used instead,\n// so a significant region never silently turns grey.\nexport const BRAIN_P_THRESHOLD = 0.05\nexport const BRAIN_NONSIG_COLOR = '#ccc'\nexport const BRAIN_NEG_COLOR = '#2166ac'\nexport const BRAIN_ZERO_COLOR = '#f7f7f7'\nexport const BRAIN_POS_COLOR = '#b2182b'\n\nexport type BrainRegionEntry = { fold_change: number; fdr: number; p_value?: number }\nexport type BrainRegionData = { [code: string]: BrainRegionEntry }\n\nexport const brainSigValue = (e: BrainRegionEntry) => e.p_value ?? e.fdr\nexport const isBrainRegionSig = (e: BrainRegionEntry | undefined) => !!e && brainSigValue(e) < BRAIN_P_THRESHOLD\n\n/** fold-change color scale over the significant regions of one isoform \u00D7 disease */\nexport function makeBrainFcScale(regionData: BrainRegionData) {\n\tconst sigFCs: number[] = []\n\tfor (const entry of Object.values(regionData)) if (isBrainRegionSig(entry)) sigFCs.push(entry.fold_change)\n\tconst maxAbsFC = sigFCs.length ? Math.max(...sigFCs.map(v => Math.abs(v))) : 1\n\tconst colorScale = scaleLinear<string>()\n\t\t.domain([-maxAbsFC, 0, maxAbsFC])\n\t\t.range([BRAIN_NEG_COLOR, BRAIN_ZERO_COLOR, BRAIN_POS_COLOR])\n\t\t.clamp(true)\n\treturn { maxAbsFC, colorScale, nSig: sigFCs.length }\n}\n\nexport function brainFillByRegion(regionData: BrainRegionData, colorScale: (v: number) => string) {\n\treturn (code: string) => {\n\t\tconst entry = regionData[code]\n\t\treturn isBrainRegionSig(entry) ? colorScale(entry.fold_change) : BRAIN_NONSIG_COLOR\n\t}\n}\n\nexport function brainTooltipByRegion(regionData: BrainRegionData) {\n\tconst fmt = (v: number) => (v >= 0.0001 ? v.toFixed(4) : v.toExponential(3))\n\treturn (code: string, label: string) => {\n\t\tconst entry = regionData[code]\n\t\tif (!entry) return `${label} (${code})\\nNo data`\n\t\tconst p = Number.isFinite(entry.p_value) ? fmt(entry.p_value as number) : 'NA'\n\t\treturn `${label} (${code})\\nlog\u2082 fold change: ${entry.fold_change.toFixed(4)}\\np-value: ${p}\\nFDR: ${fmt(\n\t\t\tentry.fdr\n\t\t)}`\n\t}\n}\n"],
+  "mappings": 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+}