@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/chunk-6FG6JFZP.js

@@ -0,0 +1,339 @@
+import {
+  matchesGvQueryEntry
+} from "./chunk-3XBG5HIV.js";
+import {
+  mclass
+} from "./chunk-SB36AUG7.js";
+
+// ../shared/utils/dist/src/termCollection.js
+function validateTermCollectionTerm(term) {
+  if (!Array.isArray(term?.termlst) || !term.termlst.length)
+    throw new Error("termCollection requires nonempty term.termlst[]");
+  const memberIds = /* @__PURE__ */ new Set();
+  const types = /* @__PURE__ */ new Set();
+  for (const t of term.termlst) {
+    if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
+    if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
+    if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
+    memberIds.add(t.id);
+    types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
+  }
+  if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
+  return memberIds;
+}
+function validateFractionMembers(numerators, denominators, memberIds) {
+  if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
+  if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
+  if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
+  if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
+  for (const id of denominators) {
+    if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
+    if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
+  }
+  for (const id of numerators) {
+    if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
+    if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
+  }
+}
+var FRACTION_TW_TYPE = "TermCollectionTWFraction";
+function isFractionTw(tw) {
+  return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
+}
+function getFractionTvsTerm(tw) {
+  if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
+  const term = structuredClone(tw.term);
+  const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
+  const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
+  const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
+  validateFractionMembers(numerators, denominators, memberIds);
+  term.numerators = numerators;
+  term.denominators = denominators;
+  return term;
+}
+function validateTermCollectionFraction(q, term) {
+  const memberIds = validateTermCollectionTerm(term);
+  validateFractionMembers(q?.numerators, q?.denominators, memberIds);
+  if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
+    throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
+}
+
+// ../shared/utils/dist/src/filter.js
+function getFilteredSamples(sampleAnno, filter) {
+  setDatasetAnnotations(filter);
+  const samples = /* @__PURE__ */ new Set();
+  for (const anno of sampleAnno) {
+    if (samples.has(anno.sample)) continue;
+    const data = anno.s || anno.data;
+    if (data && sample_match_termvaluesetting(data, filter)) {
+      samples.add(anno.sample);
+    }
+  }
+  return samples;
+}
+function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
+  const lst = filter.type == "tvslst" ? filter.lst : [filter];
+  let numberofmatchedterms = 0;
+  for (const item of lst) {
+    if ("type" in item && item.type == "tvslst") {
+      if (sample_match_termvaluesetting(row, item, _term, sample)) {
+        numberofmatchedterms++;
+      }
+    } else {
+      const itemCopy = JSON.parse(JSON.stringify(item));
+      const t = itemCopy.tvs;
+      if (_term && t.term) {
+        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
+          numberofmatchedterms++;
+          continue;
+        }
+      }
+      let samplevalue;
+      if (_term && !t.term) {
+        if (t.term$type && t.term$type !== _term.type) {
+          numberofmatchedterms++;
+          continue;
+        }
+        t.term = _term;
+        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
+      } else if (sample && t.term.$id) {
+        samplevalue = sample[t.term.$id].value;
+      } else {
+        samplevalue = t.term.id in row ? row[t.term.id] : row;
+      }
+      setDatasetAnnotations(itemCopy);
+      let thistermmatch;
+      if (t.term.type == "categorical") {
+        if (samplevalue === void 0) continue;
+        thistermmatch = t.valueset.has(samplevalue);
+      } else if (t.term.type == "integer" || t.term.type == "float") {
+        if (samplevalue === void 0) continue;
+        for (const range of t.ranges) {
+          if ("value" in range) {
+            thistermmatch = samplevalue === range.value;
+            if (thistermmatch) break;
+          } else if (samplevalue == range.name) {
+            thistermmatch = true;
+            break;
+          } else {
+            if (t.term.values) {
+              const v = t.term.values[samplevalue.toString()];
+              if (v && v.uncomputable) {
+                continue;
+              }
+            }
+            let left, right;
+            if (range.startunbounded) {
+              left = true;
+            } else if ("start" in range) {
+              if (range.startinclusive) {
+                left = samplevalue >= range.start;
+              } else {
+                left = samplevalue > range.start;
+              }
+            }
+            if (range.stopunbounded) {
+              right = true;
+            } else if ("stop" in range) {
+              if (range.stopinclusive) {
+                right = samplevalue <= range.stop;
+              } else {
+                right = samplevalue < range.stop;
+              }
+            }
+            thistermmatch = left && right;
+          }
+          if (thistermmatch) break;
+        }
+      } else if (t.term.type == "condition") {
+        const key = getPrecomputedKey(t);
+        const anno = samplevalue && samplevalue[key];
+        if (anno) {
+          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
+        }
+      } else if (t.term.type == "geneVariant") {
+        const svalues = samplevalue.values || [samplevalue];
+        for (const sv of svalues) {
+          thistermmatch = t.values.find(
+            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
+          ) && true;
+          if (thistermmatch) break;
+        }
+      } else {
+        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
+      }
+      if (t.isnot) {
+        thistermmatch = !thistermmatch;
+      }
+      if (thistermmatch) numberofmatchedterms++;
+    }
+    if (filter.join == "or") {
+      if (numberofmatchedterms && filter.in) return true;
+      if (!numberofmatchedterms && !filter.in) return true;
+    }
+  }
+  if (!("in" in filter)) filter.in = true;
+  return filter.in == (numberofmatchedterms == lst.length);
+}
+function setDatasetAnnotations(item, ds = null) {
+  if (item.type == "tvslst") {
+    for (const subitem of item.lst) {
+      setDatasetAnnotations(subitem, ds);
+    }
+  } else {
+    if (ds && typeof ds.setAnnoByTermId == "function") {
+      ds.setAnnoByTermId(item.tvs.term.id);
+    }
+    if (item.tvs.term.type == "categorical") {
+      const tvsAny = item.tvs;
+      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
+    }
+  }
+}
+function getPrecomputedKey(q) {
+  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
+  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
+  return precomputedKey;
+}
+function getWrappedTvslst(lst = [], join = "", $id = null) {
+  const filter = {
+    type: "tvslst",
+    in: true,
+    join,
+    lst
+  };
+  if ($id !== null) filter.$id = $id;
+  return filter;
+}
+function getTvsDenominators(term) {
+  if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
+  return (term?.termlst || []).map((t) => t.id);
+}
+function validateTermCollectionTvs(term) {
+  const memberIds = validateTermCollectionTerm(term);
+  if (!term.numerators) return;
+  validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
+}
+
+// ../shared/utils/dist/src/geneVariantFilter.js
+var statusClasses = /* @__PURE__ */ new Set(["WT", "Blank"]);
+function unsupported(what) {
+  return `tw.q.variantFilter does not support ${what}, which qualifies a sample rather than an individual variant. Use a groupset (q.type='custom-groupset') for a sample-level filter.`;
+}
+function validateVariantFilter(filter, term) {
+  if (!filter) return;
+  if (filter.type != "tvslst") throw `tw.q.variantFilter.type must be 'tvslst'`;
+  if (!Array.isArray(filter.lst) || !filter.lst.length) throw "tw.q.variantFilter.lst[] is empty";
+  if (filter.lst.length > 1 && filter.join != "and" && filter.join != "or")
+    throw `tw.q.variantFilter.join must be 'and' or 'or' when lst[] has more than one item`;
+  const dts = term?.childTerms?.length ? new Set(term.childTerms.map((t) => t.dt)) : null;
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      validateVariantFilter(item, term);
+      continue;
+    }
+    if (item.type != "tvs") throw `unexpected tw.q.variantFilter item.type='${item.type}'`;
+    const tvs = item.tvs;
+    if (!tvs) throw "missing tvs of a tw.q.variantFilter item";
+    if (!Number.isInteger(tvs.term?.dt)) throw "tw.q.variantFilter tvs.term must be a dt term, with an integer .dt";
+    if (dts && !dts.has(tvs.term.dt))
+      throw `tw.q.variantFilter tvs.term.dt=${tvs.term.dt} is not a dt of term '${term.name}'`;
+    if (!Array.isArray(tvs.values) || !tvs.values.length) throw "tw.q.variantFilter tvs.values[] is empty";
+    for (const v of tvs.values) {
+      if (!v.key) throw "a tw.q.variantFilter tvs.values[] entry is missing .key";
+      if (statusClasses.has(v.key))
+        throw `tw.q.variantFilter cannot select the '${v.key}' class, which is a testing status and not a variant`;
+      if (v.partnerBreakpointRange) throw unsupported("partnerBreakpointRange");
+    }
+    if (tvs.genotype && tvs.genotype != "variant") throw unsupported(`genotype='${tvs.genotype}'`);
+    if (tvs.mcount && tvs.mcount != "any") throw unsupported(`mcount='${tvs.mcount}'`);
+    if (tvs.mafFilter) throw unsupported("mafFilter");
+    if (tvs.continuousCnv) throw unsupported("continuousCnv");
+    if (tvs.selfBreakpointRange) throw unsupported("selfBreakpointRange");
+  }
+}
+function getFilterScope(filter, scope = /* @__PURE__ */ new Set()) {
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") getFilterScope(item, scope);
+    else scope.add(`${item.tvs.term.dt}:${item.tvs.term.origin || "*"}`);
+  }
+  return scope;
+}
+function isInScope(v, scope) {
+  return scope.has(`${v.dt}:*`) || scope.has(`${v.dt}:${v.origin || ""}`);
+}
+function matchTvs(v, tvs) {
+  let match = false;
+  if (v.dt == tvs.term.dt && (!tvs.term.origin || v.origin == tvs.term.origin)) {
+    match = tvs.values.some((e) => e.key == v.class && (!e.mname || e.mname == v.mname && matchesGvQueryEntry(e, v)));
+  }
+  return tvs.isnot ? !match : match;
+}
+function matchFilter(v, filter) {
+  const lst = filter.type == "tvslst" ? filter.lst : [filter];
+  let numMatched = 0;
+  for (const item of lst) {
+    const matched = item.type == "tvslst" ? matchFilter(v, item) : matchTvs(v, item.tvs);
+    if (matched) numMatched++;
+    if (filter.join == "or" && numMatched) break;
+  }
+  const pass = filter.join == "or" ? numMatched > 0 : numMatched == lst.length;
+  return filter.in === false ? !pass : pass;
+}
+function filterVariantValues(values, filter) {
+  if (!filter || !values) return values;
+  const scope = getFilterScope(filter);
+  const kept = [];
+  const annotated = /* @__PURE__ */ new Set();
+  const dropped = /* @__PURE__ */ new Map();
+  for (const v of values) {
+    if (!isInScope(v, scope)) continue;
+    const key = `${v.dt}:${v.origin || ""}`;
+    if (statusClasses.has(v.class) || matchFilter(v, filter)) {
+      kept.push(v);
+      annotated.add(key);
+    } else if (!dropped.has(key)) {
+      dropped.set(key, v);
+    }
+  }
+  for (const [key, v] of dropped) {
+    if (annotated.has(key)) continue;
+    const wt = { dt: v.dt, class: "WT", label: mclass.WT.label };
+    if (v.gene) wt.gene = v.gene;
+    if (v.origin) wt.origin = v.origin;
+    kept.push(wt);
+  }
+  return kept;
+}
+function variantFilterLabel(filter, mclassOverride, maxItems = 3) {
+  if (!filter) return "";
+  const entries = [];
+  collect(filter, false);
+  function collect(f, negated) {
+    const flipped = f.in === false ? !negated : negated;
+    for (const item of f.lst) {
+      if (item.type == "tvslst") collect(item, flipped);
+      else if (flipped === !!item.tvs.isnot) entries.push(...item.tvs.values);
+    }
+  }
+  if (!entries.length) return "";
+  const classes = mclass;
+  const names = [
+    ...new Set(entries.map((e) => e.mname || mclassOverride?.[e.key]?.label || classes[e.key]?.label || e.key))
+  ];
+  return names.length > maxItems ? `${names.slice(0, maxItems).join("/")}\u2026` : names.join("/");
+}
+
+export {
+  isFractionTw,
+  getFractionTvsTerm,
+  validateTermCollectionFraction,
+  getFilteredSamples,
+  sample_match_termvaluesetting,
+  getWrappedTvslst,
+  getTvsDenominators,
+  validateTermCollectionTvs,
+  validateVariantFilter,
+  filterVariantValues,
+  variantFilterLabel
+};
+//# sourceMappingURL=chunk-6FG6JFZP.js.map

package/dist/chunk-6G45AUSV.js

@@ -0,0 +1,237 @@
+import {
+  DataPointInteractions,
+  axisstyle,
+  createLollipopFromGene,
+  drawHoverShapes,
+  showResultsTable,
+  table2col,
+  to_svg
+} from "./chunk-C3HEDQPT.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  icons
+} from "./chunk-6RRZRISL.js";
+import {
+  axisLeft
+} from "./chunk-Z2ZITHT4.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/manhattan/manhattan.ts
+var manhattanLayoutDefaults = {
+  plotWidth: 1e3,
+  plotHeight: 400,
+  pngDotRadius: 2,
+  yAxisX: 70,
+  yAxisY: 40,
+  yAxisSpace: 20,
+  xAxisLabelPad: 30,
+  yAxisPad: 5,
+  axisColor: "#545454",
+  showYAxisLine: true,
+  fontSize: 12,
+  showLegend: true,
+  legendItemWidth: 80,
+  legendDotRadius: 3,
+  legendRightOffset: 15,
+  legendTextOffset: 12,
+  legendVerticalOffset: 4,
+  legendFontSize: 12,
+  showInteractiveDots: true,
+  interactiveDotRadius: 2,
+  interactiveDotStrokeWidth: 1,
+  showDownload: true,
+  interactiveDotsCap: 5e3,
+  maxTooltipGenes: 5
+};
+function plotManhattan(div, data, settings, app, custom = {}) {
+  const handle = { points: [], highlight: () => {
+  } };
+  settings = {
+    ...settings
+  };
+  let interactivePoints = data.plotData.points;
+  if (data.plotData.points.length > settings.interactiveDotsCap) {
+    interactivePoints = data.plotData.points.sort((a, b) => Math.abs(b.y) - Math.abs(a.y)).slice(0, settings.interactiveDotsCap);
+  }
+  const signed = data.plotData.y_min < 0;
+  div.style("position", "relative");
+  const geneTip = new Menu({ padding: "" });
+  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
+  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
+  const yPad = data.plotData.y_pad ?? settings.pngDotRadius;
+  const yAxisLow = signed ? data.plotData.y_min + yPad : 0;
+  const yAxisScale = linear().domain([yAxisLow, data.plotData.y_max - yPad]).range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)]);
+  const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
+  axisG.call(
+    axisLeft(yAxisScale).tickSizeOuter(0)
+    // removes top/bottom cap lines for clean look
+  );
+  axisstyle({
+    axis: axisG,
+    color: settings.axisColor,
+    fontsize: settings.fontSize + 2,
+    showline: settings.showYAxisLine
+  });
+  svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text((custom.yAxisLabel ?? "-log\u2081\u2080(q-value)") + (data.plotData.has_capped_points ? " [capped]" : ""));
+  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
+  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
+  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
+    const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
+    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
+    const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
+    const linkedLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
+    handle.points = interactivePoints;
+    handle.highlight = (dots) => drawHoverShapes(
+      linkedLayer,
+      dots.map((d) => ({
+        path: circlePath(settings.pngDotRadius + 2),
+        transform: `translate(${d.pixel_x},${d.pixel_y})`,
+        stroke: "black",
+        strokeWidth: 2
+      }))
+    );
+    const grin2Hover = (d, container) => {
+      const table = table2col({ holder: container.append("div"), margin: "10px" });
+      table.addRow("Gene", d.gene);
+      table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
+      const [t1, t2] = table.addRow();
+      t1.text("Type");
+      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
+      table.addRow("Q-value", d.q_value.toPrecision(3));
+      table.addRow("Subject count", d.nsubj);
+    };
+    const grin2Table = (dots) => ({
+      columns: [
+        { label: "Gene" },
+        { label: "Position" },
+        { label: "Type" },
+        { label: "Q-value", sortable: true },
+        { label: "Subject count", sortable: true }
+      ],
+      rows: dots.map((d) => [
+        { value: d.gene },
+        { value: `${d.chrom}:${d.start}-${d.end}` },
+        {
+          html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
+        },
+        { value: d.q_value.toPrecision(3) },
+        { value: d.nsubj }
+      ])
+    });
+    const interactions = new DataPointInteractions({
+      cover,
+      hoverLayer,
+      hoverTip: geneTip,
+      points: interactivePoints,
+      getX: (d) => d.pixel_x,
+      getY: (d) => d.pixel_y,
+      hitRadius: settings.pngDotRadius + 3,
+      toHoverSpec: (d) => ({
+        path: circlePath(settings.pngDotRadius),
+        transform: `translate(${d.pixel_x},${d.pixel_y})`,
+        fill: "none",
+        stroke: "black",
+        strokeWidth: settings.interactiveDotStrokeWidth
+      }),
+      maxTooltipRows: settings.maxTooltipGenes,
+      onHover: custom.onHover,
+      itemNoun: custom.itemNoun ?? "gene",
+      renderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,
+      buildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,
+      // A caller with actions gets the module's standard click flow: an action menu for one
+      // dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.
+      ...custom.getActions ? {
+        getActions: custom.getActions,
+        renderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,
+        getRowKey: custom.getRowKey
+      } : {
+        // Manhattan single-click goes straight to a lollipop launch — no menu.
+        // Release hover-suppression immediately so the cursor's next move re-engages.
+        onSingleClick: (d, _event, ctx) => {
+          ctx.dismiss();
+          if (app && d.gene) createLollipopFromGene(d.gene, app);
+        },
+        // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
+        // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
+        // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
+        // Content is built BEFORE show2 so Menu can measure the populated rect for
+        // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
+        // and extends off the right edge of the viewport.
+        onMultiClick: (dots, event, ctx) => {
+          if (!app) {
+            ctx.dismiss();
+            return;
+          }
+          ctx.clickMenu.clear();
+          const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
+          showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
+          ctx.clickMenu.show2(event.clientX, event.clientY);
+        }
+      }
+    });
+    interactions.attach();
+  }
+  if (data.plotData.chrom_data) {
+    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
+    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
+      const chromLabel = chrom.replace("chr", "");
+      if (chromLabel === "M") return;
+      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
+      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
+    });
+  }
+  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr("y", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text("Chromosomes");
+  const title = svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text(custom.title ?? "Manhattan Plot");
+  const titleWidth = title.node().getBBox?.().width || 100;
+  if (settings.showDownload) {
+    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + titleWidth + 8}px`);
+    icons["download"](downloadDiv, {
+      width: 16,
+      height: 16,
+      title: "Download Manhattan plot",
+      handler: () => {
+        const svgNode = svg.node();
+        const clone = svgNode.cloneNode(true);
+        const bbox = svgNode.getBBox();
+        clone.setAttribute("width", bbox.width.toString());
+        clone.setAttribute("height", bbox.height.toString());
+        clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
+        to_svg(clone, `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`, {
+          apply_dom_styles: true
+        });
+      }
+    });
+  }
+  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type).filter(Boolean))];
+  const legendData = custom.legend?.map((l) => ({ type: l.label, color: l.color, hollow: l.hollow })) ?? mutationTypes.map((type) => {
+    const point = data.plotData.points.find((p) => p.type === type);
+    return {
+      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
+      color: point?.color
+    };
+  });
+  if (settings.showLegend && legendData.length > 0) {
+    const legendY = settings.yAxisY / 2;
+    const totalWidth = legendData.length * settings.legendItemWidth;
+    const legendX = settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) - totalWidth - settings.legendRightOffset;
+    legendData.forEach((item, i) => {
+      const x = legendX + i * settings.legendItemWidth;
+      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.hollow ? "none" : item.color).attr("stroke", item.hollow ? item.color : "none");
+      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
+    });
+  }
+  return handle;
+}
+
+export {
+  manhattanLayoutDefaults,
+  plotManhattan
+};
+//# sourceMappingURL=chunk-6G45AUSV.js.map

package/dist/chunk-6G45AUSV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/manhattan/manhattan.ts"],
+  "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport { select } from 'd3-selection'\nimport {\n\tMenu,\n\ticons,\n\taxisstyle,\n\ttable2col,\n\tshowResultsTable,\n\tcreateLollipopFromGene,\n\tDataPointInteractions,\n\tdrawHoverShapes,\n\ttype ActionMenuItem\n} from '#dom'\nimport { to_svg } from '#src/client'\nimport type { ManhattanPoint } from './manhattanTypes'\n\n/**\n * Creates an interactive Manhattan plot on top of a PNG background plot image.\n *\n * @param {Object} div - div element to contain the plot\n * @param {Object} data - Plot data\n * @param {Object} settings - Display configuration options:\n *   @param {number} [settings.plotWidth=500] - Plot area width\n *   @param {number} [settings.plotHeight=200] - Plot area height\n *   @param {boolean} [settings.showLegend=true] - Whether to display legend\n *   @param {boolean} [settings.showDownload=true] - Whether to show download button\n *   @param {boolean} [settings.showInteractiveDots=true] - Whether to show hoverable data points\n *   @param {number} [settings.yAxisX=70] - Y-axis positioning\n *   @param {number} [settings.yAxisSpace=40] - Space between Y-axis and plot\n *   @param {number} [settings.yAxisY=40] - Top margin\n *   @param {number} [settings.fontSize=12] - Base font size\n *   @param {number} [settings.pngDotRadius=2] - Radius of dots in PNG plot\n *   @param {number} [settings.legendItemWidth=80] - Horizontal space per legend item\n *   @param {number} [settings.legendDotRadius=3] - Size of legend dots\n *   @param {number} [settings.legendRightOffset=15] - Offset from right edge\n *   @param {number} [settings.legendTextOffset=12] - Distance between dot and text\n *   @param {number} [settings.legendVerticalOffset=4] - Vertical offset for legend items\n *   @param {number} [settings.legendFontSize=12] - Font size for legend text\n *   @param {number} [settings.interactiveDotRadius=2] - Radius of interactive dots\n *   @param {number} [settings.xAxisLabelPad=20] - Amount of padding we give for x-axis title padding\n *   @param {number} [settings.interactiveDotStrokeWidth=1] - Stroke width for interactive dots\n *   @param {string} [settings.axisColor='#545454'] - Color for y-axis\n *   @param {boolean} [settings.showYAxisLine=true] - Whether to show y-axis line\n *   @param {number} [settings.interactiveDotsCap=5000] - Interactive dots cap\n *   @param {number} [settings.maxTooltipGenes=5] - Maximum number of genes to show in tooltip\n * @param {Object} [app] - Optional app context for dispatching events\n *\n *\n * @description\n * Renders a genomic Manhattan plot by overlaying interactive elements on the base PNG plot image.\n * Features include chromosome labels, legend, hoverable data points with tooltips,\n * and proper axis scaling. The plot combines a static PNG plot image of all points with dynamic SVG elements\n * including axes, labels, legend, and top genes (represented as interactive dots) for detailed information on hover.\n */\n\n/** What a caller other than GRIN2 supplies: the plot is drawn the same way, but what a dot IS --\n * what its tooltip says, what clicking it offers, what the axis is called -- belongs to the caller.\n * Every field is optional and defaults to the GRIN2 behaviour, so GRIN2 passes nothing. */\nexport type ManhattanCustom<T = any> = {\n\ttitle?: string\n\tyAxisLabel?: string\n\t/** legend entries; default derives one per point `type` from the data. `hollow` draws the\n\t * swatch as an open circle, for a plot whose dots are drawn that way */\n\tlegend?: { label: string; color: string; hollow?: boolean }[]\n\titemNoun?: string\n\trenderSingleHoverTooltip?: (d: T, container: any) => void\n\tbuildMultiHitTableData?: (dots: T[]) => { columns: any[]; rows: any[] }\n\t/** Given, clicking a dot opens the standard action menu (buttons over the info table) rather\n\t * than GRIN2's lollipop launch; multi-hit clicks open the standard pick-a-row menu. */\n\tgetActions?: (d: T) => ActionMenuItem[]\n\trenderSingleHitInfo?: (d: T, container: any) => void\n\tgetRowKey?: (d: T) => string\n\t/** see DataPointInteractionsOpts.onHover */\n\tonHover?: (dots: T[]) => void\n}\n\n/** Returned by plotManhattan: the live points, and a way to ring some of them from outside -- for a\n * hover on another plot showing the same items. Separate from the plot's own hover layer, so the two\n * never erase each other. */\nexport type ManhattanHandle = { points: any[]; highlight: (dots: any[]) => void }\n\n/** Layout settings shared by every caller. GRIN2 keeps its own copy in its settings (they are\n * part of its persisted state); a caller without such state spreads these. */\nexport const manhattanLayoutDefaults = {\n\tplotWidth: 1000,\n\tplotHeight: 400,\n\tpngDotRadius: 2,\n\tyAxisX: 70,\n\tyAxisY: 40,\n\tyAxisSpace: 20,\n\txAxisLabelPad: 30,\n\tyAxisPad: 5,\n\taxisColor: '#545454',\n\tshowYAxisLine: true,\n\tfontSize: 12,\n\tshowLegend: true,\n\tlegendItemWidth: 80,\n\tlegendDotRadius: 3,\n\tlegendRightOffset: 15,\n\tlegendTextOffset: 12,\n\tlegendVerticalOffset: 4,\n\tlegendFontSize: 12,\n\tshowInteractiveDots: true,\n\tinteractiveDotRadius: 2,\n\tinteractiveDotStrokeWidth: 1,\n\tshowDownload: true,\n\tinteractiveDotsCap: 5000,\n\tmaxTooltipGenes: 5\n}\n\nexport function plotManhattan(\n\tdiv: any,\n\tdata: any,\n\tsettings: any,\n\tapp?: any,\n\tcustom: ManhattanCustom = {}\n): ManhattanHandle {\n\tconst handle: ManhattanHandle = { points: [], highlight: () => {} }\n\t// Get our settings\n\tsettings = {\n\t\t...settings\n\t}\n\n\t// Check size of interactive data. Ranked by |y| so a signed plot (hypomethylation below the\n\t// line) keeps its strongest dots on both sides rather than only the positive ones.\n\tlet interactivePoints = data.plotData.points\n\tif (data.plotData.points.length > settings.interactiveDotsCap) {\n\t\tinteractivePoints = data.plotData.points\n\t\t\t.sort((a: any, b: any) => Math.abs(b.y) - Math.abs(a.y))\n\t\t\t.slice(0, settings.interactiveDotsCap)\n\t}\n\t// A signed plot has y_min below zero; its axis is symmetric and its zero line sits mid-plot.\n\tconst signed = data.plotData.y_min < 0\n\n\t// Set the  positioning up for download button to work properly\n\tdiv.style('position', 'relative')\n\n\t// Hover tooltip menu \u2014 DataPointInteractions writes into this on hover.\n\tconst geneTip = new Menu({ padding: '' })\n\n\tconst svg = div\n\t\t.append('svg')\n\t\t.attr('data-testid', 'sjpp-manhattan')\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4) // Extra space for x-axis labels, legend, and title\n\n\t// Add y-axis\n\t// yPlot       \u2192 full padded scale, aligns exactly with PNG coordinates\n\t// yAxisScale  \u2192 trimmed scale for axis labels, ignores PNG padding\n\t// --- Y-Axis Setup ---\n\t// This section builds two linked scales:\n\t//\n\t//   1) yPlot       \u2192 full PNG-aligned scale (includes padding added by Rust)\n\t//   2) yAxisScale  \u2192 visual axis scale (no padding; shows only real data values)\n\t//\n\t// The reason for two scales is that the PNG image itself was rendered\n\t// with top/bottom padding for dot radius. We need one scale to stay\n\t// pixel-perfect with the PNG (for dots, overlays, etc.), and another\n\t// scale to make the visible y-axis line up only with the *real* data region.\n\n\t// 1) yPlot: true positioning scale used for all pixel-aligned elements\n\t//    - Domain = padded range from Rust (includes buffer above/below real data)\n\t//    - Range  = full PNG pixel height (0 is top, png_height is bottom)\n\tconst yPlot = scaleLinear()\n\t\t.domain([data.plotData.y_min, data.plotData.y_max]) // padded domain from Rust\n\t\t.range([settings.plotHeight + 2 * settings.pngDotRadius, 0]) // full PNG height\n\n\t// 2) yAxisScale: used only for the visible axis labels/ticks\n\t//    - Domain = true data values (no padding)\n\t//    - Range  = subset of pixel space between yPlot(0) and yPlot(realMax [data.plotData.y_max - data.plotData.png_dot_radius])\n\t//               so the axis sits entirely within the real data area\n\t// the PNG pads its y range by the dot radius; older renders had that padding equal the radius\n\t// in y units, newer ones state it\n\tconst yPad = data.plotData.y_pad ?? settings.pngDotRadius\n\tconst yAxisLow = signed ? data.plotData.y_min + yPad : 0\n\tconst yAxisScale = scaleLinear()\n\t\t.domain([yAxisLow, data.plotData.y_max - yPad])\n\t\t.range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)])\n\n\t// Axis group\n\tconst axisG = svg\n\t\t.append('g')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`)\n\n\taxisG.call(\n\t\td3axis.axisLeft(yAxisScale).tickSizeOuter(0) // removes top/bottom cap lines for clean look\n\t)\n\n\taxisstyle({\n\t\taxis: axisG,\n\t\tcolor: settings.axisColor,\n\t\tfontsize: settings.fontSize + 2,\n\t\tshowline: settings.showYAxisLine\n\t})\n\n\t// Add y-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY)\n\t\t.attr('y', settings.yAxisX / 2)\n\t\t.attr('transform', 'rotate(-90)')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text((custom.yAxisLabel ?? '-log\u2081\u2080(q-value)') + (data.plotData.has_capped_points ? ' [capped]' : ''))\n\n\t// Add png image\n\tsvg\n\t\t.append('image')\n\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t.attr('width', settings.plotWidth + 2 * settings.pngDotRadius)\n\t\t.attr('height', settings.plotHeight + 2 * settings.pngDotRadius)\n\t\t.attr('href', `data:image/png;base64,${data.pngImg || data.png}`)\n\n\t// Create scales for positioning elements\n\tconst xScale = scaleLinear()\n\t\t.domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer])\n\t\t.range([0, settings.plotWidth + 2 * settings.pngDotRadius])\n\n\t// Add interactive dots layer\n\tif (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {\n\t\t// Hover-ring layer \u2014 `pointer-events: none` so rings never intercept clicks.\n\t\tconst hoverLayer = svg\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t\t.style('pointer-events', 'none')\n\n\t\t// Cover as a sibling HTML div positioned over the plot area \u2014 avoids\n\t\t// the mouse-event quirks of nesting inside SVG.\n\t\tconst cover = select(svg.node().parentNode as HTMLElement)\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('left', `${settings.yAxisX + settings.yAxisSpace}px`)\n\t\t\t.style('top', `${settings.yAxisY}px`)\n\t\t\t.style('width', `${settings.plotWidth + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('height', `${settings.plotHeight + 2 * settings.pngDotRadius}px`)\n\t\t\t.style('pointer-events', 'all')\n\n\t\t// Circle as an SVG path so it flows through the generic `drawHoverShapes`.\n\t\tconst circlePath = (r: number) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`\n\n\t\tconst linkedLayer = svg\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`)\n\t\t\t.style('pointer-events', 'none')\n\t\thandle.points = interactivePoints\n\t\thandle.highlight = dots =>\n\t\t\tdrawHoverShapes(\n\t\t\t\tlinkedLayer,\n\t\t\t\tdots.map(d => ({\n\t\t\t\t\tpath: circlePath(settings.pngDotRadius + 2),\n\t\t\t\t\ttransform: `translate(${d.pixel_x},${d.pixel_y})`,\n\t\t\t\t\tstroke: 'black',\n\t\t\t\t\tstrokeWidth: 2\n\t\t\t\t}))\n\t\t\t)\n\n\t\tconst grin2Hover = (d: ManhattanPoint, container: any) => {\n\t\t\tconst table = table2col({ holder: container.append('div'), margin: '10px' })\n\t\t\ttable.addRow('Gene', d.gene)\n\t\t\ttable.addRow('Position', `${d.chrom}:${d.start}-${d.end}`)\n\t\t\tconst [t1, t2] = table.addRow()\n\t\t\tt1.text('Type')\n\t\t\tt2.html(`<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`)\n\t\t\ttable.addRow('Q-value', d.q_value.toPrecision(3))\n\t\t\ttable.addRow('Subject count', d.nsubj)\n\t\t}\n\t\tconst grin2Table = (dots: ManhattanPoint[]) => ({\n\t\t\tcolumns: [\n\t\t\t\t{ label: 'Gene' },\n\t\t\t\t{ label: 'Position' },\n\t\t\t\t{ label: 'Type' },\n\t\t\t\t{ label: 'Q-value', sortable: true },\n\t\t\t\t{ label: 'Subject count', sortable: true }\n\t\t\t],\n\t\t\trows: dots.map(d => [\n\t\t\t\t{ value: d.gene },\n\t\t\t\t{ value: `${d.chrom}:${d.start}-${d.end}` },\n\t\t\t\t{\n\t\t\t\t\thtml: `<span style=\"color:${d.color}\">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`\n\t\t\t\t},\n\t\t\t\t{ value: d.q_value.toPrecision(3) },\n\t\t\t\t{ value: d.nsubj }\n\t\t\t])\n\t\t})\n\n\t\tconst interactions = new DataPointInteractions<ManhattanPoint>({\n\t\t\tcover,\n\t\t\thoverLayer,\n\t\t\thoverTip: geneTip,\n\t\t\tpoints: interactivePoints,\n\t\t\tgetX: d => d.pixel_x,\n\t\t\tgetY: d => d.pixel_y,\n\t\t\thitRadius: settings.pngDotRadius + 3,\n\t\t\ttoHoverSpec: d => ({\n\t\t\t\tpath: circlePath(settings.pngDotRadius),\n\t\t\t\ttransform: `translate(${d.pixel_x},${d.pixel_y})`,\n\t\t\t\tfill: 'none',\n\t\t\t\tstroke: 'black',\n\t\t\t\tstrokeWidth: settings.interactiveDotStrokeWidth\n\t\t\t}),\n\t\t\tmaxTooltipRows: settings.maxTooltipGenes,\n\t\t\tonHover: custom.onHover,\n\t\t\titemNoun: custom.itemNoun ?? 'gene',\n\t\t\trenderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,\n\t\t\tbuildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,\n\t\t\t// A caller with actions gets the module's standard click flow: an action menu for one\n\t\t\t// dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.\n\t\t\t...(custom.getActions\n\t\t\t\t? {\n\t\t\t\t\t\tgetActions: custom.getActions,\n\t\t\t\t\t\trenderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,\n\t\t\t\t\t\tgetRowKey: custom.getRowKey\n\t\t\t\t  }\n\t\t\t\t: {\n\t\t\t\t\t\t// Manhattan single-click goes straight to a lollipop launch \u2014 no menu.\n\t\t\t\t\t\t// Release hover-suppression immediately so the cursor's next move re-engages.\n\t\t\t\t\t\tonSingleClick: (d, _event, ctx) => {\n\t\t\t\t\t\t\tctx.dismiss()\n\t\t\t\t\t\t\tif (app && d.gene) createLollipopFromGene(d.gene, app)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t// Manhattan multi-click shows showResultsTable directly with `app + clickMenu`\n\t\t\t\t\t\t// so the table renders inline Matrix/Lollipop buttons. Reuses the module's\n\t\t\t\t\t\t// clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.\n\t\t\t\t\t\t// Content is built BEFORE show2 so Menu can measure the populated rect for\n\t\t\t\t\t\t// its right-edge clamp \u2014 otherwise the wide table is placed at cursor+offsetX\n\t\t\t\t\t\t// and extends off the right edge of the viewport.\n\t\t\t\t\t\tonMultiClick: (dots, event, ctx) => {\n\t\t\t\t\t\t\tif (!app) {\n\t\t\t\t\t\t\t\tctx.dismiss()\n\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tctx.clickMenu.clear()\n\t\t\t\t\t\t\tconst holder = ctx.clickMenu.d.append('div').style('margin', '10px')\n\t\t\t\t\t\t\tshowResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu })\n\t\t\t\t\t\t\tctx.clickMenu.show2(event.clientX, event.clientY)\n\t\t\t\t\t\t}\n\t\t\t\t  })\n\t\t})\n\n\t\tinteractions.attach()\n\t}\n\n\t// Add chromosome labels\n\tif (data.plotData.chrom_data) {\n\t\tconst chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10\n\n\t\tObject.entries(data.plotData.chrom_data).forEach(([chrom, chromData]: [string, any]) => {\n\t\t\tconst chromLabel = chrom.replace('chr', '')\n\n\t\t\t// Skip chrM\n\t\t\tif (chromLabel === 'M') return\n\n\t\t\t// Calculate center position for label\n\t\t\tconst centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center)\n\n\t\t\t// Append chromosome label\n\t\t\tsvg\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', centerPos)\n\t\t\t\t.attr('y', chromLabelY)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t\t\t.text(chromLabel)\n\t\t})\n\t}\n\n\t// Add x-axis label\n\tsvg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2)\n\t\t.attr('y', settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', `${settings.fontSize + 4}px`)\n\t\t.attr('fill', 'black')\n\t\t.text('Chromosomes')\n\n\t// Add title\n\tconst title = svg\n\t\t.append('text')\n\t\t.attr('x', settings.yAxisX + settings.yAxisSpace)\n\t\t.attr('y', settings.yAxisY / 2)\n\t\t.attr('font-weight', 'bold')\n\t\t.attr('font-size', `${settings.fontSize + 2}px`)\n\t\t.text(custom.title ?? 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+}