@euphrasiologist/lwphylo 1.1.15 → 1.2.1

package/dist/drawPhylogeny.cjs

@@ -0,0 +1,1103 @@
+'use strict';
+
+var d3 = require('d3');
+
+function _interopNamespaceDefault(e) {
+  var n = Object.create(null);
+  if (e) {
+    Object.keys(e).forEach(function (k) {
+      if (k !== 'default') {
+        var d = Object.getOwnPropertyDescriptor(e, k);
+        Object.defineProperty(n, k, d.get ? d : {
+          enumerable: true,
+          get: function () { return e[k]; }
+        });
+      }
+    });
+  }
+  n.default = e;
+  return Object.freeze(n);
+}
+
+var d3__namespace = /*#__PURE__*/_interopNamespaceDefault(d3);
+
+// src/radial/polarToCartesian.js
+function polarToCartesian (cx, cy, r, t) {
+  return { x: cx + r * Math.cos(t), y: cy - r * Math.sin(t) };
+}
+
+/**
+ * Draw the shortest arc between startAngle and endAngle (radians), CCW.
+ * If the CW path is shorter, swap start/end so the CCW path is still shortest.
+ * Works with Y-inverted screen coords (polarToCartesian already inverts Y).
+ */
+function describeArc(cx, cy, radius, startAngle, endAngle) {
+  const TAU = Math.PI * 2;
+  const norm = (t) => ((t % TAU) + TAU) % TAU;
+  let a0 = norm(startAngle);
+  let a1 = norm(endAngle);
+
+  // CCW and CW spans
+  const ccw = (a1 - a0 + TAU) % TAU;
+  const cw = (a0 - a1 + TAU) % TAU;
+
+  // Ensure we always take the shorter span *in CCW* by swapping if needed
+  if (cw < ccw) {
+    const tmp = a0; a0 = a1; a1 = tmp;
+  }
+
+  const delta = (a1 - a0 + TAU) % TAU;          // now the shorter CCW span
+  if (delta < 1e-9) {
+    const p = polarToCartesian(cx, cy, radius, a0);
+    return `M ${p.x} ${p.y}`;                   // degenerate span → no arc
+  }
+
+  const largeArcFlag = delta > Math.PI ? 1 : 0; // should be 0 for “shortest”, but keep for safety
+  const sweepFlag = 0;                          // CCW
+
+  const p0 = polarToCartesian(cx, cy, radius, a0);
+  const p1 = polarToCartesian(cx, cy, radius, a1);
+
+  return `M ${p0.x} ${p0.y} A ${radius} ${radius} 0 ${largeArcFlag} ${sweepFlag} ${p1.x} ${p1.y}`;
+}
+
+/**
+ * Recursive function for pre-order traversal of tree (returns array)
+ */
+function preorder(node, list = []) {
+  list.push(node);
+  for (let i = 0; i < (node.children?.length || 0); i++) {
+    list = preorder(node.children[i], list);
+  }
+  return list;
+}
+
+/**
+ * Convert parsed Newick tree from readTree() into data
+ * frame.
+ * this is akin to a "phylo" object in R.
+ */
+
+function fortify (tree, sort = true) {
+    var df = [];
+
+    for (const node of preorder(tree)) {
+        if (node.parent === null) {
+            df.push({
+                'parentId': null,
+                'parentLabel': null,
+                'thisId': node.id,
+                'thisLabel': node.label,
+                'children': node.children.map(x => x.id),
+                'branchLength': 0.,
+                'isTip': false,
+                'x': node.x,
+                'y': node.y,
+                'angle': node.angle
+            });
+        }
+        else {
+            df.push({
+                'parentId': node.parent.id,
+                'parentLabel': node.parent.label,
+                'thisId': node.id,
+                'thisLabel': node.label,
+                'children': node.children.map(x => x.id),
+                'branchLength': node.branchLength,
+                'isTip': (node.children.length == 0),
+                'x': node.x,
+                'y': node.y,
+                'angle': node.angle
+            });
+        }
+    }
+
+    if (sort) {
+        df = df.sort(function (a, b) {
+            return a.thisId - b.thisId;
+        });
+    }
+    return (df);
+}
+
+/**
+ * Compute per-node polar coordinates for radial layout:
+ *  - Tip angles: evenly spaced 0..2π in tip DFS order
+ *  - Internal angles: circular mean of child angles
+ *  - Radii: cumulative branch length from root
+ *  - x,y: cartesian projection
+ *
+ * Returns the fortified array with added {angle, r, x, y}.
+ */
+function radialData(node) {
+  const TAU = Math.PI * 2;
+  const norm = (t) => ((t % TAU) + TAU) % TAU;
+
+  const pd = fortify(node, /*sort*/ true);
+  const byId = new Map(pd.map(d => [d.thisId, d]));
+  const kids = new Map(pd.map(d => [d.thisId, d.children || []]));
+
+  // Find root id
+  let root = null;
+  for (const d of pd) {
+    if (d.parentId == null) { root = d.thisId; break; }
+  }
+
+  // Collect tip ids in DFS left->right order to preserve input ordering
+  const tipIds = [];
+  (function dfs(id) {
+    const c = kids.get(id) || [];
+    if (c.length === 0) {
+      tipIds.push(id);
+      return;
+    }
+    for (const ch of c) dfs(ch);
+  })(root);
+
+  // Assign tip angles evenly spaced 0..2π
+  const N = Math.max(1, tipIds.length);
+  const angle = new Map();
+  tipIds.forEach((id, i) => {
+    angle.set(id, (i / N) * TAU);
+  });
+
+  // Internal node angles: circular mean of child angles (post-order)
+  (function setInternalAngles(id) {
+    const c = kids.get(id) || [];
+    for (const ch of c) setInternalAngles(ch);
+    if (c.length > 0) {
+      let sx = 0, sy = 0;
+      for (const ch of c) {
+        const th = angle.get(ch);
+        sx += Math.cos(th);
+        sy += Math.sin(th);
+      }
+      angle.set(id, norm(Math.atan2(sy, sx)));
+    }
+  })(root);
+
+  // Radii: cumulative branch lengths from root (root r=0)
+  const radius = new Map();
+  radius.set(root, 0);
+  (function setR(id) {
+    const c = kids.get(id) || [];
+    const r0 = radius.get(id) || 0;
+    for (const ch of c) {
+      const child = byId.get(ch);
+      const bl = child?.branchLength ?? 0;
+      radius.set(ch, r0 + bl);
+      setR(ch);
+    }
+  })(root);
+
+  // Enrich pd rows with angle, r, x, y
+  for (const d of pd) {
+    const th = angle.get(d.thisId) ?? 0;
+    const r  = radius.get(d.thisId) ?? 0;
+    d.angle = th;
+    d.r = r;
+    d.x = r * Math.cos(th);
+    d.y = r * Math.sin(th);
+  }
+
+  return pd;
+}
+
+/**
+ * Per-edge radial segments (for highlighting and drawing).
+ * For each non-root node, draw a radial line from the parent radius to the child radius
+ * at the CHILD'S angle.
+ *
+ * Output: [{ parentId, childId, x0, y0, x1, y1, isTip }]
+ */
+function getRadii(node) {
+  const data = radialData(node);
+  const byId = new Map(data.map(d => [d.thisId, d]));
+  const root = data.find(d => d.parentId == null)?.thisId;
+
+  const segments = [];
+  for (const d of data) {
+    if (d.thisId === root) continue;
+    const parent = byId.get(d.parentId);
+    if (!parent) continue;
+
+    const theta = d.angle;
+    const r0 = parent.r;
+    const r1 = d.r;
+
+    segments.push({
+      parentId: parent.thisId,
+      childId: d.thisId,
+      x0: r0 * Math.cos(theta),
+      y0: r0 * Math.sin(theta),
+      x1: r1 * Math.cos(theta),
+      y1: r1 * Math.sin(theta),
+      isTip: !!d.isTip
+    });
+  }
+  return segments;
+}
+
+/**
+ * Build arc descriptors for each internal parent:
+ *  - One arc per internal node at radius = parent.r
+ *  - Start/end angles choose the *shortest* wrap-aware span covering the children
+ *  - Skips degenerate spans (delta ~ 0)
+ */
+function getArcs(pd) {
+  const TAU = Math.PI * 2;
+  const norm = (t) => ((t % TAU) + TAU) % TAU;
+  const EPS = 1e-6;
+
+  // Quick lookups
+  new Map(pd.map(d => [d.thisId, d]));
+  const childrenByParent = new Map();
+  let root = null;
+
+  for (const d of pd) {
+    if (d.parentId == null) root = d.thisId;
+    if (!childrenByParent.has(d.parentId)) childrenByParent.set(d.parentId, []);
+    childrenByParent.get(d.parentId).push(d);
+  }
+
+  const arcs = [];
+
+  for (const parent of pd) {
+    const pid = parent.thisId;
+    if (pid === root) continue; // no arc above root
+    const kids = childrenByParent.get(pid) || [];
+    if (kids.length < 2) continue; // need at least two children
+
+    // Collect & sort child angles
+    const A = kids.map(k => norm(k.angle)).sort((a, b) => a - b);
+    const aMin = A[0], aMax = A[A.length - 1];
+
+    // Two candidate spans: direct (aMin -> aMax) and wrapped (aMax -> aMin across 2π)
+    const direct = aMax - aMin;
+    const wrapped = TAU - direct;
+
+    // Choose the shorter span. We'll draw **CCW** (sweepFlag = 0) in describeArc.
+    let start, end, span;
+    if (direct <= wrapped) {
+      start = aMin;
+      end = aMax;
+      span = direct;
+    } else {
+      // wrapped is shorter: go CCW from aMax up through 2π to aMin
+      start = aMax;
+      end = aMin;
+      span = wrapped;
+    }
+
+    if (span < EPS || !isFinite(parent.r) || parent.r <= 0) continue;
+
+    arcs.push({
+      start,
+      end,
+      radius: parent.r,
+      thisId: pid,
+      parentId: parent.parentId
+    });
+  }
+
+  return arcs;
+}
+
+/**
+ * Simple wrapper for radial layout:
+ *  - data: per-node { angle, r, x, y, ... }
+ *  - radii: per-edge radial spokes (parent.r → child.r)
+ *  - arcs: per-internal-node arcs spanning its children at parent radius
+ */
+function radialLayout(node) {
+  const data = {};
+  data.data = radialData(node);
+  data.radii = getRadii(node);
+  data.arcs = getArcs(data.data);
+  return data;
+}
+
+/**
+ * Iterable mean
+ * Poached from https://github.com/d3/d3-array/blob/master/src/mean.js
+ * (Other array means buggered up the tree)
+ */
+
+function mean (values, valueof) {
+    let count = 0;
+    let sum = 0;
+    {
+        for (let value of values) {
+            if (value != null && (value = +value) >= value) {
+                ++count, sum += value;
+            }
+        }
+    }
+    if (count) return sum / count;
+}
+
+/**
+ * Rectangle layout: compute per-node x0,x1 and y0=y1
+ * - Tip y is assigned by input order (preserves ladderize/order)
+ * - Internal node y is mean of child y's
+ * - x1 accumulates branch lengths from root
+ */
+
+function getHorizontal(node) {
+  const pd = fortify(node);
+
+  // Fast lookup from id -> pd index
+  const idIndex = new Map(pd.map((d, i) => [d.thisId, i]));
+
+  // 1) Leaf order from the INPUT TREE (respects your child order / ladderize)
+  const leafIds = [];
+  (function dfs(n) {
+    if (!n.children || n.children.length === 0) { leafIds.push(n.id); return; }
+    n.children.forEach(dfs);
+  })(node);
+
+  // Map each leaf id to a vertical slot (1..N)
+  const tipSlot = new Map(leafIds.map((id, i) => [id, i + 1]));
+
+  // 2) Set Y for tips directly from that order; internal node Y via children mean
+  (function setY(n) {
+    const i = idIndex.get(n.id);
+    if (!n.children || n.children.length === 0) {
+      const y = tipSlot.get(n.id);
+      pd[i].y0 = y; pd[i].y1 = y;
+      return y;
+    }
+    const ys = n.children.map(setY);
+    const y = mean(ys);
+    pd[i].y0 = y; pd[i].y1 = y;
+    return y;
+  })(node);
+
+  // 3) Set X by accumulating branch lengths down the tree
+  (function setX(n, xParent) {
+    const i = idIndex.get(n.id);
+    const bl = pd[i].branchLength ?? 0;
+    const x0 = xParent ?? 0;
+    const x1 = x0 + bl;
+    pd[i].x0 = x0; pd[i].x1 = x1;
+    if (n.children && n.children.length) n.children.forEach(c => setX(c, x1));
+  })(node, 0);
+
+  // Clean up: remove fields not needed downstream without triggering no-unused-vars
+  return pd.map((row) => {
+    const { y: _y, x: _x, angle: _angle, ...item } = row;
+    return item;
+  });
+}
+
+function getVertical(node) {
+  const data = getHorizontal(node);
+
+  // Group rows by parentId (children that share a parent)
+  const byParent = new Map();
+  for (const row of data) {
+    if (row.parentId == null) continue;
+    const a = byParent.get(row.parentId);
+    if (a) a.push(row); else byParent.set(row.parentId, [row]);
+  }
+
+  const verticals = [];
+  for (const [parentId, kids] of byParent.entries()) {
+    if (!kids.length) continue;
+    // Works for binary and multifurcations:
+    const yvals = kids.map(d => d.y0);
+    const y0 = Math.min(...yvals);
+    const y1 = Math.max(...yvals);
+    // All children share the same junction x (their x0)
+    const x = kids[0].x0;
+
+    verticals.push({
+      parentId,
+      x0: x,
+      x1: x,
+      y0,
+      y1,
+      heights: y1 - y0
+    });
+  }
+
+  return verticals;
+}
+
+/**
+ * Build per-child vertical segments for a rectangular tree:
+ * For each non-root node (child), draw a vertical from (parent.x, child.y) to (parent.x, parent.y).
+ * This yields exactly one vertical per edge (child->parent), making highlighting trivial.
+ *
+ * Returns an array of:
+ *   {
+ *     parentId: number,
+ *     childId: number,
+ *     x: number,         // x of the parent junction
+ *     y0: number,        // min(child.y, parent.y)
+ *     y1: number,        // max(child.y, parent.y)
+ *   }
+ */
+function getChildVerticals(node) {
+  const data = getHorizontal(node); // has parentId, thisId, x0,x1,y0=y1
+
+  // Build a quick index to access parent's y by id
+  const byId = new Map(data.map(d => [d.thisId, d]));
+
+  const childVerticals = [];
+
+  for (const d of data) {
+    if (d.parentId == null) continue;
+    const parent = byId.get(d.parentId);
+    if (!parent) continue;
+
+    const x = d.x0;            // child’s vertical sits at parent.x == child.x0
+    const yc = d.y0;           // child y
+    const yp = parent.y0;      // parent y
+    const y0 = Math.min(yc, yp);
+    const y1 = Math.max(yc, yp);
+
+    childVerticals.push({
+      parentId: d.parentId,
+      childId: d.thisId,
+      x,
+      y0,
+      y1
+    });
+  }
+
+  return childVerticals;
+}
+
+/**
+ * Rectangle layout wrapper.
+ * Returns:
+ *  - data: per-node rows (x0,x1,y0=y1,...)
+ *  - vertical_lines: single spanning vertical per parent (baseline draw)
+ *  - child_vertical_lines: one vertical per edge (for highlighting)
+ *  - horizontal_lines: per-edge child horizontals (x0->x1 at y), with labels & tip flags
+ */
+function rectangleLayout(node) {
+  const data = getHorizontal(node);              // per-node
+  const vertical_lines = getVertical(node);      // parent spans
+  const child_vertical_lines = getChildVerticals(node); // per-edge verticals
+
+  // IMPORTANT: include y0 & y1, and carry isTip/labels for the renderer
+  new Map(data.map(d => [d.thisId, d]));
+  const horizontal_lines = data
+    .filter(d => d.parentId != null)
+    .map(d => ({
+      parentId: d.parentId,
+      childId: d.thisId,
+      thisId: d.thisId,
+      thisLabel: d.thisLabel,
+      isTip: d.isTip,
+      x0: d.x0,
+      x1: d.x1,
+      y0: d.y0,
+      y1: d.y0
+    }));
+
+  return { data, vertical_lines, child_vertical_lines, horizontal_lines };
+}
+
+/**
+ * Convert parsed Newick tree from fortify() into data frame of edges
+ * this is akin to a "phylo" object in R, where thisID and parentId
+ * are the $edge slot. I think.
+ */
+
+function edges(df, rectangular = false) {
+  const rows = [...df].sort((a, b) => a.thisId - b.thisId);
+  const byId = new Map(rows.map((r) => [r.thisId, r]));
+  const result = [];
+
+  for (const row of rows) {
+    if (row.parentId == null) continue;
+    const parent = byId.get(row.parentId);
+    if (!parent) continue;
+
+    if (rectangular) {
+      result.push({ x1: row.x, y1: row.y, id1: row.thisId, x2: parent.x, y2: row.y, id2: undefined });
+      result.push({ x1: parent.x, y1: row.y, id1: undefined, x2: parent.x, y2: parent.y, id2: row.parentId });
+    } else {
+      result.push({ x1: row.x, y1: row.y, id1: row.thisId, x2: parent.x, y2: parent.y, id2: row.parentId });
+    }
+  }
+  return result;
+}
+
+/**
+ * Recursive function for breadth-first search of a tree
+ * the root node is visited first.
+ */
+
+function levelorder(root) {
+  const queue = [root], result = [];
+  while (queue.length) {
+    const curnode = queue.shift();         // <- FIFO
+    result.push(curnode);
+    for (const child of curnode.children) queue.push(child);
+  }
+  return result;
+}
+
+
+/**
+ * Count the number of tips that descend from this node
+ */
+
+function numTips(thisnode) {
+  var result = 0;
+  for (const node of levelorder(thisnode)) {
+    if (node.children.length == 0) result++;
+  }
+  return (result);
+}
+
+/**
+ * Equal-angle layout for unrooted trees.
+ * - Precomputes ntips in O(n) to avoid repeated subtree counts
+ * - Uses angles in "π units" (0..2) to match existing API
+ * - Populates x,y positions from branchLength and angle
+ */
+
+function annotateTipCounts(root) {
+  (function post(n) {
+    if (!n.children || n.children.length === 0) {
+      n.ntips = 1; return 1;
+    }
+    let sum = 0;
+    for (const c of n.children) sum += post(c);
+    n.ntips = sum;
+    return sum;
+  })(root);
+  return root;
+}
+
+function equalAngleLayout(node) {
+  if (node.parent === null) {
+    annotateTipCounts(node);
+    node.start = 0.;     // guarantees no arcs overlap 0
+    node.end = 2.;       // *π
+    node.angle = 0.;     // irrelevant at root
+    node.ntips = numTips(node); // safe (already computed), left for compatibility
+    node.x = 0;
+    node.y = 0;
+  }
+
+  let lastStart = node.start;
+
+  for (let i = 0; i < node.children.length; i++) {
+    const child = node.children[i];
+    const arc = (node.end - node.start) * (child.ntips / node.ntips);
+
+    child.start = lastStart;
+    child.end = lastStart + arc;
+
+    // bisect the arc in π-units
+    child.angle = child.start + (child.end - child.start) / 2.;
+    lastStart = child.end;
+
+    // map to coordinates (convert π-units to radians by multiplying by Math.PI)
+    const theta = child.angle * Math.PI;
+    const bl = (child.branchLength ?? 0);
+    child.x = node.x + bl * Math.sin(theta);
+    child.y = node.y + bl * Math.cos(theta);
+
+    equalAngleLayout(child);
+  }
+
+  return node;
+}
+
+/**
+ * Simple wrapper function for equalAngleLayout()
+ */
+
+function unrooted (node) {
+  var data = {};
+  // use the Felsenstein equal angle layout algorithm
+  var eq = fortify(equalAngleLayout(node));
+  data.data = eq;
+  // make the edges dataset
+  data.edges = edges(eq);
+
+  return data;
+}
+
+/**
+ * Parse a Newick tree string into a doubly-linked list of JS Objects.
+ * Assigns labels, branch lengths, and node IDs (tips before internals if input emits them that way).
+ *
+ * Notes / limitations:
+ * - Quoted labels and NHX annotations are not fully supported.
+ * - Branch lengths in scientific notation are supported (parseFloat).
+ */
+
+function readTree(text) {
+  // Remove all whitespace (space, tabs, newlines)
+  text = String(text).replace(/\s+/g, '');
+
+  const tokens = text.split(/(;|\(|\)|,)/);
+  const root = { parent: null, children: [] };
+  let curnode = root;
+  let nodeId = 0;
+
+  for (const token of tokens) {
+    if (!token || token === ';') continue;
+
+    if (token === '(') {
+      const child = { parent: curnode, children: [] };
+      curnode.children.push(child);
+      curnode = child; // descend
+    } else if (token === ',') {
+      // back to parent, then create sibling
+      curnode = curnode.parent;
+      const child = { parent: curnode, children: [] };
+      curnode.children.push(child);
+      curnode = child;
+    } else if (token === ')') {
+      // ascend one level
+      curnode = curnode.parent;
+      if (curnode === null) break;
+    } else {
+      // label/branch-length chunk (e.g., "A:0.01" or "A")
+      const nodeinfo = token.split(':');
+      if (nodeinfo.length === 1) {
+        if (token.startsWith(':')) {
+          curnode.label = '';
+          curnode.branchLength = parseFloat(nodeinfo[0]);
+        } else {
+          curnode.label = nodeinfo[0];
+          curnode.branchLength = null;
+        }
+      } else if (nodeinfo.length === 2) {
+        curnode.label = nodeinfo[0];
+        curnode.branchLength = parseFloat(nodeinfo[1]);
+      } else {
+        console.warn(token, "Unhandled token with multiple ':' characters");
+        curnode.label = nodeinfo[0] || '';
+        curnode.branchLength = parseFloat(nodeinfo[nodeinfo.length - 1]);
+      }
+      curnode.id = nodeId++; // assign then increment
+    }
+  }
+
+  // Ensure root has an id if not assigned during parsing
+  if (root.id == null) root.id = nodeId;
+
+  return root;
+}
+
+function drawPhylogeny(
+  treeText,
+  {
+    layout = "rect", // "rect" or "radial"
+    width = 800,
+    height = 800,
+    margin = { top: 20, right: 300, bottom: 20, left: 50 },
+    radialMargin = 80,
+    strokeWidth = 1,
+    radialMode = "outer" // or "align"
+  } = {}
+) {
+  if (layout === "rect") {
+    // RECTANGULAR LAYOUT
+    const tree_df = rectangleLayout(readTree(treeText));
+    const horizontal = tree_df.horizontal_lines;
+    const vertical = tree_df.vertical_lines;
+    const tips = horizontal.filter((d) => d.isTip);
+
+    const maxY = d3__namespace.max(horizontal, (d) => d.y1);
+    const minY = d3__namespace.min(horizontal, (d) => d.y1);
+    const maxX = d3__namespace.max(horizontal, (d) => d.x1);
+
+    const yScale = d3__namespace
+      .scaleLinear()
+      .domain([minY - 1, maxY + 1])
+      .range([margin.top, height - margin.bottom]);
+
+    const xScale = d3__namespace
+      .scaleLinear()
+      .domain([0, maxX])
+      .range([margin.left, width - margin.right]);
+
+    const svg = d3__namespace
+      .create("svg")
+      .attr("width", width)
+      .attr("height", height)
+      .attr("font-family", "sans-serif")
+      .attr("font-size", 10);
+
+    const group = svg.append("g");
+
+    group
+      .selectAll(".hline")
+      .data(horizontal)
+      .join("line")
+      .attr("x1", (d) => xScale(d.x0))
+      .attr("y1", (d) => yScale(d.y0))
+      .attr("x2", (d) => xScale(d.x1))
+      .attr("y2", (d) => yScale(d.y1))
+      .attr("stroke", "#555")
+      .attr("stroke-width", strokeWidth);
+
+    group
+      .selectAll(".vline")
+      .data(vertical)
+      .join("line")
+      .attr("x1", (d) => xScale(d.x0))
+      .attr("y1", (d) => yScale(d.y0))
+      .attr("x2", (d) => xScale(d.x1))
+      .attr("y2", (d) => yScale(d.y1))
+      .attr("stroke", "#555")
+      .attr("stroke-width", strokeWidth);
+
+    group
+      .selectAll(".tip-dot")
+      .data(tips)
+      .join("circle")
+      .attr("cx", (d) => xScale(d.x1))
+      .attr("cy", (d) => yScale(d.y1))
+      .attr("r", 2)
+      .attr("fill", "black");
+
+    svg
+      .append("g")
+      .selectAll("text")
+      .data(tips)
+      .join("text")
+      .attr("x", (d) => xScale(d.x1) + 4)
+      .attr("y", (d) => yScale(d.y1))
+      .attr("dy", "0.32em")
+      .attr("font-size", 10)
+      .text((d) => d.thisLabel?.replace(/_/g, " ") ?? "");
+
+    return svg.node();
+  } else if (layout === "radial") {
+    const parsedTree = readTree(treeText);
+    const rad = radialLayout(parsedTree);
+
+    // ===== MODE / DEBUG =====
+    const TIP_MODE = radialMode; // "align" (shorten to original tips) or "outer" (project to one circle)
+    const isOuter = TIP_MODE === "outer";
+
+    // visuals (0 = let spokes reach the dots)
+    const DOT_R = 3;
+    const END_CAP = 0;
+
+    // ===== SCALES / BOUNDS =====
+    const maxRadius = d3__namespace.max(rad.data, (d) => d.r) ?? 0;
+    const scaleRadial = maxRadius + 2 * radialMargin;
+    const w = width,
+      h = height;
+    const centerX = w / 2,
+      centerY = h / 2;
+
+    const xScaleRadial = d3__namespace
+      .scaleLinear()
+      .domain([-scaleRadial, scaleRadial])
+      .range([0, w]);
+    const yScaleRadial = d3__namespace
+      .scaleLinear()
+      .domain([-scaleRadial, scaleRadial])
+      .range([h, 0]);
+    const radiusPx = (r) => r * (w / (2 * scaleRadial));
+
+    // ===== INDEXES / HELPERS =====
+    const byId = new Map(rad.data.map((d) => [d.thisId, d]));
+    const tips = rad.data.filter((d) => d.isTip);
+    const tipMaxR = tips.length ? d3__namespace.max(tips, (d) => d.r) : 0;
+
+    // Robust child-id extractor (handles multiple shapes)
+    function childIdOf(spoke) {
+      // prefer explicit child id fields; fall back to thisId; last-ditch id1 (seen in some edge shapes)
+      return spoke.childId ?? spoke.thisId ?? spoke.id1 ?? null;
+    }
+
+    // Shorten the *screen-space* end of a spoke by END_CAP px
+    function shortenSpokePx(x0, y0, x1, y1) {
+      const X0 = xScaleRadial(x0),
+        Y0 = yScaleRadial(y0);
+      const X1 = xScaleRadial(x1),
+        Y1 = yScaleRadial(y1);
+      const dx = X1 - X0,
+        dy = Y1 - Y0;
+      const len = Math.hypot(dx, dy) || 1;
+      const t = Math.max(0, (len - END_CAP) / len);
+      return { X0, Y0, X1s: X0 + dx * t, Y1s: Y0 + dy * t, len };
+    }
+
+    // ===== SVG ROOT =====
+    const svg = d3__namespace
+      .create("svg")
+      .attr("width", w)
+      .attr("height", h)
+      .attr("font-family", "sans-serif")
+      .attr("font-size", 10);
+
+    const group = svg.append("g");
+
+    // ===== ARCS (parent circles) =====
+    group
+      .append("g")
+      .attr("class", "phylo_arcs")
+      .selectAll("path")
+      .data(rad.arcs)
+      .join("path")
+      .attr("d", (d) =>
+        describeArc(
+          centerX,
+          centerY,
+          Math.max(0, radiusPx(d.radius)),
+          d.start,
+          d.end
+        )
+      )
+      .attr("fill", "none")
+      .attr("stroke", "#777")
+      .attr("stroke-width", strokeWidth);
+
+    // ===== RADII (spokes) =====
+    group
+      .append("g")
+      .attr("class", "phylo_radii")
+      .selectAll("line")
+      .data(rad.radii)
+      .join("line")
+      .each(function(s, _) {
+        // parent end (data space)
+        const x0 = s.x0,
+          y0 = s.y0;
+
+        // child end (data space), shape-agnostic
+        const cid = childIdOf(s);
+        const node = cid != null ? byId.get(cid) : undefined;
+        const isTipSpoke = !!(node && node.isTip);
+
+        // default to the original child endpoint from the spoke record
+        let x1 = s.x1,
+          y1 = s.y1;
+
+        // In "outer" mode, project only *tip* spokes to the common circle
+        if (isOuter && isTipSpoke) {
+          x1 = tipMaxR * Math.cos(node.angle);
+          y1 = tipMaxR * Math.sin(node.angle);
+        }
+
+        // Shorten in screen space so the spoke doesn’t pierce the dot (END_CAP can be 0)
+        const { X0, Y0, X1s, Y1s} = shortenSpokePx(x0, y0, x1, y1);
+
+        d3__namespace.select(this)
+          .attr("x1", X0)
+          .attr("y1", Y0)
+          .attr("x2", X1s)
+          .attr("y2", Y1s)
+          .attr("stroke", "#777")
+          .attr("stroke-width", strokeWidth);
+      });
+
+    // ===== TIP DOTS =====
+    group
+      .append("g")
+      .attr("class", "phylo_tip_dots")
+      .selectAll("circle")
+      .data(tips)
+      .join("circle")
+      .each(function(d, _) {
+        // dot at original tip (align) or projected circle (outer)
+        const x = isOuter ? tipMaxR * Math.cos(d.angle) : d.x;
+        const y = isOuter ? tipMaxR * Math.sin(d.angle) : d.y;
+
+        d3__namespace.select(this)
+          .attr("cx", xScaleRadial(x))
+          .attr("cy", yScaleRadial(y))
+          .attr("r", DOT_R)
+          .attr("fill", "black")
+          .attr("stroke", "black")
+          .attr("stroke-width", 1.5);
+      });
+
+    // ===== LABELS (unchanged) =====
+    // Labels — make them follow the tip position used by the current mode
+    group
+      .append("g")
+      .attr("class", "phylo_labels")
+      .selectAll("g.label")
+      .data(tips) // <— bind only tip nodes
+      .join("g")
+      .attr("class", "label")
+      .attr("transform", (d) => {
+        // same tip position rule as dots/spokes:
+        //  - "outer": snap to common ring (tipMaxR)
+        //  - otherwise (e.g. "align"/"phylo"): true tip radius
+        const r = isOuter ? tipMaxR : d.r;
+        const x = r * Math.cos(d.angle);
+        const y = r * Math.sin(d.angle);
+        return `translate(${xScaleRadial(x)},${yScaleRadial(y)})`;
+      })
+      .each(function(d) {
+        // rotate so text reads outward; flip when on the left side
+        let angle = (-d.angle * 180) / Math.PI;
+        let xoff = 10; // radial padding for text (px)
+        let anchor = "start";
+        if (d.angle > Math.PI / 2 && d.angle < (3 * Math.PI) / 2) {
+          angle += 180;
+          xoff *= -1;
+          anchor = "end";
+        }
+        d3__namespace.select(this)
+          .append("g")
+          .attr("transform", `rotate(${angle})`)
+          .append("text")
+          .attr("x", xoff)
+          .attr("alignment-baseline", "middle")
+          .attr("text-anchor", anchor)
+          .attr("font-size", 10)
+          .attr("fill", "black")
+          .text((d) => d.thisLabel?.replace(/_/g, " ") ?? "");
+      });
+
+    return svg.node();
+  } else if (layout === "unrooted") {
+    // UNROOTED LAYOUT
+    const parsedTree = readTree(treeText);
+    const unrootedPhylo = unrooted(parsedTree);
+
+    const w = width;
+    const h = height;
+
+    // Get spatial extent
+    const xExtent = d3__namespace.extent(unrootedPhylo.data, (d) => d.x);
+    const yExtent = d3__namespace.extent(unrootedPhylo.data, (d) => d.y);
+
+    // Find maximum absolute distance from center (0,0)
+    const maxX = Math.max(Math.abs(xExtent[0]), Math.abs(xExtent[1]));
+    const maxY = Math.max(Math.abs(yExtent[0]), Math.abs(yExtent[1]));
+    const maxRadius = Math.max(maxX, maxY);
+
+    // Add some margin
+    const scaleUnroot = maxRadius + 2 * radialMargin;
+
+    const xScaleUnroot = d3__namespace
+      .scaleLinear()
+      .domain([-scaleUnroot, scaleUnroot])
+      .range([0, w]);
+
+    const yScaleUnroot = d3__namespace
+      .scaleLinear()
+      .domain([-scaleUnroot, scaleUnroot])
+      .range([h, 0]);
+
+    const svg = d3__namespace
+      .create("svg")
+      .attr("width", w)
+      .attr("height", h)
+      .attr("font-family", "sans-serif")
+      .attr("font-size", 10);
+
+    const group = svg.append("g");
+
+    // Edges
+    group
+      .append("g")
+      .attr("class", "phylo_lines")
+      .selectAll("line")
+      .data(unrootedPhylo.edges)
+      .join("line")
+      .attr("x1", (d) => xScaleUnroot(d.x1))
+      .attr("y1", (d) => yScaleUnroot(d.y1))
+      .attr("x2", (d) => xScaleUnroot(d.x2))
+      .attr("y2", (d) => yScaleUnroot(d.y2))
+      .attr("stroke-width", strokeWidth)
+      .attr("stroke", "#777");
+
+    // Nodes
+    group
+      .append("g")
+      .attr("class", "phylo_points")
+      .selectAll("circle")
+      .data(unrootedPhylo.data)
+      .join("circle")
+      .attr("class", "dot")
+      .attr("r", (d) => (d.isTip ? 4 : 0))
+      .attr("cx", (d) => xScaleUnroot(d.x))
+      .attr("cy", (d) => yScaleUnroot(d.y))
+      .attr("stroke", "black")
+      .attr("stroke-width", 2)
+      .attr("fill", (d) => (d.isTip ? "black" : "white"));
+
+    // Tip labels
+    const tipEdges = new Map();
+    const nodesById = new Map(unrootedPhylo.data.map((d) => [d.thisId, d]));
+
+    unrootedPhylo.edges.forEach((edge) => {
+      const tipNode = nodesById.get(edge.id1);
+      if (tipNode?.isTip) {
+        tipEdges.set(edge.id1, edge);
+      }
+    });
+
+    group
+      .append("g")
+      .attr("class", "phylo_labels")
+      .selectAll("g")
+      .data(unrootedPhylo.data.filter((d) => d.isTip))
+      .join("g")
+      .attr("transform", (d) => {
+        const x = xScaleUnroot(d.x);
+        const y = yScaleUnroot(d.y);
+        return `translate(${x},${y})`;
+      })
+      .each(function(d) {
+        const edge = tipEdges.get(d.thisId);
+        if (!edge) {
+          console.warn(
+            "No incoming edge found for tip node:",
+            d.thisId,
+            d.thisLabel
+          );
+          return;
+        }
+
+        // Compute angle of the incoming edge (screen coords)
+        const x1 = xScaleUnroot(edge.x1);
+        const y1 = yScaleUnroot(edge.y1);
+        const x2 = xScaleUnroot(edge.x2);
+        const y2 = yScaleUnroot(edge.y2);
+
+        const dx = x2 - x1;
+        const dy = y2 - y1;
+        let angle = (Math.atan2(dy, dx) * 180) / Math.PI;
+
+        // Flip label if upside down
+        let xOffset = -10;
+        let anchor = "end";
+        if (angle > 90 || angle < -90) {
+          angle += 180;
+          anchor = "start";
+          xOffset = 10;
+        }
+
+        // Draw label rotated along branch direction
+        d3__namespace.select(this)
+          .append("g")
+          .attr("transform", `rotate(${angle})`)
+          .append("text")
+          .attr("x", xOffset)
+          .attr("alignment-baseline", "middle")
+          .attr("text-anchor", anchor)
+          .attr("font-size", 10)
+          .attr("fill", "black")
+          .text(d.thisLabel?.replace(/_/g, " ") ?? "");
+      });
+
+    return svg.node();
+  } else {
+    throw new Error("Unsupported layout type. Use 'rect' or 'radial'.");
+  }
+}
+
+module.exports = drawPhylogeny;
+//# sourceMappingURL=drawPhylogeny.cjs.map