@euphrasiologist/lwphylo 1.1.4 → 1.1.7

package/dist/@euphrasiologist/lwphylo.js

@@ -1,4 +1,4 @@
-// https://github.com/Euphrasiologist/lwPhylo#readme v1.1.4 Copyright 2021 Max Brown
+// https://github.com/Euphrasiologist/lwPhylo#readme v1.1.7 Copyright 2025 Max Brown
 (function (global, factory) {
 typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports) :
 typeof define === 'function' && define.amd ? define(['exports'], factory) :
@@ -393,60 +393,60 @@ function reflectAngle (rad, dir) {
  * arc from
  */
 
-function getArcs(pd) {
-    // must return start of arc and end
-    // these are pairs of edges that have the same parent
-    // start is the min(angle) of the children and end is the max(angle)
-    // radius is the radius of the parent
-    // origin is 0, 0 
-  
-    var data = [];
-    var root = pd.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
-  
-  
-    // get the branchlength of the parentID
-    function sisterAngle(current_parentId) {
-      for (var i = 0; i < pd.length; i++) {
-        if (pd[i].parentId === current_parentId) {
-          var sister_angle = pd[i].angle;
-        }
+function getArcs (pd) {
+  // must return start of arc and end
+  // these are pairs of edges that have the same parent
+  // start is the min(angle) of the children and end is the max(angle)
+  // radius is the radius of the parent
+  // origin is 0, 0 
+
+  var data = [];
+  var root = pd.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
+
+
+  // get the branchlength of the parentID
+  function sisterAngle(current_parentId) {
+    for (var i = 0; i < pd.length; i++) {
+      if (pd[i].parentId === current_parentId) {
+        var sister_angle = pd[i].angle;
       }
-      return sister_angle;
     }
-  
-    function parentRadius(current_parentId) {
-      for (var i = 0; i < pd.length; i++) {
-        if (pd[i].thisId === current_parentId) {
-          var parent_r = pd[i].r;
-        }
+    return sister_angle;
+  }
+
+  function parentRadius(current_parentId) {
+    for (var i = 0; i < pd.length; i++) {
+      if (pd[i].thisId === current_parentId) {
+        var parent_r = pd[i].r;
       }
-      return parent_r;
     }
-  
-    for (let i = 0; i < pd.length; i++) {
-      if (pd[i].thisId !== root) {
-        data.push({
-          'start': reflectAngle(Math.max(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
-          'end': reflectAngle(Math.min(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
-          'radius': parentRadius(pd[i].parentId),
-          'thisId': pd[i].thisId,
-          'parentId': pd[i].parentId
-  
-        });
-      }
+    return parent_r;
+  }
+
+  for (let i = 0; i < pd.length; i++) {
+    if (pd[i].thisId !== root) {
+      data.push({
+        'start': reflectAngle(Math.min(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
+        'end': reflectAngle(Math.max(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
+        'radius': parentRadius(pd[i].parentId),
+        'thisId': pd[i].thisId,
+        'parentId': pd[i].parentId
+
+      });
     }
-    //  TODO: understand why this works (and it may not in every case)... test!
-    for (let i = 0; i < data.length; i++) {
-      if (Math.sign(data[i].start) !== Math.sign(data[i].end)) {
-        data[i].end = Math.abs(data[i].end);
-        data[i].start = -Math.abs(data[i].start);
-      }
+  }
+  //  TODO: understand why this works (and it may not in every case)... test!
+  for (let i = 0; i < data.length; i++) {
+    if (Math.sign(data[i].start) !== Math.sign(data[i].end)) {
+      data[i].end = Math.abs(data[i].end);
+      data[i].start = -Math.abs(data[i].start);
     }
-  
-    return data.filter(d => d.start !== d.end & d.radius !== 0);
-  
   }
 
+  return data.filter(d => d.start !== d.end & d.radius !== 0);
+
+}
+
 /**
  * Simple wrapper function for getting the data,
  * radii, and arcs.
@@ -468,124 +468,79 @@ function radialLayout (node) {
  * Attempted copy of .layout.rect() function here https://github.com/ArtPoon/ggfree/blob/master/R/tree.R
  */
 
-function getHorizontal (node) {
-  // phylodata layout...
-  var pd = fortify(node);
-  // set y to null... not needed here.
-  pd.map(d => d.y = null);
-  // where y corresponds to a tip, return tip number
-  // make y0 and y1 equal.
-  var tipID = 1;
-  for (let i = 0; i < pd.length; i++) {
-    if (pd[i].isTip === true) {
-      pd[i].y0 = tipID;
-      pd[i].y1 = tipID;
-      tipID += 1;
-    }
-  }
-
-  // probably incredibly inefficient for large trees.
-  // gets the y values of two child branches by looping through the whole tree...
-  function yVals(child_1, child_2) {
-    for (var i = 0; i < pd.length; i++) {
-      if (pd[i].thisId === child_1) {
-        var y1 = pd[i].y0;
-      }
-      if (pd[i].thisId === child_2) {
-        var y2 = pd[i].y0;
-      }
-    }
-    return mean(([y1, y2]))
-  }
-
-  // if the node is not a tip...
-  for (let i = 0; i < pd.length; i++) {
-    if (pd[i].isTip === false) {
-      // then y0 === y1 and is the mean of the parental nodes
-      pd[i].y0 = yVals(pd[i].children[0], pd[i].children[1]);
-      pd[i].y1 = yVals(pd[i].children[0], pd[i].children[1]);
+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; compute Y for internal nodes via postorder
+  (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;
     }
-  }
-
-  // find root
-  var root = pd.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
-
-  // sort the data temporarily in decreasing parentId
-  pd.sort((a, b) => b.thisId - a.thisId);
-
-  // get the branchlength of the parentID
-  function getParentBranchLength(current_parentId) {
-    for (var i = 0; i < pd.length; i++) {
-      if (pd[i].thisId === current_parentId) {
-        var branchLength = pd[i].x1;
-      }
-    }
-    return branchLength;
-  }
-
-  // last loop...
-  // now get the x0 and x1 coordinates.
-  for (let i = 0; i < pd.length; i++) {
-    // special cases where parent is the root.
-    if (pd[i].parentId === root) {
-      // x0 = 0 and x1 is branch length
-      pd[i].x0 = 0;
-      pd[i].x1 = pd[i].branchLength;
-    } else {
-      // the x0 is that of the parent
-      var parent_branchLength = getParentBranchLength(pd[i].parentId);
-      pd[i].x0 = parent_branchLength;
-      // the x1 is the sum of parent and current branchlength
-      pd[i].x1 = parent_branchLength + pd[i].branchLength;
-    }
-  }
-
-  // return the original sorted data
-  pd.sort((a, b) => a.thisId - b.thisId);
-
-  // remove root?
-
-  // finally get rid of unwanted y, x and angle properties
-  /* eslint-disable no-unused-vars */
+    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 (no sorting-by-id needed)
+  (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 and return
   return pd.map(({ y, x, angle, ...item }) => item);
-  /* eslint-enable no-unused-vars */
 }
 
-/**
- * Get the vertical lines to draw.
- */
-
 function getVertical (node) {
-  var data = getHorizontal(node);
-
-  // for the current iteration of the loop find the matching parentId
-  // then take the difference
-  function findPairs(current_node) {
-    for (var i = 0; i < data.length; i++) {
-      if (data[i].parentId === current_node.parentId) {
-        var height = Math.abs(data[i].y0 - current_node.y0);
-      }
-    }
-    return height;
+  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]);
   }
 
-  var verticals = [];
-  // find root
-  var root = data.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
-
-  for (var i = 0; i < data.length; i++) {
-    if (data[i].thisId !== root) {
-
-      verticals.push({
-        'thisId': data[i].thisId,
-        'x0': data[i].x0,
-        'x1': data[i].x0, // x values remain constant
-        'y0': data[i].y0,
-        'y1': data[i].y0 + findPairs(data[i]),
-        'heights': findPairs(data[i])
-      });
-
-    }
+  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;

package/dist/@euphrasiologist/lwphylo.min.js

@@ -1,2 +1,2 @@
-// https://github.com/Euphrasiologist/lwPhylo#readme v1.1.4 Copyright 2021 Max Brown
-!function(n,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((n=n||self).lwphylo=n.lwphylo||{})}(this,(function(n){"use strict";const t={circular:()=>{var n,t,r=200,e=2,a=[0,0],i={};function l(e){var l=i.xscale(e.x)-a[0],h=i.yscale(e.y)-a[1],s=Math.sqrt(l*l+h*h);if(!s||s>=r)return{x:i.xscale(e.x),y:i.yscale(e.y),z:s>=r?1:10};var d=n*(1-Math.exp(-s*t))/s*.75+.25;return{x:a[0]+l*d,y:a[1]+h*d,z:Math.min(d,10)}}function h(){return n=(n=Math.exp(e))/(n-1)*r,t=e/r,l}return l.radius=function(n){return arguments.length?(r=+n,h()):r},l.distortion=function(n){return arguments.length?(e=+n,h()):e},l.focus=function(n){return arguments.length?(a=n,l):a},l.scales=function(n,t){return arguments.length?(i={xscale:n,yscale:t},l):i},h()}};function r(n,t,r,e){return{x:n+r*Math.cos(e),y:t+r*Math.sin(e)}}function e(n,t=!0){var r=[];for(const t of function n(t,r=[]){r.push(t);for(var e=0;e<t.children.length;e++)r=n(t.children[e],r);return r}(n))null===t.parent?r.push({parentId:null,parentLabel:null,thisId:t.id,thisLabel:t.label,children:t.children.map(n=>n.id),branchLength:0,isTip:!1,x:t.x,y:t.y,angle:t.angle}):r.push({parentId:t.parent.id,parentLabel:t.parent.label,thisId:t.id,thisLabel:t.label,children:t.children.map(n=>n.id),branchLength:t.branchLength,isTip:0==t.children.length,x:t.x,y:t.y,angle:t.angle});return t&&(r=r.sort((function(n,t){return n.thisId-t.thisId}))),r}function a(n){var t=0;for(const r of function(n){for(var t,r=[n],e=[];r.length>0;){t=r.pop(),e.push(t);for(const n of t.children)r.push(n)}return e}(n))0==r.children.length&&t++;return t}function i(n,t){let r=0,e=0;if(void 0===t)for(let t of n)null!=t&&(t=+t)>=t&&(++r,e+=t);else{let a=-1;for(let i of n)null!=(i=t(i,++a,n))&&(i=+i)>=i&&(++r,e+=i)}if(r)return e/r}function l(n){var t=e(n),r=a(n),l=1;for(let n=0;n<t.length;n++)1==t[n].isTip&&(t[n].angle=l/r*2*Math.PI,l+=1);function h(n,r){for(var e=0;e<t.length;e++){if(t[e].thisId===n)var a=t[e].angle;if(t[e].thisId===r)var l=t[e].angle}return i([a,l])}for(let n=0;n<t.length;n++)!1===t[n].isTip&&(t[n].angle=h(t[n].children[0],t[n].children[1]));var s=t.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0];function d(n){for(var r=0;r<t.length;r++)if(t[r].thisId===n)var e=t[r].r;return e}t.sort((n,t)=>t.thisId-n.thisId);for(let n=0;n<t.length;n++)if(t[n].parentId===s)!0===t[n].isTip?(t[n].r=t[n].branchLength,t[n].x=t[n].branchLength,t[n].y=0):(t[n].r=t[n].branchLength,t[n].x=t[n].branchLength*Math.cos(t[n].angle),t[n].y=t[n].branchLength*Math.sin(t[n].angle));else{var o=d(t[n].parentId);t[n].r=o+t[n].branchLength,t[n].x=(o+t[n].branchLength)*Math.cos(t[n].angle),t[n].y=(o+t[n].branchLength)*Math.sin(t[n].angle)}return t[0].r=0,t[0].x=0,t[0].y=0,t}function h(n,t){const r=Math.cos(n),e=Math.sin(n);return(a=Math.atan2(..."X"===t?[e,-r]:[-e,r])).toString().includes("3.1415")&&(a=Math.abs(a)),a;var a}function s(n){var t=e(n);t.map(n=>n.y=null);var r=1;for(let n=0;n<t.length;n++)!0===t[n].isTip&&(t[n].y0=r,t[n].y1=r,r+=1);function a(n,r){for(var e=0;e<t.length;e++){if(t[e].thisId===n)var a=t[e].y0;if(t[e].thisId===r)var l=t[e].y0}return i([a,l])}for(let n=0;n<t.length;n++)!1===t[n].isTip&&(t[n].y0=a(t[n].children[0],t[n].children[1]),t[n].y1=a(t[n].children[0],t[n].children[1]));var l=t.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0];function h(n){for(var r=0;r<t.length;r++)if(t[r].thisId===n)var e=t[r].x1;return e}t.sort((n,t)=>t.thisId-n.thisId);for(let n=0;n<t.length;n++)if(t[n].parentId===l)t[n].x0=0,t[n].x1=t[n].branchLength;else{var s=h(t[n].parentId);t[n].x0=s,t[n].x1=s+t[n].branchLength}return t.sort((n,t)=>n.thisId-t.thisId),t.map(({y:n,x:t,angle:r,...e})=>e)}n.describeArc=function(n,t,e,a,i){var l=r(n,t,e,a),h=r(n,t,e,i);return["M",l.x,l.y,"A",e,e,0,0,0,h.x,h.y].join(" ")},n.parentFisheye=function(n,t){for(let r=0;r<t.length;r++)if(n.parentId===t[r].thisId)return{px:t[r].fisheye.x,py:t[r].fisheye.y}},n.phisheye=t,n.radialLayout=function(n){var t={};return t.data=l(n),t.radii=function(n){var t=l(n);function r(n){for(var r=0;r<t.length;r++)if(t[r].thisId===n.parentId)var e=t[r].r;return e}for(var e=[],a=t.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0],i=0;i<t.length;i++)t[i].thisId!==a&&e.push({thisId:t[i].thisId,thisLabel:t[i].thisLabel,x0:t[i].x,x1:r(t[i])*Math.cos(t[i].angle),y0:t[i].y,y1:r(t[i])*Math.sin(t[i].angle),isTip:t[i].isTip});return e}(n),t.arcs=function(n){var t=[],r=n.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0];function e(t){for(var r=0;r<n.length;r++)if(n[r].parentId===t)var e=n[r].angle;return e}function a(t){for(var r=0;r<n.length;r++)if(n[r].thisId===t)var e=n[r].r;return e}for(let 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colons!"),e.id=a++}return e.id=a,r},n.rectangleLayout=function(n){var t={};return t.data=s(n),t.vertical_lines=function(n){var t=s(n);function r(n){for(var r=0;r<t.length;r++)if(t[r].parentId===n.parentId)var e=Math.abs(t[r].y0-n.y0);return e}for(var e=[],a=t.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0],i=0;i<t.length;i++)t[i].thisId!==a&&e.push({thisId:t[i].thisId,x0:t[i].x0,x1:t[i].x0,y0:t[i].y0,y1:t[i].y0+r(t[i]),heights:r(t[i])});return e}(n),t},n.subTree=function(n,t){let r={};n.data.forEach(n=>{r[n.thisId]={...n}});let e={};const a=function(n){r[n]&&(e[n]=r[n],r[n].children&&r[n].children.forEach(n=>{a(n)}))};a(t);const i=[["data",Object.values(e)]],l=i[0][1].map(n=>n.thisId);var h=[];for(const t in n)"data"!==t&&h.push([t,n[t]]);var s=h.map(n=>[n[0],n[1].filter(n=>l.includes(n.thisId))]);return Object.fromEntries(i.concat(s))},n.unrooted=function(n){var t={},r=e(function n(t){null===t.parent&&(t.start=0,t.end=2,t.angle=0,t.ntips=a(t),t.x=0,t.y=0);for(var r,e,i=t.start,l=0;l<t.children.length;l++)(r=t.children[l]).ntips=a(r),e=(t.end-t.start)*r.ntips/t.ntips,r.start=i,r.end=r.start+e,r.angle=r.start+(r.end-r.start)/2,i=r.end,r.x=t.x+r.branchLength*Math.sin(r.angle*Math.PI),r.y=t.y+r.branchLength*Math.cos(r.angle*Math.PI),n(r);return t}(n));return t.data=r,t.edges=function(n,t=!1){var r,e=[];n.sort((function(n,t){return n.thisId-t.thisId}));for(const h of n)if(null!==h.parentId&&null!=(r=n[h.parentId]))if(t){var a={x1:h.x,y1:h.y,id1:h.thisId,x2:r.x,y2:h.y,id2:void 0};e.push(a);var i={x1:r.x,y1:h.y,id1:void 0,x2:r.x,y2:r.y,id2:h.parentId};e.push(i)}else{var l={x1:h.x,y1:h.y,id1:h.thisId,x2:r.x,y2:r.y,id2:h.parentId};e.push(l)}return e}(r),t},Object.defineProperty(n,"__esModule",{value:!0})}));
+// https://github.com/Euphrasiologist/lwPhylo#readme v1.1.7 Copyright 2025 Max Brown
+!function(n,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((n=n||self).lwphylo=n.lwphylo||{})}(this,(function(n){"use strict";const t={circular:()=>{var n,t,e=200,r=2,a=[0,0],i={};function l(r){var l=i.xscale(r.x)-a[0],h=i.yscale(r.y)-a[1],s=Math.sqrt(l*l+h*h);if(!s||s>=e)return{x:i.xscale(r.x),y:i.yscale(r.y),z:s>=e?1:10};var o=n*(1-Math.exp(-s*t))/s*.75+.25;return{x:a[0]+l*o,y:a[1]+h*o,z:Math.min(o,10)}}function h(){return n=(n=Math.exp(r))/(n-1)*e,t=r/e,l}return l.radius=function(n){return arguments.length?(e=+n,h()):e},l.distortion=function(n){return arguments.length?(r=+n,h()):r},l.focus=function(n){return arguments.length?(a=n,l):a},l.scales=function(n,t){return arguments.length?(i={xscale:n,yscale:t},l):i},h()}};function e(n,t,e,r){return{x:n+e*Math.cos(r),y:t+e*Math.sin(r)}}function r(n,t=!0){var e=[];for(const t of function n(t,e=[]){e.push(t);for(var r=0;r<t.children.length;r++)e=n(t.children[r],e);return e}(n))null===t.parent?e.push({parentId:null,parentLabel:null,thisId:t.id,thisLabel:t.label,children:t.children.map(n=>n.id),branchLength:0,isTip:!1,x:t.x,y:t.y,angle:t.angle}):e.push({parentId:t.parent.id,parentLabel:t.parent.label,thisId:t.id,thisLabel:t.label,children:t.children.map(n=>n.id),branchLength:t.branchLength,isTip:0==t.children.length,x:t.x,y:t.y,angle:t.angle});return t&&(e=e.sort((function(n,t){return n.thisId-t.thisId}))),e}function a(n){var t=0;for(const e of function(n){for(var t,e=[n],r=[];e.length>0;){t=e.pop(),r.push(t);for(const n of t.children)e.push(n)}return r}(n))0==e.children.length&&t++;return t}function i(n,t){let e=0,r=0;if(void 0===t)for(let t of n)null!=t&&(t=+t)>=t&&(++e,r+=t);else{let a=-1;for(let i of n)null!=(i=t(i,++a,n))&&(i=+i)>=i&&(++e,r+=i)}if(e)return r/e}function l(n){var t=r(n),e=a(n),l=1;for(let n=0;n<t.length;n++)1==t[n].isTip&&(t[n].angle=l/e*2*Math.PI,l+=1);function h(n,e){for(var r=0;r<t.length;r++){if(t[r].thisId===n)var a=t[r].angle;if(t[r].thisId===e)var l=t[r].angle}return i([a,l])}for(let n=0;n<t.length;n++)!1===t[n].isTip&&(t[n].angle=h(t[n].children[0],t[n].children[1]));var s=t.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0];function o(n){for(var e=0;e<t.length;e++)if(t[e].thisId===n)var r=t[e].r;return r}t.sort((n,t)=>t.thisId-n.thisId);for(let n=0;n<t.length;n++)if(t[n].parentId===s)!0===t[n].isTip?(t[n].r=t[n].branchLength,t[n].x=t[n].branchLength,t[n].y=0):(t[n].r=t[n].branchLength,t[n].x=t[n].branchLength*Math.cos(t[n].angle),t[n].y=t[n].branchLength*Math.sin(t[n].angle));else{var c=o(t[n].parentId);t[n].r=c+t[n].branchLength,t[n].x=(c+t[n].branchLength)*Math.cos(t[n].angle),t[n].y=(c+t[n].branchLength)*Math.sin(t[n].angle)}return t[0].r=0,t[0].x=0,t[0].y=0,t}function h(n,t){const e=Math.cos(n),r=Math.sin(n);return(a=Math.atan2(..."X"===t?[r,-e]:[-r,e])).toString().includes("3.1415")&&(a=Math.abs(a)),a;var a}function s(n){const t=r(n),e=new Map(t.map((n,t)=>[n.thisId,t])),a=[];!function n(t){t.children&&0!==t.children.length?t.children.forEach(n):a.push(t.id)}(n);const l=new Map(a.map((n,t)=>[n,t+1]));return function n(r){const a=e.get(r.id);if(!r.children||0===r.children.length){const n=l.get(r.id);return t[a].y0=n,t[a].y1=n,n}const h=i(r.children.map(n));return t[a].y0=h,t[a].y1=h,h}(n),function n(r,a){const i=e.get(r.id),l=a??0,h=l+(t[i].branchLength??0);t[i].x0=l,t[i].x1=h,r.children&&r.children.length&&r.children.forEach(t=>n(t,h))}(n,0),t.map(({y:n,x:t,angle:e,...r})=>r)}n.describeArc=function(n,t,r,a,i){var l=e(n,t,r,a),h=e(n,t,r,i);return["M",l.x,l.y,"A",r,r,0,0,0,h.x,h.y].join(" ")},n.parentFisheye=function(n,t){for(let e=0;e<t.length;e++)if(n.parentId===t[e].thisId)return{px:t[e].fisheye.x,py:t[e].fisheye.y}},n.phisheye=t,n.radialLayout=function(n){var t={};return t.data=l(n),t.radii=function(n){var t=l(n);function e(n){for(var e=0;e<t.length;e++)if(t[e].thisId===n.parentId)var r=t[e].r;return r}for(var r=[],a=t.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0],i=0;i<t.length;i++)t[i].thisId!==a&&r.push({thisId:t[i].thisId,thisLabel:t[i].thisLabel,x0:t[i].x,x1:e(t[i])*Math.cos(t[i].angle),y0:t[i].y,y1:e(t[i])*Math.sin(t[i].angle),isTip:t[i].isTip});return r}(n),t.arcs=function(n){var t=[],e=n.map(n=>null===n.parentId?n.thisId:null).filter(n=>null!=n)[0];function r(t){for(var e=0;e<n.length;e++)if(n[e].parentId===t)var r=n[e].angle;return r}function a(t){for(var e=0;e<n.length;e++)if(n[e].thisId===t)var r=n[e].r;return r}for(let i=0;i<n.length;i++)n[i].thisId!==e&&t.push({start:h(Math.min(n[i].angle,r(n[i].parentId)),"Y"),end:h(Math.max(n[i].angle,r(n[i].parentId)),"Y"),radius:a(n[i].parentId),thisId:n[i].thisId,parentId:n[i].parentId});for(let n=0;n<t.length;n++)Math.sign(t[n].start)!==Math.sign(t[n].end)&&(t[n].end=Math.abs(t[n].end),t[n].start=-Math.abs(t[n].start));return t.filter(n=>n.start!==n.end&0!==n.radius)}(t.data),t},n.readTree=function(n){var t=(n=n.replace(/ \t/g,"")).split(/(;|\(|\)|,)/),e={parent:null,children:[]},r=e,a=0;for(const n of t)if(""!=n&&";"!=n)if("("==n){let n={parent:r,children:[]};r.children.push(n),r=n}else if(","==n){let n={parent:r=r.parent,children:[]};r.children.push(n),r=n}else if(")"==n){if(null===(r=r.parent))break}else{var i=n.split(":");1==i.length?n.startsWith(":")?(r.label="",r.branchLength=parseFloat(i[0])):(r.label=i[0],r.branchLength=null):2==i.length?(r.label=i[0],r.branchLength=parseFloat(i[1])):console.warn(n,"I don't know what to do with two colons!"),r.id=a++}return r.id=a,e},n.rectangleLayout=function(n){var t={};return t.data=s(n),t.vertical_lines=function(n){const t=s(n),e=new Map;for(const n of t){if(null==n.parentId)continue;const t=e.get(n.parentId);t?t.push(n):e.set(n.parentId,[n])}const r=[];for(const[n,t]of e.entries()){if(!t.length)continue;const e=t.map(n=>n.y0),a=Math.min(...e),i=Math.max(...e),l=t[0].x0;r.push({parentId:n,x0:l,x1:l,y0:a,y1:i,heights:i-a})}return r}(n),t},n.subTree=function(n,t){let e={};n.data.forEach(n=>{e[n.thisId]={...n}});let r={};const a=function(n){e[n]&&(r[n]=e[n],e[n].children&&e[n].children.forEach(n=>{a(n)}))};a(t);const i=[["data",Object.values(r)]],l=i[0][1].map(n=>n.thisId);var h=[];for(const t in n)"data"!==t&&h.push([t,n[t]]);var s=h.map(n=>[n[0],n[1].filter(n=>l.includes(n.thisId))]);return Object.fromEntries(i.concat(s))},n.unrooted=function(n){var t={},e=r(function n(t){null===t.parent&&(t.start=0,t.end=2,t.angle=0,t.ntips=a(t),t.x=0,t.y=0);for(var e,r,i=t.start,l=0;l<t.children.length;l++)(e=t.children[l]).ntips=a(e),r=(t.end-t.start)*e.ntips/t.ntips,e.start=i,e.end=e.start+r,e.angle=e.start+(e.end-e.start)/2,i=e.end,e.x=t.x+e.branchLength*Math.sin(e.angle*Math.PI),e.y=t.y+e.branchLength*Math.cos(e.angle*Math.PI),n(e);return t}(n));return t.data=e,t.edges=function(n,t=!1){var e,r=[];n.sort((function(n,t){return n.thisId-t.thisId}));for(const h of n)if(null!==h.parentId&&null!=(e=n[h.parentId]))if(t){var a={x1:h.x,y1:h.y,id1:h.thisId,x2:e.x,y2:h.y,id2:void 0};r.push(a);var i={x1:e.x,y1:h.y,id1:void 0,x2:e.x,y2:e.y,id2:h.parentId};r.push(i)}else{var l={x1:h.x,y1:h.y,id1:h.thisId,x2:e.x,y2:e.y,id2:h.parentId};r.push(l)}return r}(e),t},Object.defineProperty(n,"__esModule",{value:!0})}));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@euphrasiologist/lwphylo",
-  "version": "1.1.4",
+  "version": "1.1.7",
   "description": "A lightweight, low level javascript library to plot phylogenies from Newick files.",
   "main": "dist/@euphrasiologist/lwphylo.js",
   "unpkg": "dist/@euphrasiologist/lwphylo.min.js",
@@ -16,7 +16,7 @@
   "scripts": {
     "pretest": "rollup -c",
     "test": "eslint src",
-    "prepublishOnly": "rm -rf dist && /Users/mb39/homebrew/bin/yarn test"
+    "prepublishOnly": "rm -rf dist && npm run test"
   },
   "repository": {
     "type": "git",
@@ -38,4 +38,4 @@
     "rollup": "1",
     "rollup-plugin-terser": "5"
   }
-}
+}

package/src/radial/getArcs.js

@@ -6,56 +6,56 @@ import reflectAngle from "./reflectAngle.js"
  * arc from
  */
 
-export default function(pd) {
-    // must return start of arc and end
-    // these are pairs of edges that have the same parent
-    // start is the min(angle) of the children and end is the max(angle)
-    // radius is the radius of the parent
-    // origin is 0, 0 
-  
-    var data = [];
-    var root = pd.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
-  
-  
-    // get the branchlength of the parentID
-    function sisterAngle(current_parentId) {
-      for (var i = 0; i < pd.length; i++) {
-        if (pd[i].parentId === current_parentId) {
-          var sister_angle = pd[i].angle;
-        }
+export default function (pd) {
+  // must return start of arc and end
+  // these are pairs of edges that have the same parent
+  // start is the min(angle) of the children and end is the max(angle)
+  // radius is the radius of the parent
+  // origin is 0, 0 
+
+  var data = [];
+  var root = pd.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
+
+
+  // get the branchlength of the parentID
+  function sisterAngle(current_parentId) {
+    for (var i = 0; i < pd.length; i++) {
+      if (pd[i].parentId === current_parentId) {
+        var sister_angle = pd[i].angle;
       }
-      return sister_angle;
     }
-  
-    function parentRadius(current_parentId) {
-      for (var i = 0; i < pd.length; i++) {
-        if (pd[i].thisId === current_parentId) {
-          var parent_r = pd[i].r;
-        }
+    return sister_angle;
+  }
+
+  function parentRadius(current_parentId) {
+    for (var i = 0; i < pd.length; i++) {
+      if (pd[i].thisId === current_parentId) {
+        var parent_r = pd[i].r;
       }
-      return parent_r;
     }
-  
-    for (let i = 0; i < pd.length; i++) {
-      if (pd[i].thisId !== root) {
-        data.push({
-          'start': reflectAngle(Math.max(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
-          'end': reflectAngle(Math.min(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
-          'radius': parentRadius(pd[i].parentId),
-          'thisId': pd[i].thisId,
-          'parentId': pd[i].parentId
-  
-        })
-      }
+    return parent_r;
+  }
+
+  for (let i = 0; i < pd.length; i++) {
+    if (pd[i].thisId !== root) {
+      data.push({
+        'start': reflectAngle(Math.min(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
+        'end': reflectAngle(Math.max(pd[i].angle, sisterAngle(pd[i].parentId)), "Y"),
+        'radius': parentRadius(pd[i].parentId),
+        'thisId': pd[i].thisId,
+        'parentId': pd[i].parentId
+
+      })
     }
-    //  TODO: understand why this works (and it may not in every case)... test!
-    for (let i = 0; i < data.length; i++) {
-      if (Math.sign(data[i].start) !== Math.sign(data[i].end)) {
-        data[i].end = Math.abs(data[i].end);
-        data[i].start = -Math.abs(data[i].start);
-      }
+  }
+  //  TODO: understand why this works (and it may not in every case)... test!
+  for (let i = 0; i < data.length; i++) {
+    if (Math.sign(data[i].start) !== Math.sign(data[i].end)) {
+      data[i].end = Math.abs(data[i].end);
+      data[i].start = -Math.abs(data[i].start);
     }
-  
-    return data.filter(d => d.start !== d.end & d.radius !== 0);
-  
-  }
+  }
+
+  return data.filter(d => d.start !== d.end & d.radius !== 0);
+
+}

package/src/rectangle/getHorizontal.js

@@ -6,85 +6,46 @@ import fortify from "../utils/fortify.js"
  * Attempted copy of .layout.rect() function here https://github.com/ArtPoon/ggfree/blob/master/R/tree.R
  */
 
-export default function (node) {
-  // phylodata layout...
-  var pd = fortify(node);
-  // set y to null... not needed here.
-  pd.map(d => d.y = null);
-  // where y corresponds to a tip, return tip number
-  // make y0 and y1 equal.
-  var tipID = 1;
-  for (let i = 0; i < pd.length; i++) {
-    if (pd[i].isTip === true) {
-      pd[i].y0 = tipID;
-      pd[i].y1 = tipID;
-      tipID += 1;
+export default function(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; compute Y for internal nodes via postorder
+  (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;
     }
-  }
-
-  // probably incredibly inefficient for large trees.
-  // gets the y values of two child branches by looping through the whole tree...
-  function yVals(child_1, child_2) {
-    for (var i = 0; i < pd.length; i++) {
-      if (pd[i].thisId === child_1) {
-        var y1 = pd[i].y0;
-      }
-      if (pd[i].thisId === child_2) {
-        var y2 = pd[i].y0;
-      }
-    }
-    return mean(([y1, y2]))
-  }
-
-  // if the node is not a tip...
-  for (let i = 0; i < pd.length; i++) {
-    if (pd[i].isTip === false) {
-      // then y0 === y1 and is the mean of the parental nodes
-      pd[i].y0 = yVals(pd[i].children[0], pd[i].children[1]);
-      pd[i].y1 = yVals(pd[i].children[0], pd[i].children[1]);
-    }
-  }
-
-  // find root
-  var root = pd.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
-
-  // sort the data temporarily in decreasing parentId
-  pd.sort((a, b) => b.thisId - a.thisId);
-
-  // get the branchlength of the parentID
-  function getParentBranchLength(current_parentId) {
-    for (var i = 0; i < pd.length; i++) {
-      if (pd[i].thisId === current_parentId) {
-        var branchLength = pd[i].x1;
-      }
-    }
-    return branchLength;
-  }
-
-  // last loop...
-  // now get the x0 and x1 coordinates.
-  for (let i = 0; i < pd.length; i++) {
-    // special cases where parent is the root.
-    if (pd[i].parentId === root) {
-      // x0 = 0 and x1 is branch length
-      pd[i].x0 = 0;
-      pd[i].x1 = pd[i].branchLength;
-    } else {
-      // the x0 is that of the parent
-      var parent_branchLength = getParentBranchLength(pd[i].parentId);
-      pd[i].x0 = parent_branchLength;
-      // the x1 is the sum of parent and current branchlength
-      pd[i].x1 = parent_branchLength + pd[i].branchLength;
-    }
-  }
-
-  // return the original sorted data
-  pd.sort((a, b) => a.thisId - b.thisId);
-
-  // remove root?
-
-  // finally get rid of unwanted y, x and angle properties
-  /* eslint-disable no-unused-vars */
+    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 (no sorting-by-id needed)
+  (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 and return
   return pd.map(({ y, x, angle, ...item }) => item);
-  /* eslint-enable no-unused-vars */
-}
+}

package/src/rectangle/getVertical.js

@@ -1,41 +1,35 @@
 import getHorizontal from "./getHorizontal.js"
 
-/**
- * Get the vertical lines to draw.
- */
-
 export default function (node) {
-  var data = getHorizontal(node);
-
-  // for the current iteration of the loop find the matching parentId
-  // then take the difference
-  function findPairs(current_node) {
-    for (var i = 0; i < data.length; i++) {
-      if (data[i].parentId === current_node.parentId) {
-        var height = Math.abs(data[i].y0 - current_node.y0);
-      }
-    }
-    return height;
+  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]);
   }
 
-  var verticals = [];
-  // find root
-  var root = data.map(d => d.parentId === null ? d.thisId : null).filter(d => d != null)[0];
-
-  for (var i = 0; i < data.length; i++) {
-    if (data[i].thisId !== root) {
-
-      verticals.push({
-        'thisId': data[i].thisId,
-        'x0': data[i].x0,
-        'x1': data[i].x0, // x values remain constant
-        'y0': data[i].y0,
-        'y1': data[i].y0 + findPairs(data[i]),
-        'heights': findPairs(data[i])
-      })
-
-    }
+  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;
-}
+}