| license: gpl-3.0 | |
| height: 960 | |
| border: no | |
| scrolling: yes |
A re-implementation of Jason Davies’ Phylogenetic Tree of Life, with faded gray lines to connect the leaf nodes of the tree to their corresponding labels inspired by a figure from Nature.
This implementation modifies the depth of interior nodes in a cluster layout to show branch lengths. Toggle the checkbox in the top-left corner to show or hide branch lengths, and mouseover a label to highlight its path to the root.
forked from mbostock's block: Tree of Life
| <!DOCTYPE html> | |
| <meta charset="utf-8"> | |
| <style> | |
| body { | |
| font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; | |
| margin: 0; | |
| } | |
| .links { | |
| fill: none; | |
| stroke: #000; | |
| } | |
| .link-extensions { | |
| fill: none; | |
| stroke: #000; | |
| stroke-opacity: .25; | |
| } | |
| .labels { | |
| font: 10px sans-serif; | |
| font-weight: bold; | |
| } | |
| </style> | |
| <label id="show-length"> | |
| </label> | |
| <!-- Copyright 2011 Jason Davies https://github.com/jasondavies/newick.js --> | |
| <script>function parseNewick(a){for(var e=[],r={},s=a.split(/\s*(;|\(|\)|,|:)\s*/),t=0;t<s.length;t++){var n=s[t];switch(n){case"(":var c={};r.branchset=[c],e.push(r),r=c;break;case",":var c={};e[e.length-1].branchset.push(c),r=c;break;case")":r=e.pop();break;case":":break;default:var h=s[t-1];")"==h||"("==h||","==h?r.name=n:":"==h&&(r.length=parseFloat(n))}}return r}</script> | |
| <!-- Copyright 2016 Mike Bostock https://d3js.org --> | |
| <script src="https://d3js.org/d3.v4.min.js"></script> | |
| <script src="https://unpkg.com/[email protected]/build/d3-jetpack.js"></script> | |
| <script> | |
| const outerRadius = 900/2, | |
| innerRadius = outerRadius - 150; | |
| const color = d3 | |
| .scaleOrdinal() | |
| .domain(["1.", "2.", "3.", "4.", "5.", "6.", "7."]) | |
| .range(d3.schemeCategory10); | |
| const cluster = d3 | |
| .cluster() | |
| .size([360, innerRadius]) | |
| .separation(function(a, b) { | |
| return 1; | |
| }); | |
| const svg = d3 | |
| .select('body') | |
| .append('svg') | |
| .at({ | |
| width: outerRadius * 2, | |
| height: outerRadius * 2, | |
| }); | |
| const chart = svg.append('g').translate([outerRadius, outerRadius]); | |
| d3.text( | |
| 'https://gist.githubusercontent.com/basilesimon/fa37a436836e3556b1cc36a5067e5e33/raw/a4dddacc9e4332219ac5b94568818e7272977cdd/tlp.txt', | |
| function(error, life) { | |
| if (error) throw error; | |
| const root = d3 | |
| .hierarchy(parseNewick(life), d => d.branchset) | |
| .sum(d => (d.branchset ? 0 : 1)) | |
| .sort( | |
| (a, b) => | |
| a.value - b.value || d3.ascending(a.data.length, b.data.length) | |
| ); | |
| cluster(root); | |
| setRadius(root, (root.data.length = 0), innerRadius / maxLength(root)); | |
| setColor(root); | |
| const linkExtension = chart | |
| .append('g') | |
| .attr('class', 'link-extensions') | |
| .selectAll('path') | |
| .data(root.links().filter(d => !d.target.children)) | |
| .enter() | |
| .append('path') | |
| .each(function(d) { | |
| d.target.linkExtensionNode = this; | |
| }) | |
| .attr('d', linkExtensionConstiable); | |
| const link = chart | |
| .append('g') | |
| .attr('class', 'links') | |
| .selectAll('path') | |
| .data(root.links()) | |
| .enter() | |
| .append('path') | |
| .each(function(d) { | |
| d.target.linkNode = this; | |
| }) | |
| .attr('d', linkConstant) | |
| .attr('stroke', d => d.target.color); | |
| chart | |
| .append('g') | |
| .attr('class', 'labels') | |
| .selectAll('text') | |
| .data(root.leaves()) | |
| .enter() | |
| .append('text') | |
| .attr('dy', '.31em') | |
| .attr( | |
| 'transform', | |
| d => | |
| 'rotate(' + | |
| (d.x - 90) + | |
| ')translate(' + | |
| (innerRadius + 4) + | |
| ',0)' + | |
| (d.x < 180 ? '' : 'rotate(180)') | |
| ) | |
| .attr('text-anchor', d => (d.x < 180 ? 'start' : 'end')) | |
| .text(d => (d.data.name.length < 3 ? d.data.name : '')); | |
| } | |
| ); | |
| // Compute the maximum cumulative length of any node in the tree. | |
| const maxLength = d => | |
| d.data.length + (d.children ? d3.max(d.children, maxLength) : 0); | |
| // Set the radius of each node by recursively summing and scaling the distance from the root. | |
| const setRadius = (d, y0, k) => { | |
| d.radius = (y0 += d.data.length) * k; | |
| if (d.children) | |
| d.children.forEach(function(d) { | |
| setRadius(d, y0, k); | |
| }); | |
| }; | |
| // Set the color of each node by recursively inheriting. | |
| const setColor = d => { | |
| const name = d.data.name.substring(0,2); | |
| d.color = | |
| color.domain().indexOf(name) >= 0 | |
| ? color(name) | |
| : d.parent ? d.parent.color : null; | |
| if (d.children) d.children.forEach(setColor); | |
| }; | |
| const linkConstiable = d => | |
| linkStep(d.source.x, d.source.radius, d.target.x, d.target.radius); | |
| const linkConstant = d => | |
| linkStep(d.source.x, d.source.y, d.target.x, d.target.y); | |
| const linkExtensionConstiable = d => | |
| linkStep(d.target.x, d.target.radius, d.target.x, innerRadius); | |
| const linkExtensionConstant = d => | |
| linkStep(d.target.x, d.target.y, d.target.x, innerRadius); | |
| // Like d3.svg.diagonal.radial, but with square corners. | |
| function linkStep(startAngle, startRadius, endAngle, endRadius) { | |
| const c0 = Math.cos((startAngle = (startAngle - 90) / 180 * Math.PI)), | |
| s0 = Math.sin(startAngle), | |
| c1 = Math.cos((endAngle = (endAngle - 90) / 180 * Math.PI)), | |
| s1 = Math.sin(endAngle); | |
| return ( | |
| 'M' + | |
| startRadius * c0 + | |
| ',' + | |
| startRadius * s0 + | |
| (endAngle === startAngle | |
| ? '' | |
| : 'A' + | |
| startRadius + | |
| ',' + | |
| startRadius + | |
| ' 0 0 ' + | |
| (endAngle > startAngle ? 1 : 0) + | |
| ' ' + | |
| startRadius * c1 + | |
| ',' + | |
| startRadius * s1) + | |
| 'L' + | |
| endRadius * c1 + | |
| ',' + | |
| endRadius * s1 | |
| ); | |
| } | |
| </script> |
