chart = {
const root = d3.hierarchy(data, 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 svg = d3.create("svg")
.attr("viewBox", [-outerRadius, -outerRadius, width, width])
.attr("font-family", "sans-serif")
.attr("font-size", 10);
svg.append("g")
.call(legend);
svg.append("style").text(`
.link--active {
stroke: #000 !important;
stroke-width: 1.5px;
}
.link-extension--active {
stroke-opacity: .6;
}
.label--active {
font-weight: bold;
}
`);
const linkExtension = svg.append("g")
.attr("fill", "none")
.attr("stroke", "#000")
.attr("stroke-opacity", 0.25)
.selectAll("path")
.data(root.links().filter(d => !d.target.children))
.join("path")
.each(function(d) { d.target.linkExtensionNode = this; })
.attr("d", linkExtensionConstant);
const link = svg.append("g")
.attr("fill", "none")
.attr("stroke", "#000")
.selectAll("path")
.data(root.links())
.join("path")
.each(function(d) { d.target.linkNode = this; })
.attr("d", linkConstant)
.attr("stroke", d => d.target.color);
svg.append("g")
.selectAll("text")
.data(root.leaves())
.join("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.replace(/_/g, " "))
.on("mouseover", mouseovered(true))
.on("mouseout", mouseovered(false));
function update(checked) {
const t = d3.transition().duration(750);
linkExtension.transition(t).attr("d", checked ? linkExtensionVariable : linkExtensionConstant);
link.transition(t).attr("d", checked ? linkVariable : linkConstant);
}
function mouseovered(active) {
return function(event, d) {
d3.select(this).classed("label--active", active);
d3.select(d.linkExtensionNode).classed("link-extension--active", active).raise();
do d3.select(d.linkNode).classed("link--active", active).raise();
while (d = d.parent);
};
}
return Object.assign(svg.node(), {update});
}
update = chart.update(showLength)
cluster = d3.cluster()
.size([360, innerRadius])
.separation((a, b) => 1)
color = d3.scaleOrdinal()
.domain(["Bacteria", "Eukaryota", "Archaea"])
.range(d3.schemeCategory10)
// Compute the maximum cumulative length of any node in the tree.
function maxLength(d) {
return 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.
function setRadius(d, y0, k) {
d.radius = (y0 += d.data.length) * k;
if (d.children) d.children.forEach(d => setRadius(d, y0, k));
}
// Set the color of each node by recursively inheriting.
function setColor(d) {
var name = d.data.name;
d.color = color.domain().indexOf(name) >= 0 ? color(name) : d.parent ? d.parent.color : null;
if (d.children) d.children.forEach(setColor);
}
function linkVariable(d) {
return linkStep(d.source.x, d.source.radius, d.target.x, d.target.radius);
}
function linkConstant(d) {
return linkStep(d.source.x, d.source.y, d.target.x, d.target.y);
}
function linkExtensionVariable(d) {
return linkStep(d.target.x, d.target.radius, d.target.x, innerRadius);
}
function linkExtensionConstant(d) {
return linkStep(d.target.x, d.target.y, d.target.x, innerRadius);
}
function linkStep(startAngle, startRadius, endAngle, endRadius) {
const c0 = Math.cos(startAngle = (startAngle - 90) / 180 * Math.PI);
const s0 = Math.sin(startAngle);
const c1 = Math.cos(endAngle = (endAngle - 90) / 180 * Math.PI);
const 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;
}
legend = svg => {
const g = svg
.selectAll("g")
.data(color.domain())
.join("g")
.attr("transform", (d, i) => `translate(${-outerRadius},${-outerRadius + i * 20})`);
g.append("rect")
.attr("width", 18)
.attr("height", 18)
.attr("fill", color);
g.append("text")
.attr("x", 24)
.attr("y", 9)
.attr("dy", "0.35em")
.text(d => d);
}
data = parseNewick(await FileAttachment("Getah_virus_ml_tree_midpoint@1.newick").text())
width = 954
outerRadius = width / 2
innerRadius = outerRadius - 170
// https://github.com/jasondavies/newick.js
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}
d3 = require("d3@6")
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