orthoxml-parser
Version:
library to parse ortoxml and extract hog tree as json
188 lines (139 loc) • 6.22 kB
HTML
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Example to parse an orthoxml</title>
<script src="../dist/orthoxml-parser.js"></script>
<script src="https://d3js.org/d3.v7.min.js"></script>
</head>
<body>
<div id="test"> </div>
<script>
var example_file = './data/HOG_C0348246.orthoxml';
fetch(example_file)
.then(response => response.text())
.then((d) => {
console.log(example_file)
var data = OrthoxmlParser.parse(d);
console.log(data);
var width = 700
margin = ({top: 10, right: 120, bottom: 10, left: 40})
dy = width / 6
dx = 15
tree = d3.tree().nodeSize([dx, dy])
//diagonal = d3.linkHorizontal().x(d => d.y).y(d => d.x)
function diagonal(d) {
return "M" + d.source.y + "," + d.source.x
+ "V" + d.target.x + "H" + d.target.y;
}
const root = d3.hierarchy(data);
root.x0 = dy / 2;
root.y0 = 0;
root.descendants().forEach((d, i) => {
d.id = i;
d._children = d.children;
});
const svg = d3.select("body").append("svg")
.attr("viewBox", [-margin.left, -margin.top, width, dx])
.style("font", "10px sans-serif")
.style("user-select", "none");
const gLink = svg.append("g")
.attr("fill", "none")
.attr("stroke", "#555")
.attr("stroke-opacity", 0.4)
.attr("stroke-width", 1.5);
const gNode = svg.append("g")
.attr("cursor", "pointer")
.attr("pointer-events", "all");
function update(event, source) {
const duration = event?.altKey ? 2500 : 250;
const nodes = root.descendants().reverse();
const links = root.links();
// Compute the new tree layout.
tree(root);
let left = root;
let right = root;
root.eachBefore(node => {
if (node.x < left.x) left = node;
if (node.x > right.x) right = node;
});
const height = right.x - left.x + margin.top + margin.bottom;
const transition = svg.transition()
.duration(duration)
.attr("viewBox", [-margin.left, left.x - margin.top, width, height])
.tween("resize", window.ResizeObserver ? null : () => () => svg.dispatch("toggle"));
// Update the nodes…
const node = gNode.selectAll("g")
.data(nodes, d => d.id);
// Enter any new nodes at the parent's previous position.
const nodeEnter = node.enter().append("g")
.attr("transform", d => `translate(${source.y0},${source.x0})`)
.attr("fill-opacity", 0)
.attr("stroke-opacity", 0)
.on("click", (event, d) => {
d.children = d.children ? null : d._children;
update(event, d);
});
nodeEnter.append("circle")
.attr("r", 2.5)
.attr("fill", d => d.data.paralog ? 'red' : d._children ? "#555" : "#999")
.attr("stroke-width", 10);
nodeEnter.append("text")
.attr("dy", "0.31em")
.attr("x", d => d._children ? -6 : 6)
.attr("text-anchor", d => d._children ? "end" : "start")
.text(d => String(d.data.id) +'_' + d.data.species)
.clone(true).lower()
.attr("stroke-linejoin", "round")
.attr("stroke-width", 3)
.attr("stroke", "white");
// Transition nodes to their new position.
const nodeUpdate = node.merge(nodeEnter).transition(transition)
.attr("transform", d => `translate(${d.y},${d.x})`)
.attr("fill-opacity", 1)
.attr("stroke-opacity", 1);
// Transition exiting nodes to the parent's new position.
const nodeExit = node.exit().transition(transition).remove()
.attr("transform", d => `translate(${source.y},${source.x})`)
.attr("fill-opacity", 0)
.attr("stroke-opacity", 0);
// Update the links…
const link = gLink.selectAll("path")
.data(links, d => d.target.id);
// Enter any new links at the parent's previous position.
const linkEnter = link.enter().append("path")
.attr("d", d => {
const o = {x: source.x0, y: source.y0};
return diagonal({source: o, target: o});
});
// Transition links to their new position.
link.merge(linkEnter).transition(transition)
.attr("d", diagonal);
// Transition exiting nodes to the parent's new position.
link.exit().transition(transition).remove()
.attr("d", d => {
const o = {x: source.x, y: source.y};
return diagonal({source: o, target: o});
});
// Stash the old positions for transition.
root.eachBefore(d => {
d.x0 = d.x;
d.y0 = d.y;
});
}
update(null, root);
svg.node();
})
/*
var example_file = './data/HOG_C0348246_augmented.orthoxml';
fetch(example_file)
.then(response => response.text())
.then((data) => {
console.log(example_file)
var hog_tree = OrthoxmlParser.parse(data, true);
console.log(hog_tree);
})
*/
</script>
</body>
</html>