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@Jverma /README.md
Last active Aug 29, 2015

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Visualizing a genome annotation file (gff)

D3 JavaScript interactive visualization of a genome feature file(GFF). More information on how to parse the gff file and create the parent-child CSV file is on the GitHub Repository.

<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Tree Example</title>
<style>
.node {
cursor: pointer;
}
.node circle {
fill: #fff;
stroke: steelblue;
stroke-width: 3px;
}
.node text {
font: 12px sans-serif;
}
.link {
fill: none;
stroke: #ccc;
stroke-width: 2px;
}
.tooltip{
position: absolute;
width: 200px;
height: 28px;
pointer-events: none;
}
</style>
</head>
<body>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script>
// ************** Generate the tree diagram *****************
var margin = {top: 20, right: 120, bottom: 20, left: 120},
width = 2000 - margin.right - margin.left,
height = 1000 - margin.top - margin.bottom;
var i = 0,
duration = 750,
root;
var tree = d3.layout.tree()
.size([height, width]);
var diagonal = d3.svg.diagonal()
.projection(function(d) { return [d.y, d.x]; });
var svg = d3.select("body").append("svg")
.attr("width", width + margin.right + margin.left)
.attr("height", height + margin.top + margin.bottom)
.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
var tooltip = d3.select("body").append("div")
.attr("class", "tooltip")
.style("opacity", 0);
d3.csv("parentChild.csv", function(error, data) {
// create a name: node map
var dataMap = data.reduce(function(map, node) {
map[node.name] = node;
return map;
}, {});
// create the tree array
var treeData = [];
data.forEach(function(node) {
// add to parent
var parent = dataMap[node.parent];
var start = dataMap[node.start];
if (parent) {
// create child array if it doesn't exist
(parent.children || (parent.children = []))
// add node to child array
.push(node);
} else {
// parent is null or missing
treeData.push(node);
}
});
root = treeData[0];
update(root);
});
function update(source) {
// Compute the new tree layout.
var nodes = tree.nodes(root).reverse(),
links = tree.links(nodes);
// Normalize for fixed-depth.
nodes.forEach(function(d) { d.y = d.depth * 180; });
// Update the nodes…
var node = svg.selectAll("g.node")
.data(nodes, function(d) { return d.id || (d.id = ++i); });
// Enter any new nodes at the parent's previous position.
var nodeEnter = node.enter().append("g")
.attr("class", "node")
.attr("transform", function(d) { return "translate(" + source.y0 + "," + source.x0 + ")"; })
.on("click", click);
nodeEnter.append("circle")
.attr("r", 1e-6)
.style("fill", function(d) { return d._children ? "lightsteelblue" : "#fff"; });
nodeEnter.append("text")
.attr("x", function(d) { return d.children || d._children ? -13 : 13; })
.attr("dy", ".35em")
.attr("text-anchor", function(d) { return d.children || d._children ? "end" : "start"; })
.text(function(d) { return d.name; })
.style("fill-opacity", 1e-6)
.on("mouseover", function(d){
tooltip.transition()
.duration(200)
.style("opacity", .9);
tooltip.html(d.type + "<br/>" + "(" + d.start + "," + d.end + ")" )
.style("left", (d3.event.pageX) + 5 + "px")
.style("top", (d3.event.pageY) - 50 + "px" );
})
.on("mouseout", function(d){
tooltip.transition()
.duration(500)
.style("opacity", 0);
});
// Transition nodes to their new position.
var nodeUpdate = node.transition()
.duration(duration)
.attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; });
nodeUpdate.select("circle")
.attr("r", 10)
.style("fill", function(d) { return d._children ? "lightsteelblue" : "#fff"; });
nodeUpdate.select("text")
.style("fill-opacity", 1);
// Transition exiting nodes to the parent's new position.
var nodeExit = node.exit().transition()
.duration(duration)
.attr("transform", function(d) { return "translate(" + source.y + "," + source.x + ")"; })
.remove();
nodeExit.select("circle")
.attr("r", 1e-6);
nodeExit.select("text")
.style("fill-opacity", 1e-6);
// Update the links…
var link = svg.selectAll("path.link")
.data(links, function(d) { return d.target.id; });
// Enter any new links at the parent's previous position.
link.enter().insert("path", "g")
.attr("class", "link")
.attr("d", function(d) {
var o = {x: source.x0, y: source.y0};
return diagonal({source: o, target: o});
});
// Transition links to their new position.
link.transition()
.duration(duration)
.attr("d", diagonal);
// Transition exiting nodes to the parent's new position.
link.exit().transition()
.duration(duration)
.attr("d", function(d) {
var o = {x: source.x, y: source.y};
return diagonal({source: o, target: o});
})
.remove();
// Stash the old positions for transition.
nodes.forEach(function(d) {
d.x0 = d.x;
d.y0 = d.y;
});
}
// Toggle children on click.
function click(d) {
if (d.children) {
d._children = d.children;
d.children = null;
} else {
d.children = d._children;
d._children = null;
}
update(d);
}
</script>
</body>
</html>
name parent start end type
chromosomeI null 1 50000 chromosome
cassava4.1_012921m.g chromosomeI 8260 15046 gene
cassava4.1_012921m cassava4.1_012921m.g 8260 15046 transcript
PAC:17967856.CDS.1 cassava4.1_012921m 9850 10232 CDS
PAC:17967856.CDS.2 cassava4.1_012921m 14217 14721 CDS
cassava4.1_032021m.g chromosomeI 17167 18209 gene
cassava4.1_032021m cassava4.1_032021m.g 17167 18209 transcript
PAC:17967858.CDS.1 cassava4.1_032021m 17167 17314 CDS
PAC:17967858.CDS.2 cassava4.1_032021m 17404 17484 CDS
PAC:17967858.CDS.3 cassava4.1_032021m 17607 17881 CDS
PAC:17967858.CDS.4 cassava4.1_032021m 18009 18209 CDS
cassava4.1_018871m.g chromosomeI 39560 40433 gene
cassava4.1_018871m cassava4.1_018871m.g 39560 40433 transcript
PAC:17967850.CDS.1 cassava4.1_018871m 39623 39765 CDS
PAC:17967850.CDS.2 cassava4.1_018871m 39877 40144 CDS
cassava4.1_007010m.g chromosomeI 42479 46245 gene
cassava4.1_007010m cassava4.1_007010m.g 42479 46245 transcript
PAC:17967843.CDS.1 cassava4.1_007010m 44750 45416 CDS
PAC:17967843.CDS.2 cassava4.1_007010m 44420 44641 CDS
PAC:17967843.CDS.3 cassava4.1_007010m 43532 43779 CDS
PAC:17967843.CDS.4 cassava4.1_007010m 43159 43298 CDS
PAC:17967843.CDS.5 cassava4.1_007010m 42809 42935 CDS
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