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.
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August 29, 2015 14:24
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Visualizing a genome annotation file (gff)
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<!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> |
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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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