An alignment chart that takes read positions and generates an efficient pileup
Last active
May 2, 2016 16:43
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Iobio.viz Alignment Chart
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<!DOCTYPE html> | |
<html> | |
<head> | |
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js" charset="utf-8"></script> | |
<script src="http://iobio.io/public/js/iobio.viz.min.js"></script> | |
<link rel="stylesheet" type="text/css" href="http://iobio.io/public/css/iobio.viz.min.css"> | |
<style type="text/css"> | |
body { | |
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; | |
margin: auto; | |
position: relative; | |
width: 960px; | |
} | |
#alignment-viz .iobio-alignment polygon { fill: rgb(120,176,194); } | |
</style> | |
</head> | |
<body> | |
<div id="alignment-viz"></div> | |
<script> | |
var m = [30, 60, 44, 70], | |
w = 960, | |
h = 500; | |
d3.json('reads.json', function(data) { | |
var pileup = iobio.viz.layout.pileup().sort(null).size(w + m[1] + m[3]); | |
var selection = d3.select("#alignment-viz").datum( pileup(data) ); | |
var chart = iobio.viz.alignment() | |
.width(w) | |
.height(h) | |
.margin({top: m[0], right: m[1], bottom: m[2], left:m[3]}) | |
.xValue(function(d) { return d.x; }) | |
.yValue(function(d) { return d.y; }) | |
.wValue(function(d) { return d.w; }) | |
.margin({top: m[0], right: m[1], bottom: m[2], left:m[3]}) | |
.id(function(d) { return 'read-' + d.data.id; }) | |
.tooltip(function(d) { return "id: " + d.data.id + "<br/>" + "pos: " + d.data.start + ' - ' + d.data.end }) | |
chart(selection); | |
}); | |
</script> | |
</body> | |
</html> |
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