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index.html
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<html>
<head>
<meta charset='utf-8'>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script src="http://d3js.org/queue.v1.min.js"></script>
<script src="underscore.js"></script>
<style>
svg {
border: 1px solid black;
}
.grid-horizontal {
stroke: grey;
}
.grid-vertical {
stroke: grey;
}
.synteny {
stroke: green;
stroke-width: 2;
}
.extent {
fill: grey;
opacity: .2;
}
.textInPlot {
font-family: Verdana, geneva, sans-serif;
font-size: 14pt;
}
.xAxis > line {
stroke-width: 2;
}
</style>
</head>
<body>
<script>
'use strict'
function cumulative_counts(data) {
var ret = []
var count = 0;
for(var i = 0; i < data.length; i++) {
ret[i] = count;
count += data[i];
}
ret[i] = count;
return ret;
}
queue()
.defer(d3.json, 'data/homo_chimp.json')
.defer(d3.json, 'lengths/11691.json')
.defer(d3.json, 'lengths/25577.json')
.await(function(error, data, aLengths, bLengths) {
if(error) { console.log(error); return; }
//Make sure we gave the length files in the right order.
var aID = data[0].header.aID_c.split('_')[0];
aID = aID.substring(1, aID.length);
var bID = data[0].header.bID_c.split('_')[0];
bID = bID.substring(1, bID.length);
if(aID !== aLengths.id) {
console.log('You got the length files backwards, swapping...');
var t = aLengths;
aLengths = bLengths;
bLengths = t;
}
if(aID !== aLengths.id || bID !== bLengths.id) {
console.log('Are you using the right length files?');
console.log('Length files have ID\'s: ' + aLengths.id
+ ' and ' + bLengths.id);
console.log('Data file has ID\'s: '+aID+' and '+bID);
return;
}
// Compute cumulative BP counts
var xLengths = _.map(aLengths.lengths, function(d) {
return { name: d.name, length: Number(d.length) };
});
var yLengths = _.map(bLengths.lengths, function(d) {
return { name: d.name, length: Number(d.length) };
});
xLengths.sort(function(a,b) { return a.length < b.length; });
yLengths.sort(function(a,b) { return a.length < b.length; });
var xNames = _.pluck(xLengths, 'name');
var yNames = _.pluck(yLengths, 'name');
var xCumBPCount = cumulative_counts(_.pluck(xLengths, 'length'));
var yCumBPCount = cumulative_counts(_.pluck(yLengths, 'length'));
var xShiftScale = d3.scale.ordinal().domain(xNames).range(xCumBPCount);
var yShiftScale = d3.scale.ordinal().domain(yNames).range(yCumBPCount);
// Compute absolute BP offset from chromosome and relative offset
for(var i = 0; i < data.length; i++) {
var group = data[i].data;
var aChrom = group[0].chr1;
var bChrom = group[0].chr2;
var xShift = xShiftScale(aChrom);
var yShift = yShiftScale(bChrom);
for(var j = 0; j < group.length; j++) {
var match = group[j];
match.adjustedStart1 = Number(match.start1) + xShift;
match.adjustedStop1 = Number(match.stop1) + xShift;
match.adjustedStart2 = Number(match.start2) + yShift;
match.adjustedStop2 = Number(match.stop2) + yShift;
}
}
// Combine all chunks
data = _.flatten(_.pluck(data, 'data'));
var xTotalBPs = _.last(xCumBPCount);
var yTotalBPs = _.last(yCumBPCount);
var width = 600;
var height = width * (yTotalBPs / xTotalBPs);
var xExtent = [0, xTotalBPs];
var yExtent = [0, yTotalBPs];
var xScale = d3.scale.linear().domain(xExtent).range([0, width]);
var yScale = d3.scale.linear().domain(yExtent).range([height, 0]);
var zoom = d3.behavior.zoom().x(xScale).y(yScale).on('zoom', zoom);
var brush = d3.svg.brush().x(xScale).y(yScale)
.on('brush', function() {
updatePlot(brush.extent());
})
.on('brushend', function() {
if(brush.empty()) {
console.log('empty');
updatePlot([[0,0],[1e15,1e15]]);
}
});
var svg = d3.select('body').append('svg')
.attr({width: width, height: height}).classed('main', true)
.call(zoom).on('mousedown.zoom', null) //disable panning
.call(brush).append('g');
var plotWidth = 600, plotHeight = 600;
var plot = d3.select('body').append('svg')
.attr({width: plotWidth, height: plotHeight});
// Grid lines
svg.selectAll('.grid-vertical')
.data(xCumBPCount).enter().append('path')
.classed('grid-vertical', true)
.attr('d', function(d) {
var x = xScale(d);
var y1 = 0, y2 = height;
return 'M ' + x + ' ' + y1 + ' L ' + x + ' ' + y2;
});
svg.selectAll('.grid-horizontal')
.data(yCumBPCount).enter().append('path')
.classed('grid-horizontal', true)
.attr('d', function(d) {
var y = yScale(d);
var x1 = 0, x2 = width;
return 'M ' + x1 + ' ' + y + ' L ' + x2 + ' ' + y;
});
// Data
var dataSel = svg.selectAll('.synteny').data(data).enter()
.append('line')
.classed('synteny', true)
.attr('x1', function(d) { return xScale(d.adjustedStart1); })
.attr('y1', function(d) { return yScale(d.adjustedStart2); })
.attr('x2', function(d) { return xScale(d.adjustedStop1); })
.attr('y2', function(d) { return yScale(d.adjustedStop2); });
function zoom() {
svg.attr("transform", "translate(" + d3.event.translate + ")scale(" + d3.event.scale + ")");
var modifiedXExtent = xScale.domain();
var modifiedYExtent = yScale.domain();
var screenWidth = modifiedXExtent[1] - modifiedXExtent[0]; // Ratio is same using x or y
var original = xExtent[1] - xExtent[0];
var strokeWidth = 2;
var scaling = strokeWidth * screenWidth / original;
var xMax = modifiedXExtent[1], xMin = modifiedXExtent[0];
var yMax = modifiedYExtent[1], yMin = modifiedYExtent[0];
console.log(xMax, xMin);
console.log(yMax, yMin);
dataSel
.filter(function(d) { return d.adjustedStart1 < xMax && d.adjustedStart1 > xMin && d.adjustedStart2 < yMax && d.adjustedStart2 > yMin; })
.style('stroke-width', scaling);
d3.selectAll('.grid-horizontal', scaling).style('stroke-width', scaling);
d3.selectAll('.grid-vertical', scaling).style('stroke-width', scaling);
updatePlot(brush.extent());
}
var numTicks = 20;
plot.selectAll('rect').data(d3.range(numTicks)).enter().append('rect');
function updatePlot(extent) {
var e = extent;
var field = 'Kn';
var filteredData = _.chain(data).filter(function(d) {
return d.adjustedStart1 > e[0][0] && d.adjustedStart1 < e[1][0] &&
d.adjustedStart2 > e[0][1] && d.adjustedStart2 < e[1][1];
}).pluck(field).value();
var plotData = d3.layout.histogram()
.bins(d3.scale.linear().ticks(numTicks))(filteredData);
var margin = 50;
var xPlotScale = d3.scale.linear()
.range([margin, plotWidth - margin]);
var yPlotScale = d3.scale.linear()
.domain([0, data.length/4])
.range([plotHeight - margin, margin]);
var xAxis = d3.svg.axis().scale(xPlotScale).orient('bottom');
var yAxis = d3.svg.axis().scale(yPlotScale).orient('left');
plot.selectAll('rect').data(plotData)
.attr('x', function(d) { return xPlotScale(d.x); })
.attr('width', function(d) { return xPlotScale(d.dx) - margin; })
.attr('y', function(d) { return yPlotScale(d.y); })
.attr('height', function(d) { return plotHeight - margin - yPlotScale(d.y); })
.attr('fill', 'steelblue')
plot.select('text').remove();
plot.selectAll('.xAxis').remove();
plot.selectAll('.yAxis').remove();
plot.append('text')
.attr('x', 2 * plotHeight / 3)
.attr('width', plotHeight / 3)
.attr('y', 50)
.attr('height', 50)
.classed('textInPlot', true)
.text(field);
plot.append('g')
.attr('transform', 'translate(0,' + (plotHeight - 50) + ')')
.classed('xAxis', true).call(xAxis);
plot.append('g')
.attr('transform', 'translate(50,0)')
.classed('yAxis', true).call(yAxis);
}
});
</script>
</body>
</html>