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chords.js
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chords.js
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var gieStainColor = {
gpos100: 'rgb(0,0,0)',
gpos: 'rgb(0,0,0)',
gpos75: 'rgb(130,130,130)',
gpos66: 'rgb(160,160,160)',
gpos50: 'rgb(200,200,200)',
gpos33: 'rgb(210,210,210)',
gpos25: 'rgb(200,200,200)',
gvar: 'rgb(220,220,220)',
gneg: 'rgb(255,255,255)',
acen: 'rgb(217,47,39)',
stalk: 'rgb(100,127,164)',
select: 'rgb(135,177,255)'
}
var drawCircos = function (error, GRCh37, cytobands, data) {
var width = document.getElementsByClassName('mdl-card__supporting-text')[0].offsetWidth
var circos = new Circos({
container: '#chordsChart',
width: width,
height: width
})
cytobands = cytobands.map(function (d) {
return {
block_id: d.chrom,
start: parseInt(d.chromStart),
end: parseInt(d.chromEnd),
gieStain: d.gieStain,
name: d.name
}
})
data = data.map(function (d) {
return {
source: {
id: d.source_id,
start: parseInt(d.source_breakpoint) - 2000000,
end: parseInt(d.source_breakpoint) + 2000000
},
target: {
id: d.target_id,
start: parseInt(d.target_breakpoint) - 2000000,
end: parseInt(d.target_breakpoint) + 2000000
}
}
})
circos
.layout(
GRCh37,
{
innerRadius: width/2 - 80,
outerRadius: width/2 - 40,
labels: {
radialOffset: 70
},
ticks: {
display: true,
labelDenominator: 1000000
}
}
)
.highlight('cytobands', cytobands, {
innerRadius: width/2 - 80,
outerRadius: width/2 - 40,
opacity: 0.3,
color: function (d) {
return gieStainColor[d.gieStain]
},
tooltipContent: function (d) {
return d.name
}
})
.chords(
'l1',
data,
{
logScale: false,
opacity: 0.7,
color: '#ff5722',
tooltipContent: function (d) {
return d.source.id + ' ➤ ' + d.target.id + ': ' + d.value
}
}
)
.render()
}
d3.queue()
.defer(d3.json, './data/GRCh37.json')
.defer(d3.csv, './data/cytobands.csv')
.defer(d3.csv, './data/fusion-genes.csv')
.await(drawCircos)