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Last active August 29, 2015 14:06
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Rough d3 volcano plot
Raw
README.md

This is an attempt to produce an interactive volcano plot from a csv data file using d3. A volcano plot displays significance against substance, to allow visual discrimination of data points with strongly significant & large effects (located in the top left/ top right hand corners) from those with small or insignificant effects.

The idea here is that hovering over a point displays the feature name, and clicking on a data point generates a table of information for that feature.

Raw
colorbrewer.js
// This product includes color specifications and designs developed by Cynthia Brewer (http://colorbrewer.org/).
var colorbrewer = {YlGn: {
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},YlGnBu: {
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},Greens: {
3: ["#e5f5e0","#a1d99b","#31a354"],
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}};
Raw
index.html
<!DOCTYPE html>
<meta charset="utf-8">
<style>
body
{
font-family: "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif;
width: 1000px;
background: #fff;
}
.fig
{
font-family: "HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif;
float: left;
width: 1000px;
}
.chart
{
clear: left;
float: left;
width: 800px;
display: inline;
}
.table
{
float: right;
width: 200px;
display: inline;
}
.xlabel, .ylabel {
font-weight: bold;
}
.axis path,
.axis line {
fill: none;
stroke: black;
shape-rendering: crispEdges;
}
.axis text {
font-family: sans-serif;
font-size: 12px;
}
</style>
<link href="http://cdnjs.cloudflare.com/ajax/libs/jquery.tipsy/1.0.2/jquery.tipsy.css" rel="stylesheet" type="text/css" />
<body>
<script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/d3/3.4.11/d3.min.js"></script>
<script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<script type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/jquery.tipsy/1.0.2/jquery.tipsy.min.js"></script>
<script type="text/javascript" src="colorbrewer.js"></script>
<div class='fig'>
<div class='chart'></div>
<table id="info">
<tr>
<td><b>Name:</b></td> <td><div id="gene_name"></div></td>
</tr>
<tr>
<td><b>x-value:</b></td> <td><div id="xval"></div></td>
</tr>
<tr>
<td><b>y-value:</b></td> <td><div id="yval"></div></td>
</tr>
</table>
</div>
<script type="text/javascript">
//Width and height
var w = 800;
var h = 500;
var padding = 100;
var svg = d3.select(".chart")
.append("svg")
.attr("width", w)
.attr("height", h);
var highlightElement = null;
var info = function(d) {
$("#gene_name").html(d.name);
$("#xval").html(parseFloat(d.x).toPrecision(5));
$("#yval").html(parseFloat(d.y).toPrecision(5));
var element = d3.select(this);
element.transition().duration(100)
.attr("stroke", element.attr("fill"))
.attr("stroke-width", 5);
if (highlightElement) {
highlightElement.transition().duration(100)
.attr("stroke","none");
}
highlightElement = element;
};
d3.text("voldat.csv", function(text) {
var data = d3.csv.parse(text);
var len = d3.max(data, function(d) { return d.f; } );
var xmin = d3.min(data, function(d) { return parseFloat(d.x); });
var xmax = d3.max(data, function(d) { return parseFloat(d.x); });
var ymin = d3.min(data, function(d) { return parseFloat(d.y); });
var ymax = d3.max(data, function(d) { return parseFloat(d.y); });
var xScale = d3.scale.linear()
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.on("click", info)
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$('svg circle').tipsy({
gravity: 'w',
html: true,
title: function() {
return this.__data__.name;
}
});
var xAxis = d3.svg.axis()
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var yAxis = d3.svg.axis()
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svg.append("g")
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svg.append("g")
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.call(yAxis);
svg.append("text")
.attr("class", "xlabel")
.attr("text-anchor", "end")
.attr("x", w/2)
.attr("y", h-40)
.text("Effect Size");
svg.append("text")
.attr("class", "ylabel")
.attr("text-anchor", "end")
.attr("y", 40)
.attr("x", -h/2+50)
.attr("transform", "rotate(-90)")
.text("-log10(p-value)");
});
</script>
</body>
</html>
Raw
voldat.csv
name x y f
1007_s_at -0.0230094474977989 0.0700112788795897 1
1053_at -0.243246619250137 0.419891060038732 2
117_at -0.114195484177306 0.101709511529968 3
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1255_g_at -0.138486244087801 0.426744520780239 5
1294_at 0.299874493964433 1.05803836493541 1
1316_at 0.181376088620303 0.756766103194458 2
1320_at 1.0460452234141 0.422445793530649 3
1405_i_at -0.705068932445943 0.330486434476635 4
1431_at 0.578857052144552 0.298111849341176 5
1438_at -0.636216417856751 0.248112029150025 1
1487_at -0.167843905991122 0.474015890488526 2
1494_f_at 0.0197349940147529 0.0178209339714631 3
1598_g_at 0.151746546837035 1.15230728131822 4
160020_at -0.0340081599477884 0.0773232423096207 5
1729_at 0.0277876027058852 0.0534903115231976 1
1773_at -0.204320939512136 0.329644270864909 2
177_at 0.289240041982212 0.372570568489228 3
179_at 0.0618311750801137 0.214205872683665 4
1861_at 0.0852115260481803 0.34061495659972 5
200000_s_at -0.0358969790980233 0.37039804136262 1
200001_at -0.0293550198140107 0.275774993422481 2
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200003_s_at -0.0640972852730428 1.12278806918456 4
200004_at -0.0305027346656992 0.294277068620035 5
200005_at -0.0243243717249708 0.0958454743774591 1
200006_at -0.018198951955247 0.276873262594597 2
200007_at 0.0469305427739872 0.408268595516531 3
200008_s_at 0.0149034106772579 0.278799771790002 4
200009_at -0.0457885217632157 0.272367895075269 5
200010_at -0.0674101274423293 0.749371331383503 1
200011_s_at -0.0193466195111345 0.0636321542155141 2
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200013_at 0.0368592187909691 0.225867479810232 4
200014_s_at -0.0303416302441342 0.233069537628999 5
200015_s_at -0.0144420928503202 0.038100227241368 1
200016_x_at 0.0036556802987171 0.0185417919465305 2
200017_at 0.081734537920692 0.574321079794997 3
200018_at 0.0316719316255316 0.198954863805869 4
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200034_s_at 0.111487780666637 0.724772466943685 5
200035_at 0.0795966571724342 0.0833771406378778 1
200036_s_at -0.0544994598528934 0.553286460061676 2
200037_s_at 0.0968459504444077 2.10749076207417 3
200038_s_at 0.0059477704718045 0.0340662407610335 4
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200059_s_at 0.13899965352841 0.691982959835147 5
200060_s_at 0.0380208380772249 0.100299179308256 1
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