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Yeast PPI Network Generated in Cytoscape
Raw
README.md
Raw
index.html
<!DOCTYPE html>
<head>
<meta charset="utf-8">
<link type="text/css" rel="stylesheet" href="style.css"/>
</head>
<body>
<div id="d3view"></div>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script src="src.js"></script>
</body>
</html>
Raw
net1.json
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"shared_name" : "YLR264W (pp) YER112W",
"shared_interaction" : "pp"
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"SUID" : 366,
"name" : "YEL015W (pp) YML064C",
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"shared_name" : "YEL015W (pp) YML064C",
"shared_interaction" : "pp"
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"shared_name" : "YNR050C (pp) YMR138W",
"shared_interaction" : "pp"
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"EdgeBetweenness" : 6283.85994006,
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"name" : "YJR022W (pp) YNR053C",
"interaction" : "pp",
"shared_name" : "YJR022W (pp) YNR053C",
"shared_interaction" : "pp"
}, {
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"SUID" : 119,
"name" : "YJR022W (pp) YLR264W",
"interaction" : "pp",
"shared_name" : "YJR022W (pp) YLR264W",
"shared_interaction" : "pp"
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"shared_interaction" : "pp"
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"name" : "YJR022W (pp) YEL015W",
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"shared_name" : "YJR022W (pp) YEL015W",
"shared_interaction" : "pp"
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"shared_interaction" : "pp"
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}, {
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} ]
}
Raw
src.js
d3.unconf = function () {
var DEF_NETWORK_FILE = 'net1.json';
var WIDTH = 960;
var HEIGHT = 500;
var D3_VIEW = '#d3view';
var GraphRenderer = function (width, height) {
this.force = d3.layout.force()
.charge(-20)
.gravity(0.05)
.linkDistance(35)
.size([width, height]);
this.svg = d3.select(D3_VIEW).append('svg');
};
GraphRenderer.prototype.render = function (graph) {
this.force.nodes(graph.nodes).links(graph.links).start();
var link = this.svg.selectAll('.link')
.data(graph.links)
.enter().append('line')
.attr('class', 'link')
.attr('stroke-width', function (d) {
return Math.log(d.EdgeBetweenness) / Math.LN10;
});
var node = this.svg.selectAll('.node')
.data(graph.nodes)
.enter().append('g')
.attr('class', 'node')
.call(this.force.drag);
// Render label (use name attr)
node.append('text')
.attr('dx', 8)
.attr('dy', '.25em')
.text(function (d) {
return d.name;
});
// Use circle for node shape
node.append('circle')
.attr('class', 'node')
.attr('r', function (d) {
return d.Degree;
});
this.force.on('tick', function () {
link.attr('x1', function (d) {
return d.source.x;
})
.attr('y1', function (d) {
return d.source.y;
})
.attr('x2', function (d) {
return d.target.x;
})
.attr('y2', function (d) {
return d.target.y;
});
node.attr('transform', function (d) {
return 'translate(' + d.x + ',' + d.y + ')';
});
});
};
var TreeRenderer = function (width, height) {
this.cluster = d3.layout.cluster()
.size([height, width - 80]);
this.diagonal = d3.svg.diagonal()
.projection(function (d) {
return [d.y, d.x];
});
this.svg = d3.select(D3_TREE_VIEW).append("svg")
.attr("width", width)
.attr("height", height)
.append("g")
.attr("transform", "translate(50,0)");
};
TreeRenderer.prototype.render = function (tree) {
var nodes = this.cluster.nodes(tree),
links = this.cluster.links(nodes);
var link = this.svg.selectAll(".link")
.data(links)
.enter().append("path")
.attr("class", "link")
.attr("d", this.diagonal);
var node = this.svg.selectAll(".node")
.data(nodes)
.enter().append("g")
.attr("class", "node")
.attr("transform", function (d) {
return "translate(" + d.y + "," + d.x + ")";
});
node.append("circle")
.attr("r", 6);
node.append("text")
.attr("dx", function (d) {
return d.children ? -10 : 10;
})
.attr("dy", 20)
.style("text-anchor", function (d) {
return d.children ? "end" : "start";
})
.text(function (d) {
return d.name;
});
};
var RadialTreeRenderer = function (diameter) {
this.tree = d3.layout.tree()
.size([2500, 400])
.separation(function (a, b) {
return (a.parent == b.parent ? 1 : 2) / a.depth;
});
this.diagonal = d3.svg.diagonal.radial()
.projection(function (d) {
return [d.y, d.x / 180 * Math.PI];
});
this.svg = d3.select(D3_CTREE_VIEW).append("svg")
.attr("width", diameter)
.attr("height", diameter)
.append("g")
.attr("transform", "translate(" + (diameter / 2 - 30) + "," + diameter / 2 + ")");
};
RadialTreeRenderer.prototype.render = function (treeData) {
var nodes = this.tree.nodes(treeData),
links = this.tree.links(nodes);
var link = this.svg.selectAll(".link")
.data(links)
.enter().append("path")
.attr("class", "link")
.attr("d", this.diagonal);
var node = this.svg.selectAll(".node")
.data(nodes)
.enter().append("g")
.attr("class", "node")
.attr("transform", function (d) {
return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")";
});
node.append("circle")
.attr("r", 2);
node.append("text")
.attr("dy", ".31em")
.attr("text-anchor", function (d) {
return d.x < 180 ? "start" : "end";
})
.attr("transform", function (d) {
return d.x < 180 ? "translate(8)" : "rotate(180)translate(-8)";
})
.text(function (d) {
return d.name;
});
};
// Main //
console.log('Network rendering start...');
var gr = new GraphRenderer(WIDTH, HEIGHT);
d3.json(DEF_NETWORK_FILE, function (graphData) {
gr.render(graphData);
});
};
d3.unconf();
Raw
style.css
@import url("//fonts.googleapis.com/css?family=Open+Sans:300italic,400italic,700italic,400,300,700");
body {
font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Helvetica, Arial, sans-serif;
}
.d3-unconf {
color: #222;
font-size: 44px;
font-style: normal;
font-weight: 100;
text-rendering: optimizelegibility;
}
.d3view {
width: 960px;
height: 500px;
margin-top: 1em;
margin-bottom: 1em;
}
.node {
stroke: #1987E5;
fill-opacity:0.1;
stroke-opacity:0.5;
fill: white;
stroke-width: 2.5px;
}
.node text {
stroke-width: 1px;
stroke-opacity: 1.0;
stroke: #555555;
pointer-events: none;
font-size: 8px;
}
line.link {
fill: none;
stroke: #c1c1c1;
}
path.link {
fill: none;
stroke: #a0a0a0;
stroke-width: 1.5px;
}
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