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Clustering a Force layout with a Quadtree
Raw
README.md

#Clustering a Force layout with a quadtree#

This is an example of how to use a Quadtree to cluster the nodes that are close to each other in a Force Layout.

With the slider you can select how deep you want to explore the quadtree, and it creates cluster-nodes representing the points that are not going to be displayed.

Raw
index.html
<!DOCTYPE html>
<meta charset="utf-8">
<style>
.node {
stroke: #fff;
stroke-width: 1.5px;
}
.link {
stroke: #999;
stroke-opacity: .3;
}
</style>
<script src="http://d3js.org/d3.v3.min.js"></script>
<body>
<label for='slider_cluster'>Cluster</label>
<input id='slider_cluster' type='range' min='1' max='5' value='8'/><br/>
</body>
<script>
var width = 960,
height = 500;
var color = d3.scale.category20();
var force = d3.layout.force()
.charge(-120)
.linkDistance(30)
.size([width, height]);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
var _shouldCluster = false,
_currentNode = null,
_howDeep = 2,
_nthCluster = 0;
var pruneNodes= function(original_nodes){
var nodes =[],q;
//when the clustering is disable return all the proteins
if (!_shouldCluster)
return original_nodes;
//get the current quadtree
q = d3.geom.quadtree(original_nodes);
q.depth = 0; // root
q.quadrant="0";
//Tag all the proteins to be hidden
original_nodes.forEach(function(o, i) { o.toshow=false; });
//To use in quadtree.visit, to select what to show.
var what2show = function(node, x1, y1, x2, y2){
//determine the depth of the children
for (var i=0; i<4; i++) {
if (node.nodes[i]){
node.nodes[i].depth = node.depth+1;
}
}
if (node.leaf && node.point!=null) {
node.point.toshow = true; //tag the node to show if has reach a leaf
}else{
node.cluster=null;
//takes the decision of going deeper into the tree
if (!shouldGoDeeper(node)){// && node.cluster==null){
//in case it is determined to stop at this node, it creates a new cluster in that node.
node.cluster= {
id: "Cluster_"+_nthCluster,
name: "cluster "+ (_nthCluster++),
nodes:[],
isCluster: true,
px: x1,
py: y1,
size: 1,
weight: 1,
x: x1,
y: y1,
fixed:true,
group:15
};
nodes.push(node.cluster);
return true;
}
}
return false;
};
//To use in quadtree.visit, to find the cluster that a protein belongs to.
var addCurrentNodeToCluster = function(node, x1, y1, x2, y2){
if (_currentNode==null)
return true;
if (x1<=_currentNode.x && _currentNode.x<=x2 && y1<=_currentNode.y && _currentNode.y<=y2){
if (node.cluster != null){
node.cluster.nodes.push(_currentNode);
_currentNode.cluster=node.cluster;
return true;
}
if (node.leaf)
return true;
return false;
}
return true;
};
//goes trhought the tree marking what to show and creating clusters.
q.visit(what2show);
//Goes through all the proteins to include the ones to show in the nodes array() or to find its cluster
original_nodes.forEach(function(o, i) {
if (o.toshow){
nodes.push(o);
}else{
_currentNode=o;
_currentNode.cluster=null;
q.visit(addCurrentNodeToCluster);
calculateCentroid(_currentNode.cluster);
_currentNode=null;
}
});
return nodes;
};
var shouldGoDeeper = function(node){
return _howDeep > node.depth;
};
var calculateCentroid = function(cluster){
var centroid ={x:0,y:0};
cluster.nodes.forEach(function(p,i){
centroid.x +=p.px;
centroid.y +=p.py;
});
cluster.px=cluster.x= centroid.x/cluster.nodes.length;
cluster.py=cluster.y= centroid.y/cluster.nodes.length;
};
var pruneLinks= function(original_links){
var links =[];
if (!_shouldCluster)
return original_links;
original_links.forEach(function(o, i) {
if (o.source.toshow){
if (o.target.toshow){
links.push(o);
}else{
links.push({
source: o.source,
target: o.target.cluster
});
}
}else{
if (o.target.toshow){
links.push({
source: o.source.cluster,
target: o.target
});
}else{
if (o.source.cluster.id != o.target.cluster.id)
links.push({
source: o.source.cluster,
target: o.target.cluster
});
}
}
});
return links;
};
var response=null;
d3.json("miserables.json", function(error, graph) {
response=graph;
update();
force.on("tick", function() {
svg.selectAll(".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; });
svg.selectAll(".node").attr("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; });
});
});
var update=function(){
var data_nodes = pruneNodes(response.nodes),
data_links = pruneLinks(response.links);
force
.nodes(data_nodes)
.links(data_links)
.start();
var links = svg.selectAll(".link")
.data(data_links);
var link =links
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return Math.sqrt(d.value); });
links.exit().remove();
var nodes = svg.selectAll(".node")
.data(data_nodes);
var node = nodes
.enter().append("circle")
.attr("class", "node")
.call(force.drag);
nodes.attr("r", function(d) {
return 5* Math.sqrt((d.isCluster)?d.nodes.length:1);
})
.style("fill", function(d) { return color(d.group); });
node.append("title")
.text(function(d) { return d.name; });
nodes.exit().remove();
};
d3.select("input[type=range]").on("change", function() {
_shouldCluster=true;
_howDeep=+this.value;
update();
});
</script>
Raw
miserables.json
{
"nodes":[
{"name":"Myriel","group":1},
{"name":"Napoleon","group":1},
{"name":"Mlle.Baptistine","group":1},
{"name":"Mme.Magloire","group":1},
{"name":"CountessdeLo","group":1},
{"name":"Geborand","group":1},
{"name":"Champtercier","group":1},
{"name":"Cravatte","group":1},
{"name":"Count","group":1},
{"name":"OldMan","group":1},
{"name":"Labarre","group":2},
{"name":"Valjean","group":2},
{"name":"Marguerite","group":3},
{"name":"Mme.deR","group":2},
{"name":"Isabeau","group":2},
{"name":"Gervais","group":2},
{"name":"Tholomyes","group":3},
{"name":"Listolier","group":3},
{"name":"Fameuil","group":3},
{"name":"Blacheville","group":3},
{"name":"Favourite","group":3},
{"name":"Dahlia","group":3},
{"name":"Zephine","group":3},
{"name":"Fantine","group":3},
{"name":"Mme.Thenardier","group":4},
{"name":"Thenardier","group":4},
{"name":"Cosette","group":5},
{"name":"Javert","group":4},
{"name":"Fauchelevent","group":0},
{"name":"Bamatabois","group":2},
{"name":"Perpetue","group":3},
{"name":"Simplice","group":2},
{"name":"Scaufflaire","group":2},
{"name":"Woman1","group":2},
{"name":"Judge","group":2},
{"name":"Champmathieu","group":2},
{"name":"Brevet","group":2},
{"name":"Chenildieu","group":2},
{"name":"Cochepaille","group":2},
{"name":"Pontmercy","group":4},
{"name":"Boulatruelle","group":6},
{"name":"Eponine","group":4},
{"name":"Anzelma","group":4},
{"name":"Woman2","group":5},
{"name":"MotherInnocent","group":0},
{"name":"Gribier","group":0},
{"name":"Jondrette","group":7},
{"name":"Mme.Burgon","group":7},
{"name":"Gavroche","group":8},
{"name":"Gillenormand","group":5},
{"name":"Magnon","group":5},
{"name":"Mlle.Gillenormand","group":5},
{"name":"Mme.Pontmercy","group":5},
{"name":"Mlle.Vaubois","group":5},
{"name":"Lt.Gillenormand","group":5},
{"name":"Marius","group":8},
{"name":"BaronessT","group":5},
{"name":"Mabeuf","group":8},
{"name":"Enjolras","group":8},
{"name":"Combeferre","group":8},
{"name":"Prouvaire","group":8},
{"name":"Feuilly","group":8},
{"name":"Courfeyrac","group":8},
{"name":"Bahorel","group":8},
{"name":"Bossuet","group":8},
{"name":"Joly","group":8},
{"name":"Grantaire","group":8},
{"name":"MotherPlutarch","group":9},
{"name":"Gueulemer","group":4},
{"name":"Babet","group":4},
{"name":"Claquesous","group":4},
{"name":"Montparnasse","group":4},
{"name":"Toussaint","group":5},
{"name":"Child1","group":10},
{"name":"Child2","group":10},
{"name":"Brujon","group":4},
{"name":"Mme.Hucheloup","group":8}
],
"links":[
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]
}
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