Clustering with Links

<!DOCTYPE html>

var nodes = [];
  var links = [];
  var clusters = {};
  var linked = {};

for (var i = 0; i < numClusters; i++) {
    clusters["c" + i] = [];
    for (var j = 0; j < nodesPerCluster; j++) {
      var node = {name: "c" + i + "n" + j, cluster: "c" + i};
      nodes.push(node);
      clusters["c" + i].push(node);

if (nodes.length > 1) {
        var numLinks = Math.floor(Math.random() * 1.5);
        for (var k = 0; k < numLinks; k++) {
          var pred = nodes[Math.floor(Math.random() * (nodes.length - 1))];
          var key = pred.name + ":" + node.name;
          if (!(key in linked)) {
            linked[key] = true;
            links.push({source: pred, target: node}); 
          }
        }
      }
    }
  }

var colors = d3.scale.category20()
    .domain(d3.keys(clusters));

var width = 960,
      height = 600;

function zoom() {
    svg.attr("transform", "translate(" + d3.event.translate + ") scale(" + d3.event.scale + ")"); 
  }

var svgRoot = d3.select("#chart")
    .attr("width", "100%")
    .attr("height", "100%");

svgRoot.append("rect")
    .attr("width", "100%")
    .attr("height", "100%")
    .attr("pointer-events", "all")
    .style("fill-opacity", 0)
    .call(d3.behavior.zoom().on("zoom", zoom));

svg = svgRoot.append("g");

var force = d3.layout.force()
    .charge(-250)
    .linkDistance(100)
    .size([width, height])
    .nodes(nodes)
    .links(links)
    .start();

var hullPadding = 10;
  function clusterPath(d) {
    var points = [];
    clusters[d].forEach(function(e) {
      points.push([e.x - hullPadding, e.y - hullPadding]);
      points.push([e.x - hullPadding, e.y + hullPadding]);
      points.push([e.x + hullPadding, e.y - hullPadding]);
      points.push([e.x + hullPadding, e.y + hullPadding]);
    });
    return "M" + d3.geom.hull(points).join("L") + "Z";
  }

var hull = svg.selectAll("path.hull")
    .data(d3.keys(clusters))
    .enter()
      .append("path")
      .classed("hull", true)
      .attr("d", clusterPath)
      .style("fill", function(d) { return colors(d); })
      .style("fill-opacity", "0.5");

var link = svg.selectAll("line.link")
    .data(links)
    .enter()
      .append("line")
      .classed("link", true)
      .style("stroke", "black")
      .style("stroke-width", "1.5px");

var node = svg.selectAll("circle.node")
    .data(nodes)
    .enter()
      .append("circle")
      .classed("node", true)
      .style("fill", function(d) { return colors(d.cluster); })
      .attr("r", 5)
      .call(force.drag);

node
    .append("title")
    .text(function(d) { return d.name; });

force.on("tick", function(e) {
    d3.values(clusters).forEach(function(cluster) {
      var x = 0, y = 0;
      cluster.forEach(function(n) {
        x += n.x;
        y += n.y;
      });
      x = x / cluster.length;
      y = y / cluster.length;

var k = e.alpha * 2.0;
      cluster.forEach(function(n) {
        n.x += (x - n.x) * k;
        n.y += (y - n.y) * k; 
      });

});

hull
      .attr("d", clusterPath);

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("cx", function(d) { return d.x; })
      .attr("cy", function(d) { return d.y; });
  });
</script>

Modified http://mbostock.github.com/d3/d3.v2.min.js to a secure url

https://mbostock.github.com/d3/d3.v2.min.js