Clustered Force Layout

<!DOCTYPE html>
<meta charset="utf-8">
<style>

circle {
  stroke: #fff;
}

</style>
<body>
<script src="https://cdn.jsdelivr.net/npm/d3@2.7.4/d3.js"></script>
<script src="https://cdn.jsdelivr.net/npm/d3@2.7.4/d3.geom.js"></script>
<script src="https://cdn.jsdelivr.net/npm/d3@2.7.4/d3.layout.js"></script>
<script>

var margin = {top: 0, right: 0, bottom: 0, left: 0},
    width = 960 - margin.left - margin.right,
    height = 500 - margin.top - margin.bottom;

var n = 200,
    m = 10,
    padding = 6,
    radius = d3.scale.sqrt().range([0, 12]),
    color = d3.scale.category10().domain(d3.range(m));

var nodes = d3.range(n).map(function() {
  var i = Math.floor(Math.random() * m),
      v = (i + 1) / m * -Math.log(Math.random());
  return {
    radius: radius(v),
    color: color(i)
  };
});

var force = d3.layout.force()
    .nodes(nodes)
    .size([width, height])
    .gravity(.005)
    .charge(0)
    .on("tick", tick)
    .start();

var svg = d3.select("body").append("svg")
    .attr("width", width + margin.left + margin.right)
    .attr("height", height + margin.top + margin.bottom)
  .append("g")
    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");

var circle = svg.selectAll("circle")
    .data(nodes)
  .enter().append("circle")
    .attr("r", function(d) { return d.radius; })
    .style("fill", function(d) { return d.color; })
    .call(force.drag);

function tick(e) {
  circle
      .each(cluster(10 * e.alpha * e.alpha))
      .each(collide(.5))
      .attr("cx", function(d) { return d.x; })
      .attr("cy", function(d) { return d.y; });
}

// Move d to be adjacent to the cluster node.
function cluster(alpha) {
  var max = {};

// Find the largest node for each cluster.
  nodes.forEach(function(d) {
    if (!(d.color in max) || (d.radius > max[d.color].radius)) {
      max[d.color] = d;
    }
  });

return function(d) {
    var node = max[d.color],
        l,
        r,
        x,
        y,
        i = -1;

if (node == d) return;

x = d.x - node.x;
    y = d.y - node.y;
    l = Math.sqrt(x * x + y * y);
    r = d.radius + node.radius;
    if (l != r) {
      l = (l - r) / l * alpha;
      d.x -= x *= l;
      d.y -= y *= l;
      node.x += x;
      node.y += y;
    }
  };
}

// Resolves collisions between d and all other circles.
function collide(alpha) {
  var quadtree = d3.geom.quadtree(nodes);
  return function(d) {
    var r = d.radius + radius.domain()[1] + padding,
        nx1 = d.x - r,
        nx2 = d.x + r,
        ny1 = d.y - r,
        ny2 = d.y + r;
    quadtree.visit(function(quad, x1, y1, x2, y2) {
      if (quad.point && (quad.point !== d)) {
        var x = d.x - quad.point.x,
            y = d.y - quad.point.y,
            l = Math.sqrt(x * x + y * y),
            r = d.radius + quad.point.radius + (d.color !== quad.point.color) * padding;
        if (l < r) {
          l = (l - r) / l * alpha;
          d.x -= x *= l;
          d.y -= y *= l;
          quad.point.x += x;
          quad.point.y += y;
        }
      }
      return x1 > nx2
          || x2 < nx1
          || y1 > ny2
          || y2 < ny1;
    });
  };
}

</script>

Modified http://mbostock.github.com/d3/d3.js?2.7.4 to a secure url

Modified http://mbostock.github.com/d3/d3.geom.js?2.7.4 to a secure url

Modified http://mbostock.github.com/d3/d3.layout.js?2.7.4 to a secure url

https://mbostock.github.com/d3/d3.js?2.7.4

https://mbostock.github.com/d3/d3.geom.js?2.7.4

https://mbostock.github.com/d3/d3.layout.js?2.7.4