clusters

<!DOCTYPE html>
<meta charset="utf-8">
<body>
<script src="//d3js.org/d3.v4.min.js"></script>
<script>

var width = 960,
    height = 500,
    padding = 1.5, // separation between same-color nodes
    clusterPadding = 6, // separation between different-color nodes
    maxRadius = 80;

var n = 5, // total number of nodes
    m = 1; // number of distinct clusters

var color = d3.scaleSequential(d3.interpolateRainbow)
    .domain(d3.range(m));

// The largest node for each cluster.
var clusters = new Array(m);

var nodes = d3.range(n).map(function() {
  var i = Math.floor(Math.random() * m),
      r = Math.sqrt((i + 1) / m * -Math.log(Math.random())) * maxRadius,
      d = {
        cluster: i,
        radius: r,
        x: Math.cos(i / m * 2 * Math.PI) * 200 + width / 2 + Math.random(),
        y: Math.sin(i / m * 2 * Math.PI) * 200 + height / 2 + Math.random()
      };
  if (!clusters[i] || (r > clusters[i].radius)) clusters[i] = d;
  return d;
});

var force = d3.forceSimulation()
  // keep entire simulation balanced around screen center
  .force('center', d3.forceCenter(width/2, height/2))

// cluster by section
  .force('cluster', cluster()
    .strength(0.2))

// apply collision with padding
  .force('collide', d3.forceCollide(d => d.radius + padding)
    .strength(0.7))

.on('tick', layoutTick)
	.nodes(nodes);
  
var svg = d3.select("body").append("svg")
    .attr("width", width)
    .attr("height", height);

var node = svg.selectAll("circle")
    .data(nodes)
  .enter().append("circle")
    .style("fill", function(d) { return color(d.cluster/1); });

function layoutTick(e) {
  node
      .attr("cx", function(d) { return d.x; })
      .attr("cy", function(d) { return d.y; })
      .attr("r", function(d) { return d.radius; });
}

// Move d to be adjacent to the cluster node.
// from: https://bl.ocks.org/mbostock/7881887
function cluster () {

var nodes,
    strength = 0.1;

function force (alpha) {

// scale + curve alpha value
    alpha *= strength * alpha;

nodes.forEach(function(d) {
			var cluster = clusters[d.cluster];
    	if (cluster === d) return;
      
      let x = d.x - cluster.x,
        y = d.y - cluster.y,
        l = Math.sqrt(x * x + y * y),
        r = d.radius + cluster.radius;

if (l != r) {
        l = (l - r) / l * alpha;
        d.x -= x *= l;
        d.y -= y *= l;
        cluster.x += x;
        cluster.y += y;
      }
    });

}

force.initialize = function (_) {
    nodes = _;
  }

force.strength = _ => {
    strength = _ == null ? strength : _;
    return force;
  };

return force;

}
  
</script>

https://d3js.org/d3.v4.min.js