Force-Directed Graph with Scaled Nodes

This simple force-directed graph shows identifier mappings for the disease "Ehlers Danlos Syndrome"; more background can be found here: https://github.com/monarch-initiative/ont-review/blob/master/docs/xrefs.md.

Compare this display to a force layout with curved links, a force layout with fisheye distortion and a matrix diagram.

forked from mbostock's block: Force-Directed Graph

Modifications include scaling of the size of the nodes.

forked from jmcmurry's block: Force-Directed Graph with Scaled Nodes

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

.links line {
  stroke: #999;
  stroke-opacity: 0.4;
}

.nodes circle {
  stroke: #fff;
  stroke-width: 2px;
  opacity: 0.6;
}

</style>
<svg width="960" height="600"></svg>
<script src="https://d3js.org/d3.v4.min.js"></script>
<script>

var svg = d3.select("svg"),
    width = +svg.attr("width"),
    height = +svg.attr("height");

var color = d3.scaleOrdinal(d3.schemeCategory20);

var simulation = d3.forceSimulation()
    .force("link", d3.forceLink().id(function(d) { return d.id; }))
    .force("charge", d3.forceManyBody())
    .force("center", d3.forceCenter(width / 2, height / 2));

d3.json("miserables.json", function(error, graph) {
  if (error) throw error;

var link = svg.append("g")
      .attr("class", "links")
    .selectAll("line")
    .data(graph.links)
    .enter().append("line")
      .attr("stroke-width", function(d) { return Math.sqrt(d.value); });

var node = svg.append("g")
      .attr("class", "nodes")
    .selectAll("circle")
    .data(graph.nodes)
    .enter().append("circle")
      .attr("r", function(d) { return d.group; })
      .attr("fill", function(d) { return color(d.group); })
      .call(d3.drag()
          .on("start", dragstarted)
          .on("drag", dragged)
          .on("end", dragended));

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

simulation
      .nodes(graph.nodes)
      .on("tick", ticked);

simulation.force("link")
      .links(graph.links);

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

function dragstarted(d) {
  if (!d3.event.active) simulation.alphaTarget(0.3).restart();
  d.fx = d.x;
  d.fy = d.y;
}

function dragged(d) {
  d.fx = d3.event.x;
  d.fy = d3.event.y;
}

function dragended(d) {
  if (!d3.event.active) simulation.alphaTarget(0);
  d.fx = null;
  d.fy = null;
}

</script>

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