Grouping nodes in a Force-Directed Graph

Example of a force-directed graph with an extra layer for grouping nodes.

Nodes and groups can be dragged indepedently. The type of curve and the scale of the shape can be tuned in order to define the contour of the group shapes

forked from XavierGimenez's block: Grouping nodes in a Force-Directed Graph

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

body {
  font-family: sans-serif, Arial;  
  font-size: 12px;
  font-weight: bold;
}
.links line {
  stroke: #999;
  stroke-opacity: 0.6;
}

.nodes circle {
  stroke: #fff;
  stroke-width: 1.5px;
}

path {
  fill-opacity: .1;
  stroke-opacity: 1;
}

</style>
<div id="scaleFactorSettings">
  <p>Scale of the groups: <span id='scaleFactorLabel'>1.2</span></p>
  <input type="range" min="1" max="3" value="1.2" step=".1" 
    oninput="scaleFactor = value; d3.select('#scaleFactorLabel').text(scaleFactor); updateGroups()">
</div>
<div id="curveSettings">
  <p>Type of curve: <span id='curveLabel'>curveCatmullRomClosed</span></p>
</div>
<svg width='960' height='600'></svg>
<script src='https://d3js.org/d3.v4.min.js'></script>
<script>

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

// create selector for curve types
  var select = d3.select('#curveSettings')
    .append('select')
    .attr('class','select')
    .on('change', function() {
      var val = d3.select('select').property('value');
      d3.select('#curveLabel').text(val);
      valueline.curve(d3[val]);
      updateGroups();
    });
  var options = select
    .selectAll('option')
    .data(curveTypes).enter()
    .append('option')
      .text(function (d) { return d; });

// create groups, links and nodes
  groups = svg.append('g').attr('class', 'groups');

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); });

node = svg.append('g')
      .attr('class', 'nodes')
    .selectAll('circle')
    .data(graph.nodes)
    .enter().append('circle')
      .attr('r', 5)
      .attr('fill', function(d) { return color(d.group); })
      .call(d3.drag()
          .on('start', dragstarted)
          .on('drag', dragged)
          .on('end', dragended));

// count members of each group. Groups with less
  // than 3 member will not be considered (creating
  // a convex hull need 3 points at least)
  groupIds = d3.set(graph.nodes.map(function(n) { return +n.group; }))
    .values()
    .map( function(groupId) {
      return { 
        groupId : groupId,
        count : graph.nodes.filter(function(n) { return +n.group == groupId; }).length
      };
    })
    .filter( function(group) { return group.count > 2;})
    .map( function(group) { return group.groupId; });

paths = groups.selectAll('.path_placeholder')
    .data(groupIds, function(d) { return +d; })
    .enter()
    .append('g')
    .attr('class', 'path_placeholder')
    .append('path')
    .attr('stroke', function(d) { return color(d); })
    .attr('fill', function(d) { return color(d); })
    .attr('opacity', 0);

paths
    .transition()
    .duration(2000)
    .attr('opacity', 1);

// add interaction to the groups
  groups.selectAll('.path_placeholder')
    .call(d3.drag()
      .on('start', group_dragstarted)
      .on('drag', group_dragged)
      .on('end', group_dragended)
      );

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

simulation
      .nodes(graph.nodes)
      .on('tick', ticked)
      .force('link')
      .links(graph.links);

});

// select nodes of the group, retrieve its positions
// and return the convex hull of the specified points
// (3 points as minimum, otherwise returns null)
var polygonGenerator = function(groupId) {
  var node_coords = node
    .filter(function(d) { return d.group == groupId; })
    .data()
    .map(function(d) { return [d.x, d.y]; });
    
  return d3.polygonHull(node_coords);
};

function updateGroups() {
  groupIds.forEach(function(groupId) {
    var path = paths.filter(function(d) { return d == groupId;})
      .attr('transform', 'scale(1) translate(0,0)')
      .attr('d', function(d) {
        polygon = polygonGenerator(d);          
        centroid = d3.polygonCentroid(polygon);

// to scale the shape properly around its points:
        // move the 'g' element to the centroid point, translate
        // all the path around the center of the 'g' and then
        // we can scale the 'g' element properly
        return valueline(
          polygon.map(function(point) {
            return [  point[0] - centroid[0], point[1] - centroid[1] ];
          })
        );
      });

d3.select(path.node().parentNode).attr('transform', 'translate('  + centroid[0] + ',' + (centroid[1]) + ') scale(' + scaleFactor + ')');
  });
}

// drag nodes
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;
}

// drag groups
function group_dragstarted(groupId) {
  if (!d3.event.active) simulation.alphaTarget(0.3).restart();
  d3.select(this).select('path').style('stroke-width', 3);
}

function group_dragged(groupId) {
  node
    .filter(function(d) { return d.group == groupId; })
    .each(function(d) {
      d.x += d3.event.dx;
      d.y += d3.event.dy;
    })
}

function group_dragended(groupId) {
  if (!d3.event.active) simulation.alphaTarget(0.3).restart();
  d3.select(this).select('path').style('stroke-width', 1);
}

</script>

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