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// Create the input graph
var g = new dagreD3.graphlib.Graph({compound:true})
  .setGraph({})
  .setDefaultEdgeLabel(function() { return {}; });

// Here we're setting the nodes
g.setNode('a', {label: 'A'});
g.setNode('b', {label: 'B'});
g.setNode('c', {label: 'C'});
g.setNode('d', {label: 'D'});
g.setNode('e', {label: 'E'});
g.setNode('f', {label: 'F'});
g.setNode('g', {label: 'G'});
g.setNode('group', {label: 'Group', clusterLabelPos: 'top', style: 'fill: #ae9'});
g.setNode('top_group', {label: 'Top Group', clusterLabelPos: 'bottom', style: 'fill: #ffd47f'});
g.setNode('bottom_group', {label: 'Bottom Group', style: 'fill: #5f9488'});

// Set the parents to define which nodes belong to which cluster
g.setParent('top_group', 'group');
g.setParent('bottom_group', 'group');
g.setParent('b', 'top_group');
g.setParent('c', 'bottom_group');
g.setParent('d', 'bottom_group');
g.setParent('e', 'bottom_group');
g.setParent('f', 'bottom_group');

// Set up edges, no special attributes.
g.setEdge('a', 'b');
g.setEdge('b', 'c');
g.setEdge('b', 'd');
g.setEdge('b', 'e');
g.setEdge('b', 'f');
g.setEdge('b', 'g');

g.nodes().forEach(function(v) {
  var node = g.node(v);
  // Round the corners of the nodes
  node.rx = node.ry = 5;
});


// Create the renderer
var render = new dagreD3.render();

// Set up an SVG group so that we can translate the final graph.
var svg = d3.select("svg"),
    svgGroup = svg.append("g");

// Run the renderer. This is what draws the final graph.
render(d3.select("svg g"), g);

// Center the graph
var xCenterOffset = (svg.attr("width") - g.graph().width) / 2;
svgGroup.attr("transform", "translate(" + xCenterOffset + ", 20)");
svg.attr("height", g.graph().height + 40);

<h1>D3js graph Clusters</h1>
<svg id="svg-canvas" width=960 height=600></svg>

body {
  font-family: sans-serif;
  color: #444;
}
.clusters rect {
  fill: #00ffd0;
  stroke: #999;
  stroke-width: 1.5px;
}

text {
  font-weight: 300;
  font-family: "Helvetica Neue", Helvetica, Arial, sans-serf;
  font-size: 14px;
}

.node rect {
  stroke: #999;
  fill: #fff;
  stroke-width: 1.5px;
}

.edgePath path {
  stroke: #333;
  stroke-width: 1.5px;
}