Visulalized clusters of CRAN packeges dependency network. Genereted by cytoscape 3.0.2 MCODE plugin.

README.md

Visulalized clusters of CRAN packeges dependency network (20130927 only connected nodes).

clusterM.json

{"directed": false, "graph": [],
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{"id": "MonetDB.R", "weight": 1.0},
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{"id": "RcmdrPlugin.EZR", "weight": 1.0},
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{"id": "MALDIquant", "weight": 1.0},
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{"id": "chron", "weight": 1.0},
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{"id": "cubature", "weight": 1.0},
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"multigraph": false}

index.html

<!DOCTYPE html>
<meta charset="utf-8">
<script src="http://d3js.org/d3.v2.min.js?2.9.3"></script>
<style>

.link {
  stroke: #aaa;
}

.node text {
  fill: #333;
  pointer-events: none;
  font: 10px sans-serif;
}

body {
  fill: #fff;
}

</style>
<body>
<script>

var width = 960,
    height = 500,
    nodes, _nodes,
    links, _links;

var color = d3.scale.category20();

var svg = d3.select("body").append("svg")
    .attr("width", width)
    .attr("height", height)
  .append("svg:g")
    .call(d3.behavior.zoom().on("zoom", redraw))
  .append("svg:g");

svg.append('svg:rect')
    .attr('x', -100000)
    .attr('y', -100000)
    .attr('width', 200000)
    .attr('height', 200000);

function redraw() {
  svg.attr("transform",
      "translate(" + d3.event.translate + ")"
      + " scale(" + d3.event.scale + ")");
}

var force = d3.layout.force()
    .gravity(.05)
    .distance(100)
    .charge(-100)
    .size([width, height]);

d3.json("clusterM.json", function(json) {
  nodes = json.nodes;
  links = json.links;
  update();
});

function update() {
  force
      .nodes(nodes)
      .links(links)
      .linkDistance(function(d) { return d.coauthor ? 10 : 50; })
      // .charge(function(d) { return -Math.sqrt(d.weight)*10; })
      // .gravity(function(d) { return Math.sqrt(d.weight)/100; })
      .start();

  var link = svg.selectAll(".link")
      .data(links)
    .enter().append("line")
      .attr("class", "link")
      .style("stroke", function(d) { return d.coauthor ? "#f77" : "#ccc"; })
      .style("stroke-width", function(d) { return Math.sqrt(d.weight); });

  var node = svg.selectAll(".node")
      .data(nodes)
    .enter().append("g")
      .attr("class", "node")
      .on("click", click)
      .call(force.drag);

  node.append("circle")
    // .attr("r", 4)
    .attr("r", function(d) { return Math.sqrt(d.weight) * 5; })
    .style("fill", function(d) { return color(d.group); });

  node.append("text")
      .attr("dx", 12)
      .attr("dy", ".35em")
      .text(function(d) { return d.id });

  force.on("tick", function() {
    link.attr("x1", function(d) { return d.source.x; })
        .attr("y1", function(d) { return d.source.y; })
        .attr("x2", function(d) { return d.target.x; })
        .attr("y2", function(d) { return d.target.y; });

    node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
  });
}

function click(d) {
}

</script>
</body>
</html>