Creating Network Visualizations

  • Network visualizations are a method of finding patterns in large datasets.
  • It can be used to define natural groups of objects.

Protein Simulation Example

  • I have a long simulation of a protein molecule.
  • There are 1000 snapshots with (x, y, z) coordinates of the atoms in the protein.
  • Define the deviation between two snapshots as the root mean squared deviations of the atoms between the snapshots.
  • Define a cutoff distance.
  • Each snapshot is a node on a network.
  • Two nodes are connected if the distance between them is less than the cutoff.
  • This network is then processed to generate a visual representation.

Using a cutoff of 5.


Using a cutoff of 8.

Using Tulip to Generate Network Visualizations

from tulip import tlp

def generate_svg(distances, cutoff, output, alg="GEM (Frick)", fillcolors=None):
    nodenumbers = range(0, len(distances))
    # Create the network in tulip (add nodes and edges).
    graph = tlp.newGraph()
    graphnodes = [graph.addNode() for n in nodenumbers]
    for i, j in itertools.product(nodenumbers, nodenumbers) if i > j:
        if distances[i][j] <= cutoff:
            graph.addEdge(graphnodes[i], graphnodes[j])
    # Use tulip to do a force directed layout.
    dataSet = tlp.getDefaultPluginParameters(alg, graph)
    viewlayout = graph.getLayoutProperty("viewLayout")
    graph.computeLayoutProperty(alg, viewlayout, dataSet)
    # Generate and write svgs
    svgtext = svg_from_graph(graph, fillcolors, viewlayout)
    svgfile = open(output, "w")

linetempl = '<line x1="{x1}" y1="{y1}" x2="{x2}" y2="{y2}" style="stroke:black;stroke-width:2"/>'
circltempl = '<circle cx="{cx}" cy="{cy}" r="{r}" stroke="black" stroke-width="2" fill="{fillcolor}" />'
svg_header = '<svg xmlns="" version="1.1">'
svg_footer = '</svg>'
display_r = 10

def svg_from_graph(graph, fillcolors, viewlayout):
    svgoutput = []
    nodes = list(graph.getNodes())
    for node in nodes:
        cx, cy = viewlayout[node]
        for node2 in graph.getOutNodes(node):
            x2, y2 = viewlayout[node2]
            svgoutput.append(linetempl.format(x1=cx, y1=cy, x2=x2, y2=y2))
    if fillcolors is None:
        fillcolors = [default_fillcolor,] * len(nodes)
    for fillcolor, node in zip(fillcolors, nodes):
        cx, cy = viewlayout[node]
        svgoutput.append(circltempl.format(cx=cx, cy=cy, r=display_r, fillcolor=fillcolor))
    svgtext = '\n'.join(svgoutput)
    return svgtext