clusterplot.py

#!/usr/bin/env python
# GistID: 3148850
import json
import fileinput
from igraph import Graph
from itertools import permutations
from optparse import OptionParser
from ndd.graphs import PGraph, partition_graph


def _partition(n, edges, weights):
    edgemap = dict(zip(edges, weights))
    pg = PGraph()
    pg.nodes = range(n)
    pg.edges = [(b1, b2, w) for (b1, b2), w in edgemap.iteritems()]

    partitions = partition_graph(pg)

    pedges = set(e for p in partitions for e in permutations(p, 2) if e in set(edges))

    pig = Graph(n)
    pig.add_edges(edges)
    pig.es['weight'] = weights
    pig.es['color'] = ['black' if e in pedges else 'white' for e in edges]
    return pig


def readjlist(fo):
    row = (json.loads(line) for line in fo)
    for _, nodes, scorededges in row:
        nodemap = dict((n, x) for x, n in enumerate(nodes))
        edges = []
        weights = []
        for n1, n2, score in scorededges:
            edges.append((nodemap[n1], nodemap[n2]))
            weights.append(score)

        cid = min(nodes)
        n = len(nodes)
        ig = Graph(n)
        ig.add_edges(edges)
        ig.es['weight'] = weights
        ig.es['label'] = ['%s-%s' % tuple(e) for e in edges]
        # partitioned graph
        pig = _partition(n, edges, weights)
        yield cid, ig, pig


def main():
    op = OptionParser()
    op.add_option('--layout', default='lgl')
    opts, args = op.parse_args()

    fo = fileinput.input(args)
    for cid, ig, pig in readjlist(fo):
        print '\n#### Cluster'
        print ig.summary()
        print '\n#### Partitioned'
        print pig.summary()
        ig.save(cid + '.svg', layout=opts.layout, format='svg',
                width=800, height=600, font_size=7)
        pig.save(cid + '-parted.svg', layout=opts.layout, format='svg',
                width=800, height=600, font_size=7)


if __name__ == '__main__':
    main()

example run:

$ head -n1 pcsample.jl |python clusterplot.py 

#### Cluster
10 nodes, 17 edges, undirected

Number of components: 1
Diameter: 4
Density: 0.3778
Average path length: 2.0889

#### Partitioned
10 nodes, 12 edges, undirected

Number of components: 3
Diameter: 1
Density: 0.2667
Average path length: 1.0000