graphing.py 文件源码

def visualize_frags(outdir, graphs, options):
    from rpy2.robjects import r

    utilities.ensure_dir(outdir)

    for i, graph in enumerate(graphs):
        r.pdf(os.path.join(outdir, "fragments.cluster_{}.pdf".format(i)))

        for component in networkx.connected_components(graph):
            subgraph = graph.subgraph(component)

            ends = [node for node,degree in subgraph.degree_iter() if degree==1]
            breakends = [node for node in list(networkx.shortest_simple_paths(subgraph, ends[0], ends[1]))[0]]
            # breakends = [breakend_from_label(node) for node in breakends]
            breakends = breakends[:-1:2] + breakends[-1:]
            # print ")"*100, breakends

            for sample, dataset in sorted(options.iter_10xdatasets()):
                plot_frags(breakends, options, sample, dataset)
        # plot_frags(breakpoints, options, sample, dataset)
        r["dev.off"]()