graph-tool

Very briefly, two-three basic questions about the minimize_nested_blockmodel_dl function in graph-tool library . Is there a way to figure out which vertex falls onto which block? In other words, to extract a list from each block, containing the labels of its vertices. The hierarchical visualization is rather difficult to understand for amateurs in network theory, e.g. are the squares with directed edges that are drawn meant to implicate the main direction of the underlying edges between two blocks under consideration? The blocks are nicely shown using different colors, but on a very conceptual

How should I create a graph using graph-tool in python, out of an adjacency matrix? Assume we have adj matrix as the adjacency matrix. What I do now is like this: g = graph_tool.Graph(directed = False) g.add_vertex(len(adj)) edge_weights = g.new_edge_property('double') for i in range(adj.shape[0]): for j in range(adj.shape[1]): if i > j and adj[i,j] != 0: e = g.add_edge(i, j) edge_weights[e] = adj[i,j] But it doesn't feel right, do we have any better solution for this? (and I guess a proper tag for this would be graph-tool , but I can't add it, some kind person with enough privileges could

Can anyone recommend a Python library that can do interactive graph visualization? I specifically want something like d3.js but for python and ideally it would be 3D as well. I have looked at: NetworkX - it only does Matplotlib plots and those seem to be 2D. I didn't see any sort of interactiveness, like one that d3.js gives, such as pulling nodes around. graph-tool - it does only 2D plots and has very slow interactive graphs. Vincent Agnus You could use d3py a python module that generate xml pages embedding d3.js script. For example : import d3py import networkx as nx import logging logging

I am using Python 2.7 and am trying to import graph_tool, and it seems that my libboost_thread-mt.dylib is located in /opt/local/lib rather than /usr/local/lib. If I start an X11 terminal and type in export DYLD_LIBRARY_PATH='/opt/local/lib' then Python successfully imports graph_tool. On the other hand, if I add export DYLD_LIBRARY_PATH='/opt/local/lib':$DYLD_LIBRARY_PATH to ~/.bash_profile , X11 stops working. I am really confused as to what is happening here. Why can't I add /opt/local/lib to $DYLD_LIBRARY_PATH permanently without destroying my computer? Any help is much appreciated. Thanks

After looking at the impressive performance comparison , I decided that I would give a try to graph-tool. So for comparison, I wrote codes to generate a random tree using both packages. The graph-tool code: import numpy as np import graph_tool.all as gt # construct an initial graph with two nodes and one link n = 5000 G = gt.Graph(directed = False) G.add_edge(0, 1) for t in range(2, n): # connect the new vertex to one of the old vertices randomly G.add_edge(np.random.choice(range(t)), t) The Networkx code: import networkx as nx import numpy as np n = 5000 # initial graph G = nx.Graph() G.add