[graph-tool] Building (and working with) bipartite graphs

Davide Cittaro cittaro.davide at gmail.com
Thu Jul 9 14:37:34 CEST 2020

I'm trying to build a bipartite graph from a MxN array. So far I've been able to do this:

# adjacency is the original np.array

S = []
E = []
W = []
for x in range(adjacency.shape[0]):
    for y in np.where(adjacency[x] > 0)[0]:
        E.append(y + adjacency.shape[0]) # so that node index starts with an offset)
        W.append(adjacency[x, y])

g = gt.Graph(directed=True)

g.add_edge_list(np.hstack([np.array(S)[:, None], np.array(E)[:, None]]))

ew = g.new_edge_property("double")
ew.a = W
g.ep['weight'] = ew

recs = [g.ep.weight]
rec_types = ['real-exponential']

state = gt.NestedBlockState(g, state_args=dict(recs=recs,


I'm pretty sure this is not the most efficient way to go, but gt.is_bipartite(g) returns True. Can anybody suggest a more straightforward approach? Also, is it necessary to specify a VertexPropertyMap with node type (i.e. M or N)?
Anyhow, after I had the graph and the final model, I tried to draw:

gt.draw_hierarchy(state, layout='bipartite')

but I get this error

                                Traceback (most recent call last)

<ipython-input-67-d7655416181e> in <module>
----> 1 gt.draw_hierarchy(state, layout='bipartite')

~/anaconda3/envs/schist/lib/python3.8/site-packages/graph_tool/draw/cairo_draw.py in draw_hierarchy(state, pos, layout, beta, node_weight, vprops, eprops, hvprops, heprops, subsample_edges, rel_order, deg_size, vsize_scale, hsize_scale, hshortcuts, hide, bip_aspect, empty_branches, **kwargs)

   1774     elif layout == "bipartite":
-> 1775
         tpos = get_bip_hierachy_pos(state, aspect=bip_aspect,


   1777         tpos = t.own_property(tpos)

~/anaconda3/envs/schist/lib/python3.8/site-packages/graph_tool/draw/cairo_draw.py in get_bip_hierachy_pos(state, aspect, node_weight)
   2145         t.add_edge(root, p2)
   2146         for p in ps:
-> 2147             if bc.a[tb[p]] == 0:
   2148                 t.add_edge(p2, p)
   2149             else:

: index 1 is out of bounds for axis 0 with size 1

Any help is appreciated


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