Viewing Subgraph in Networkx

[Subhabrata Banerjee]

Dear Group,

I have two questions, if I take a subseries of the matrix as in eigenvalue here,
provided I have one graph of the full form in G, how may I show it, as if I do the nx.draw(G) it takes only the original graph.

>>> import numpy
>>> import networkx as nx
>>> import matplotlib.pyplot as plt
>>> G=nx.Graph()
>>> G.add_edges_from([(1,2),(1,3),(1,3),(1,4),(1,5),(1,6),(1,7),(1,8)])
>>> L =nx.laplacian(G)
>>> print L
[[ 7. -1. -1. -1. -1. -1. -1. -1.]
 [-1.  1.  0.  0.  0.  0.  0.  0.]
 [-1.  0.  1.  0.  0.  0.  0.  0.]
 [-1.  0.  0.  1.  0.  0.  0.  0.]
 [-1.  0.  0.  0.  1.  0.  0.  0.]
 [-1.  0.  0.  0.  0.  1.  0.  0.]
 [-1.  0.  0.  0.  0.  0.  1.  0.]
 [-1.  0.  0.  0.  0.  0.  0.  1.]]
>>> print numpy.linalg.eigvals(L)
[  8.00000000e+00   2.22044605e-16   1.00000000e+00   1.00000000e+00
   1.00000000e+00   1.00000000e+00   1.00000000e+00   1.00000000e+00]

for more than 1000 nodes it is coming too slow on Windows 7 machine with 3GB RAM.

If any one of the learned members can help.

Apology for any indentation error etc.

Thanking all in Advance,

Regards,
Subhabrata Banerjee.

[Aric Hagberg]

If you don't need all of the eigenvalues you can try the scipy sparse
eigenvalue solver
http://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.linalg.eigsh.html
instead of the numpy.linalg.eigvals() solver.

Aric

[Subhabrata Banerjee]

Thanks Aric. But Scipy does not seem to have sparse.
>>> vals, vecs = sp.sparse.linalg.eigsh(id, k=6)

Traceback (most recent call last):
  File "<pyshell#3>", line 1, in <module>
    vals, vecs = sp.sparse.linalg.eigsh(id, k=6)
AttributeError: 'module' object has no attribute 'sparse'
>>>

And my question was not the values but I wanted to view in plotting graph as we can see it in nx.subgraph(

Regards,
Subhabrata Banerjee.

--
You received this message because you are subscribed to the Google Groups "networkx-discuss" group.

To post to this group, send email to networkx...@googlegroups.com.
To unsubscribe from this group, send email to networkx-discu...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/networkx-discuss?hl=en.

--

Sree Subhabrata Banerjee

PDF(2007-2010)[IISc, Bangalore]

Call:09873237945

Member, IEEE(USA), ACM(USA).

 

[Aric Hagberg]

On Sun, Jan 13, 2013 at 1:51 PM, Subhabrata Banerjee
<subhaba...@gmail.com> wrote:
>
>>>>


Maybe your scipy installation isn't complete?


In [1]: from scipy.sparse import linalg

In [2]: linalg.e
linalg.eigen linalg.eigs linalg.eigsh

In [2]: linalg.eigsh?


Can you be more specific about your drawing question?

Aric

[Subhabrata Banerjee]

Hi Eric,
This is fine.
>>> linalg.eigsh
<function eigsh at 0x038E3BB0>

My drawing question is,
Suppose I have a graph like,
>>> g = nx.DiGraph()
>>> g.add_path(['A','B','C',])
>>> g.add_path(['X','Y','Z',])

I can draw it and see the plotting(provided I imported "import matplotlib.pyplot as plt")
with,
>>> nx.draw(g)
>>> plt.show()

and I can also see the
>>> u = g.to_undirected()
>>> nodes = nx.shortest_path(u,'B').keys()
>>> s = g.subgraph(nodes)
>>> s = g.subgraph(nx.shortest_path(g.to_undirected(),'B'))
>>> nx.draw(s)
>>>plt.show()

In the same way, I like to see the drawing and plotting of numpy.linalg.eigvals(L) which is a subset of L as a subgraph,
that is to say first my graph -G is drawn and then my subgraph is drawn. Getting values I am facing no problem. Numpy is going fine.

Regards,
Subhabrata Banerjee.