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I'm trying to represent some numbers as edges of a graph with connected components. For this, I've been using python's networkX module.
My graph is G, and has nodes and edges initialised as follows: 

    G = nx.Graph()
    for (x,y) in my_set:
       G.add_edge(x,y)

    print G.nodes() #This prints all the nodes
    print G.edges() #Prints all the edges as tuples
    adj_matrix = nx.to_numpy_matrix(G)

Once I add the following line,

    pos = nx.spring_layout(adj_matrix)

I get the abovementioned error. If it might be useful, all the nodes are numbered in 9-15 digits. There are 412 nodes and 422 edges.

Detailed error:

      File "pyjson.py", line 89, in <module>
      mainevent()        
      File "pyjson.py", line 60, in mainevent
      pos = nx.spring_layout(adj_matrix)
      File "/usr/local/lib/python2.7/dist-packages/networkx/drawing/layout.py", line 244, in fruchterman_reingold_layout
      A=nx.to_numpy_matrix(G,weight=weight)
      File "/usr/local/lib/python2.7/dist-packages/networkx/convert_matrix.py", line 128, in to_numpy_matrix
      nodelist = G.nodes()
      AttributeError: 'matrix' object has no attribute 'nodes'

Edit: Solved below. Useful information: pos creates a dict with coordinates for each node. Doing nx.draw(G,pos) creates a pylab figure. But it doesn't display it, because pylab doesn't display automatically.

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  • Unclear what you're trying here spring_layout takes a graph as the first param, not a matrix array Commented May 18, 2015 at 18:43
  • @EdChum: I didn't know that, thank you. How do I actually get the drawing to appear? nx.draw(G) doesn't throw any errors but it doesn't appear either. Commented May 18, 2015 at 18:53
  • sprint_layout returns the node positions, you need to pass this to nx.draw so nx.draw(G, nx.spring_layout(G)) would work, I can post an example Commented May 18, 2015 at 18:56

2 Answers 2

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(some of this answer addresses some things in your comments. Can you add those to your question so that later users get some more context)

pos creates a dict with coordinates for each node. Doing nx.draw(G,pos) creates a pylab figure. But it doesn't display it, because pylab doesn't display automatically.

import networkx as nx
import pylab as py

G = nx.Graph()
for (x,y) in my_set:
   G.add_edge(x,y)

print G.nodes() #This prints all the nodes
print G.edges() #Prints all the edges as tuples
pos = nx.spring_layout(G)
nx.draw(G,pos)
py.show() # or py.savefig('graph.pdf') if you want to create a pdf, 
          # similarly for png or other file types

The final py.show() will display it. py.savefig('filename.extension') will save as any of a number of filetypes based on what you use for extension.

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Comments

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spring_layout takes a network graph as it's first param and not a numpy array. What it returns are the positions of the nodes according to the Fruchterman-Reingold force-directed algorithm.

So you need to pass this to draw example:

import networkx as nx
%matplotlib inline
G=nx.lollipop_graph(14, 3)
nx.draw(G,nx.spring_layout(G))

yields:

enter image description here

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2 Comments

I tried this, do I need to include the nx.lollipop_graph part? My program doesn't actually display the graph with this though no errors are thrown. Edit: Got it once I added a show
the lollipop graph was just a graph generator, I don't know what graph you're trying to construct but I thought this would demonstrate how it works and how it is displayed. If my answer fully resolved your question then please accept it, there will be an empty tick mark at the top left of the answer, thanks

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