Visualizing graph in Python using NetworkX

Question

I'm trying to visualize graph in NetworkX. I need to colorize the graph like this: center node needs to be colored dark. Then, all nodes that are further away will need to be colored lighter, but when i run the code i get this error :

error: Cannot convert argument type < class 'numpy.ndarray' > to rgba array on the line :

  nx.draw_networkx_nodes(G,pos,nodelist=p.keys(),node_size=90,
  node_color=p.values(),cmap=plt.cm.Reds_r)

I think the problem is in:

node_color=p.values()

The code is:

import numpy
import pandas
import networkx as nx
import unicodecsv as csv
import community
import matplotlib.pyplot as plt

# Generate the Graph
G=nx.davis_southern_women_graph()

# Create a Spring Layout
pos=nx.spring_layout(G)

# Find the center Node
dmin=1
ncenter=0
for n in pos:
   x,y=pos[n]
   d=(x-0.5)**2+(y-0.5)**2
   if d<dmin:
      ncenter=n
      dmin=d

""" returns a dictionary of nodes and their distance to the node 
supplied as an argument. We will then use these distances 
to determine colors"""
p=nx.single_source_shortest_path_length(G,ncenter)

plt.figure(figsize=(8,8))
nx.draw_networkx_edges(G,pos,nodelist=[ncenter],alpha=0.4)
nx.draw_networkx_nodes(G,pos,nodelist=p.keys(),node_size=90,
   node_color=p.values(),cmap=plt.cm.Reds_r)

plt.show()

Full Traceback

Traceback (most recent call last):

  File "<ipython-input-4-da1414ba5e14>", line 1, in <module>
   runfile('C:/Users/Desktop/Marvel/finding_key_players.py',        wdir='C:/Users/Desktop/Marvel')

  File "C:\Users\Anaconda33\lib\site-   packages\spyderlib\widgets\externalshell\sitecustomize.py", line 685, in runfile
   execfile(filename, namespace)

  File "C:\Users\Anaconda33\lib\site packages\spyderlib\widgets\externalshell\sitecustomize.py", line 85, in execfile
exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)

  File "C:/Users/Desktop/Marvel/finding_key_players.py", line 70, in
   <module>
      cmap=plt.cm.Reds_r)

  File "C:\Users\Anaconda33\lib\site-packages\networkx\drawing\nx_pylab.py", line 399, in draw_networkx_nodes
label=label)

  File "C:\Users\Anaconda33\lib\site-packages\matplotlib\axes\_axes.py", line 3606, in scatter
colors = mcolors.colorConverter.to_rgba_array(c, alpha)

  File "C:\Users\Anaconda33\lib\site-packages\matplotlib\colors.py",   line 391, in to_rgba_array
if alpha > 1 or alpha < 0:

ValueError: Cannot convert argument type <class 'numpy.ndarray'> to rgba array

Maybe you have a broken (or just older) version of either matplotlib or networkx? I have matplotlib-1.3.1 and networkx-1.11 and it works with those. — Aric
– Aric, Commented Feb 15, 2016 at 22:48
OK - to help you we'll need the full traceback with the error details. I believe your code is correct. It likely is a mismatch or problem with one of the libraries, likely matplotlib or numpy. — Aric
– Aric, Commented Feb 15, 2016 at 23:32
I put the whole traceback under the code. I thought the error is in matplotlib/colors.py, so i run over the original colors.py file with another, but obviously the previous file was OK too, because the error stays the same. Thank you for your help — D.Fig
– D.Fig, Commented Feb 16, 2016 at 13:18
Thanks for the traceback. I can see the error but I don't understand why it is getting triggered. Maybe someone else is familiar with this issue. It doesn't look like a networkx bug to me. — Aric
– Aric, Commented Feb 17, 2016 at 1:51

Abolfazl · Accepted Answer · 2017-08-27 09:38:04Z

1

The error is in the function for drawing nodes. p.keys()values must be put in a list for nodelist, and node_color, otherwise it's not working.

So the correct line is:

nx.draw_networkx_nodes(G,pos,nodelist=list(p.keys()),node_size=80,node_color=list(p.values()), cmap=plt.cm.Reds_r)
plt.axis('off')
plt.show()

edited Aug 27, 2017 at 9:38

Abolfazl

1,2372 gold badges16 silver badges36 bronze badges

answered Feb 29, 2016 at 20:15

D.Fig

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