Plot NetworkX Graph from Adjacency Matrix in CSV file

I made a small csv called mycsv.csv that has the following:

,a,b,c,d
a,0,1,0,1
b,1,0,1,0
c,0,1,0,1
d,1,0,1,0

You don’t have a ‘,’ as the first character on the first row, but instead you have a space, so if this is an error on my part let me know. The general idea will be the same. Read in the csv as such:

from numpy import genfromtxt
import numpy as np
mydata = genfromtxt('mycsv.csv', delimiter=",")
print(mydata)
print(type(mydata))

This prints:

[[ nan  nan  nan  nan  nan]
 [ nan   0.   1.   0.   1.]
 [ nan   1.   0.   1.   0.]
 [ nan   0.   1.   0.   1.]
 [ nan   1.   0.   1.   0.]]
<type 'numpy.ndarray'>

Now that we have the csv read in as a numpy array we need to extract just the adjacency matrix:

adjacency = mydata[1:,1:]
print(adjacency)

This prints:

[[ 0.  1.  0.  1.]
 [ 1.  0.  1.  0.]
 [ 0.  1.  0.  1.]
 [ 1.  0.  1.  0.]]

You can just slice your numpy array as needed if my small example isn’t exactly as yours.

To plot the graph you will need to import matplotlib and networkx:

import matplotlib.pyplot as plt
import networkx as nx

def show_graph_with_labels(adjacency_matrix, mylabels):
    rows, cols = np.where(adjacency_matrix == 1)
    edges = zip(rows.tolist(), cols.tolist())
    gr = nx.Graph()
    gr.add_edges_from(edges)
    nx.draw(gr, node_size=500, labels=mylabels, with_labels=True)
    plt.show()

show_graph_with_labels(adjacency, make_label_dict(get_labels('mycsv.csv')))

Here’s a short tutorial on graphs with python.