Efficiently create adjacency matrix from network graph (vice versa) Python NetworkX

Question

I'm trying to get into creating network graphs and generating sparse matrices from them. From the wikipedia Laplacian matrix example, I decided to try and recreate the following network graph using networkx

How can one EFFICIENTLY convert between an adjacency matrix and a network graph?

For example, if I have a network graph, how can I quickly convert it to an adjacency matrix and if I have an adjacency graph how can I efficiently convert it to a network graph.

Below is my code for doing it and I feel like it's pretty inefficient for larger networks.

#!/usr/bin/python

import networkx as nx
import numpy as np
import matplotlib.pyplot as plt
import scipy as sp
import pandas as pd

%matplotlib inline

#Adjacent matrix
adj_matrix = np.matrix([[0,1,0,0,1,0],[1,0,1,0,1,0],[0,1,0,1,0,0],[0,0,1,0,1,1],[1,1,0,1,0,0],[0,0,0,1,0,0]])
adj_sparse = sp.sparse.coo_matrix(adj_matrix, dtype=np.int8)
labels = range(1,7)
DF_adj = pd.DataFrame(adj_sparse.toarray(),index=labels,columns=labels)
print DF_adj

#   1  2  3  4  5  6
#1  0  1  0  0  1  0
#2  1  0  1  0  1  0
#3  0  1  0  1  0  0
#4  0  0  1  0  1  1
#5  1  1  0  1  0  0
#6  0  0  0  1  0  0

#Network graph
G = nx.Graph()
G.add_nodes_from(labels)

#Connect nodes
for i in range(DF_adj.shape[0]):
    col_label = DF_adj.columns[i]
    for j in range(DF_adj.shape[1]):
        row_label = DF_adj.index[j]
        node = DF_adj.iloc[i,j]
        if node == 1:
            G.add_edge(col_label,row_label)


#Draw graph
nx.draw(G,with_labels = True)

#DRAWN GRAPH MATCHES THE GRAPH FROM WIKI

#Recreate adjacency matrix
DF_re = pd.DataFrame(np.zeros([len(G.nodes()),len(G.nodes())]),index=G.nodes(),columns=G.nodes())
for col_label,row_label in G.edges():
    DF_re.loc[col_label,row_label] = 1
    DF_re.loc[row_label,col_label] = 1
print G.edges()
#[(1, 2), (1, 5), (2, 3), (2, 5), (3, 4), (4, 5), (4, 6)]

print DF_re
#   1  2  3  4  5  6
#1  0  1  0  0  1  0
#2  1  0  1  0  1  0
#3  0  1  0  1  0  0
#4  0  0  1  0  1  1
#5  1  1  0  1  0  0
#6  0  0  0  1  0  0

Answer 1

How to convert from graph to adjacency matrix:

import scipy as sp
import networkx as nx
G=nx.fast_gnp_random_graph(100,0.04)
adj_matrix = nx.adjacency_matrix(G)

Here's the documentation.

And from adjacency matrix to graph:

H=nx.Graph(adj_matrix)  #if it's directed, use H=nx.DiGraph(adj_matrix)

Here's the documentation.

Answer 2

I was confronted with the same problem, and found a solution. We can use the function from_numpy_matrix, which is depicted in official website http://networkx.github.io/documentation/networkx-1.7/reference/generated/networkx.convert.from_numpy_matrix.html. Pay attention that the input data usually needs to be modified by numpy.matrix(). The example given is that:

    import numpy
    A=numpy.matrix([[1,1],[2,1]])
    G=nx.from_numpy_matrix(A)

It's really useful.