Construct NetworkX graph from Pandas DataFrame

Question

I\'d like to create some NetworkX graphs from a simple Pandas DataFrame:

        Loc 1   Loc 2   Loc 3   Loc 4   Loc 5   Loc 6   Loc 7
Foo     0       0              


        

Answer 1

You can also use scipy to create the square matrix like this:

import scipy.sparse as sp

cols = df.columns
X = sp.csr_matrix(df.astype(int).values)
Xc = X.T * X  # multiply sparse matrix
Xc.setdiag(0)  # reset diagonal

# create dataframe from co-occurence matrix in dense format
df = pd.DataFrame(Xc.todense(), index=cols, columns=cols)

Later on you can create an edge list from the dataframe and import it into Networkx:

df = df.stack().reset_index()
df.columns = ['source', 'target', 'weight']

df = df[df['weight'] != 0]  # remove non-connected nodes

g = nx.from_pandas_edgelist(df, 'source', 'target', ['weight'])