python-3.xnetworkxgephi

Store networkx graph with location and weight attributes for Gephi visualization

Given a dataset X and an weight matrix W a networkx graph G is given by

G = nx.Graph(W.todense())
pos = {i: list(p) for i, p in enumerate(X)}
nx.set_node_attributes(G, pos, 'pos')

The graph G has the following structure: enter image description here

Can we store the graph G with the attributes weight and node position in such way to load G in Gephi and visualize the graph using these attributes?

Thank you in advance.

Solution

  • You have already defined nodes' attributes, so you just need to save it as a file which is acceptable in Gephi by below code:

    nx.write_gexf(
G,
path,
encoding='utf-8',
prettyprint=True)

    BTW, later on, you can assign any attribute to nodes or edges in .csv format and read and add them to your current graph in Gephi (this could be another option)