How to store a networkx graph for visualizing in Gephi?

Question

I am working on a pagerank algorithm using Networkx module in Python. I have a dictionary of lists, where key of the dictionary is the Title of the page and its value is all the Titles referenced through that page.

So in order to create a visualization, I first did this:

G = nx.DiGraph()
G = nx.from_dict_of_lists(ref_dict)

where ref_dict is the dictionary mentioned above.

After creating the graph, I am using Networkx's write_edgelist function to store the Graph in the csv format.

nx.write_edgelist(subG,'PageRanks2.csv')

Herein lies my problem. The csv file is storing edges as:

node1 node2 {} node1 node3 {}

When I am using this file directly in Gephi, it treats the {} as a node and shows visualization accordingly. So what should be the best format to store the networkx graph to visualize it?

Answer 1

Use write_gexf function like: nx.write_gexf(G, "test.gexf"), and open the file using Gephi, then you'll see it.

Reference https://networkx.github.io/documentation/networkx-1.10/reference/generated/networkx.readwrite.gexf.write_gexf.html#write-gexf

Answer 2

You can specify data argument to tell networkx not to add {}:

nx.write_edgelist(subG,'PageRanks2.csv', data=False)

There are other formats which both networkx and gephy support (e.g. GraphML), and you can accomplish much more complex data visualization tasks if your data has attributes associated with it.