How to create Gephi network graphs from Python?

Question

I have just found out about GephiStreamer. https://pypi.python.org/pypi/GephiStreamer

Using this package one can send instructions from python to Gephi to create nodes and edges in Gephi.

# Create a node with a custom_property
node_a = graph.Node("A",custom_property=1)

# Create edge 
edge_ab = graph.Edge(node_a,node_b,custom_property="hello")
stream.add_edge(edge_ab)

Similarly I want to do everything in Gephi through Python. Here is what I typically do.

ex:

steps:

1. load nodes

2. load edges

3. calculate betweeness centrality

4. change the size/color of nodes as per their centrality scores

5. change the graph layout (such as forceatlas2)

6. give the output graph

Below is the output I have got manually, but I want to produce the same by sending instructions from python to Gephi. Documentation doesn't tell anything beyond creating nodes, edges and graphs.

I have also found out about NetworKit. https://networkit.iti.kit.edu/data/uploads/docs/NetworKit-Doc/python/html/gephi.html

This is slightly better than gephistramer, but this requires python 3.4 or higher and most of the packages like pandas, numpy or sickit are in 2.7.

also Is there a way to send the file I have created in gephi back to python.

Please suggest.

PS: I have edited the entire question details so that it's easier to understand now (hopefully).

Answer 1

I found this question while looking for the answer myself. I picked Gephi as my visualizer and then wanted to build a graph that was well supported by the tool by pulling data from around my org with Python.

I found GephiStreamer and it looks a simple yet comprehensive way to build graphs in Gephi from an external python environment (command line, or IDE)

The other options at this point are:

• The Gephi Python Scripting Console
• Any Graph Lib that can export in a Gephi readable format
  • NetworkX
  • python-igraph
  • graph-tool
• Any of the python GEFX writers (Google "python GEFX")

Answer 2

There is no simple answer to that. The people at the Facebook group might be knowing something but IMO the best way to do it would be to call the Gephi toolkit , ie the available jar, from jython, check here for an example use. The thing is that jython doesn't allow to install numpy and a series of other libraries but I guess you could get around this issue by piping the output of one script to the other or using a queue like Celery.

So I would write a script let's call it graph_construction.py that uses networkx, construct the graph and then write it in the standard output in gexf. Then I would write a second script, gephi.py that would execute things in gephi and let's say write the graph to a pdf and then do something like:

python graph_construction.py | jython gephi.py output.pdf

and pray for it to work.