Clustering in Gephi 0.8.2
I'm working with a dataset in Gephi that is derived from a friends table from a Buddypress site. I've done a number of things to the graph which are useful using the built in functionality, but would be interested in a better clustering algorithm than what's included (I'm using Force Atlas 2 to arrange the nodes). For instance, I'd like to use my modularity property to group nodes into clusters. I tried downloading two plugins (Girvan Newman and a Markov clustering algorithm), but can't figure out how to apply them to my graph. They show up in the "clustering" window on the workflow, but when I select them the "Run" button is grayed out. They also don't show up in the "plugin" drop down on the main UI. Any ideas?
Answer
This is a bit tricky. The Girvan-Newman is also greying out for me but after some Gephi restarts, I managed to get it work. I think the best think to do is to close Gephi and then open your .gephi file from the filesystem, with the Gephi still closed.
If you cannot run the algorithm then try to compute from the Statistics, the graph Modularity which applies the Louvain community detection method to your graph. After modularity or Girvan-Newman run, they assign each node a cluster number which is the cluster they belong to
You can then color the graph to indicate the various different partitions with separate colors. This is done through the Partition window in Gephi.
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You can then run Force Atlas 2 to layout the clusters accordingly.