I am using GeneNet (R-package) to reconstruct a genetic network from time-series data. Does anyone have an idea if it limits the number of genes (nodes) that can be visualized in a graph (using "igraph") as an output? i.e. can I visualize up to 3000 genes e.g. in a single network, assuming they all turn out to be associated with each other?
I don't think they have any hard limits on the number of edges or nodes. I use it for the Mycobacterium tuberculosis, and it works fine with over a thousand nodes. If you happen to get an error trying to simulate a large network, maybe we can check the code for GeneNet::ggm.test.edges() and see if there is anything there causing the problem. Have you run into any difficulty running a large net?
Thanks Daniel: I just noticed indeed everything does run fine now, except that it only visualizes the first ~100 genes and the rest of the nodes are somewhere hidden in the background of the network with all the dense connections. Perhaps I can try using something like Cystoscape to have a more close look at the structural or topolgical configuration of hubs etc.
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