Cytoscape Input

[zebasilio]

I think it would be a plus if the output of MONET would be compatible with cytoscape input. In this way we could better visualize the network modules.
Thank you.
Best Regards, José

[mattiat]

This is a very interesting suggestion.
Thank you, José

TODO:
http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html

[sergio-gomez]

Since the output of the three methods is homogenized, a common conversion script to all of them could be added to MONET, and even executed at the end of each method. However, which one is a compatible format for cytoscape? The link before was about networks, not partitions. Do we have to annotate the network with the partition? It seems an inefficient solution.

[mattiat]

I imagined we would create a cystoscope network for each partition outputted by MONET - each partition would be visualized separately. This should not be hard?

[sergio-gomez]

Please prepare an example of the desired output for a small network (e.g. 10 nodes) and the corresponding partition, I'm not familiar with cytoscape (and indicate the differences in format between directed and undirected networks).

Should be easy, but I hope not to repeat the work three times. Each method has a script file to which we could add the call to make the conversion, e.g. with a python function, and triggered by a command-line option to decide whether to make the conversion or not.