I want to build a network based on correlation analysis from taxonomic and functional profiles of soil metagenomes (obtained form MG-RAST) by using Gephi. However, I am unable to figure out how to input data to Gephi, can any one help me out with this?
Dear Binu,
Gephi accepts a series of standard graph file formats as input; personally, I have had best experiences with *.graphml files which can be annotated with rich metadata. However, Gephi is essentially a network visualization tool, it will not get you very far when it comes to *analyzing* networks. Generally, you will have to pre-compute and -process your networks using another framework before exporting them to Gephi for visualization. The igraph project (attached link) may be a good starting point for this; it has implementations/libraries/packages for different environments, including R. Once you have generated a graph from correlation / association matrices (or other input data), you can annotate it with metadata and then export it for visualization or further exploration in Gephi.
Best,
Sebastian
http://igraph.org/redirect.html
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