With WGCNA_stage6.R you can generate edge- and node-files for Cytoscape. Nodes represent individual gene-expression profiles, while edges are the weighted connections between those expression profiles. Using the module specific edge- and node-files allows for depiction of individual module with Cytoscape.

Prepare WGCNA_stage6.R script

Setup your working directory and decide on the threshold of connectivity strength you want to filter out. By default "adj_threshold = 0.05" will remove all "edges" (connections) that have an adjacency value of < 0.05. Remember that the adjacency is a value between 0 and 1, and represents the strength of a connection between two nodes (gene-expression profiles). Remember that if you created the recommended "unsigned" network, positive- and negative-correlated expression profiles are connected. Therefore, the more weak connections you filter out, the more likely it is to observe interactions between genes that are biologically meaningful.

Output

In your "Data" directory a directory called "cytoscape" has been generated. In the "cytoscape" directory you will find an edge- and a node-file for each of the modules in your network.