Hello, I’ve been looking for ways to visualize interactions between taxa and function from DNA and RNA seq data using networks and discovered mixOmics! When I export the network as suggested elsewhere using write.graph (network$gR) and input this output into Cytoscape I get a nice network. mixOmics, though, shows the positive and negative correlation in the network, but this is something I’m not sure how to export to visualize in Cytoscape since I cannot seem to locate the correlation values in the network$gR output. Hope this makes sense!
If you type
?network
You will find the following as output:
Value
network return a list containing the following components:
M |
the correlation matrix used by network. |
|---|---|
gR |
a graph object to save the graph for cytoscape use (requires to load the igraph package). |
So have a look at the M output.
Kim-Anh