I have used the Pearson correlation method to infer a network of interacting genes from microarray data. And ultimately, I would like to study this network with 'WGCNA'. However as useful as some of the commands in WGCNA seem, I can't find anywhere in the tutorials a command that actually allows me to visualise the networks.... So I instead used the package 'network' to plot and visualise this network.....
p1<-cor(t(E.rna[1:20,1:20]),use="p") #pearson correlation
plot(as.network.matrix(p1)) #network package
RCyjs(portRange=9047:9057, quiet=TRUE, graph=as.network.matrix(p1)); #RCyjs
Error in validObject(.Object) :
invalid class “RCyjsClass” object: invalid object for slot "graph" in class "RCyjsClass": got class "network", should be or extend class "graph"
RCyjs does not seem to accept networks and instead only takes 'graphs'.... how can I rectify this? If possible could anyone recommend alternate packages?