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rgraphnodesigraphedges

visualizing clr network in cytoscape

Does anyone know how I can proceed from generating a clr network to visualizing the network nicely using cystoscape? I used minet package to generate a clr network as follows:

source("http://bioconductor.org/biocLite.R")
biocLite("minet")
library(Rgraphviz)
library(minet)

data(syn.data)
mim <- build.mim(syn.data,estimator="spearman")
#net<-minet(syn.data,"mrnet","mi.shrink","equalwidth",10)
net <- clr( mim, skipDiagonal=1 )
graph <- as(net, "graphNEL")

The above code visualizes the network in my rstudio, but I would like to have a nicer looking network from cytoscape where I can also have the flexibility of colouring nodes. Thanks

Solution

  • You have adjacency matrix in which row.names and col names are your genes. Then you should convert this matrix file to an edge list file:

    graph_adj=as.data.frame(as.table(as.matrix(net)))
write.table(graph_adj, "graph_adj.txt", sep="\t")

    Now you can open the file in excel, edit it and finally import to cytoscape.