r - visualizing clr network in cytoscape -


does know how can proceed generating clr network visualizing network nicely using cystoscape? used minet package generate clr network 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 network in rstudio, have nicer looking network cytoscape can have flexibility of colouring nodes. thanks

you have adjacency matrix in row.names , col names genes. should convert matrix file edge list file:

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

now can open file in excel, edit , import cytoscape.


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