Problem with edgesfile into cytoscape for network plot

Question

[Biologist]

I was using 30,000 protein-coding genes and lncRNAs for network construction on WGCNA. I have got 25 modules. And I'm interested in creating a network plot. I see that everyone is using cytoscape. So, I got the edges and nodes files with the following commands.

genes = colnames(datExpr)
dimnames(TOM) <- list(genes, genes)
module_colors2= dynamicColors[restGenes]
cyt = exportNetworkToCytoscape(TOM,
                               edgeFile = paste("samples_wgcna", ".edges.txt", sep=""),
                               nodeFile = paste("samples_wgcna", ".nodes.txt", sep=""),
                               weighted = TRUE, threshold = 0,
                               nodeNames = genes, nodeAttr = module_colors2)

I see that edges file is about 6GB. It looks very problematic to upload that in cytoscape. Not working properly. Is there any other way to make network with all the modules with genes and lncRNAs?

Answer 1

[andres.firrincieli]

Hi,

just increase the threshold value