I’ve used the WGCNA packages (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/) to generate edge and node files for use in Cytoscape.
cyt = exportNetworkToCytoscape(modTOM,
edgeFile = file.path("./environment", paste(label, "_CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep="")),
nodeFile = file.path("./environment", paste(label, "_CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep="")),
weighted = TRUE,
threshold = 0.02,
nodeNames = modProbes,
altNodeNames = modGenes,
nodeAttr = moduleColors[inModule])
I’ve read about importing these to Cytoscape here Importing Network From Wgcna Into Cytoscape
However, when I import, I can’t get the node names to appear (see image linked below). Any help please!
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