lnames=load(file="ES-networkConstruction-stepByStep.RData")
KMEColors=moduleColors

TMEList = moduleEigengenes(datExprT, colors = KMEColors)
TMEs = TMEList$eigengenes
NMEList = moduleEigengenes(datExprN, colors = KMEColors)
NMEs = NMEList$eigengenes

nGenes = ncol(datExprT)
nSamples = nrow(datExprT)
TNames = substring(names(TMEs), 3)
TModuleMembership = as.data.frame(cor(datExprT, TMEs, use = "p"))
TPvalue = as.data.frame(corPvalueStudent(as.matrix(TModuleMembership), nSamples))
names(TModuleMembership) = paste("T", TNames, sep="")
names(TPvalue) = paste("T.MM", TNames, sep="")


mGenes = ncol(datExprN)
mSamples = nrow(datExprN)
NNames = substring(names(NMEs), 3)
NModuleMembership = as.data.frame(cor(datExprN, NMEs, use = "p"))
NPvalue = as.data.frame(corPvalueStudent(as.matrix(NModuleMembership), mSamples))
names(NModuleMembership) = paste("N", NNames, sep="")
names(NPvalue) = paste("N.MM", NNames, sep="")



##########example:royalblue and CK
Tmodule="lightyellow"
Tcolumn = match(Tmodule, TNames)
TmoduleGenes = KMEColors==Tmodule

Nmodule="lightyellow"
Ncolumn = match(Nmodule, NNames)
NmoduleGenes = KMEColors==Nmodule

modulecolor="yellow"
sizeGrWindow(8, 8)

par(mfrow = c(1,1))
verboseScatterplot(abs(TModuleMembership[TmoduleGenes, Tcolumn]),
                   abs(NModuleMembership[NmoduleGenes, Ncolumn]),
                   xlab = paste("kME in", "ES"),
                   ylab = paste("kME in", "RS"),
                   main = paste("lightyellow"),
                   cex.main = 1.7, cex.lab = 1.6, cex.axis = 1.6, col = modulecolor)



# Select each module
moduleColors=KMEColors
for (mod in 1:nrow(table(moduleColors)))
{
  
  modules = names(table(moduleColors))[mod]
  # Select module probes
  probes = names(datExprT)
  inModule = (moduleColors == modules)
  modProbes = probes[inModule]
  modGenes = modProbes
  # Select the corresponding Topological Overlap
  modTOM = TOM[inModule, inModule]
  
  dimnames(modTOM) = list(modProbes, modProbes)
  # Export the network into edge and node list files Cytoscape can read
  cyt = exportNetworkToCytoscape(modTOM,
                                 edgeFile = paste("ES_CytoscapeInput-edges-", modules , ".txt", sep=""),
                                 nodeFile = paste("ES_CytoscapeInput-nodes-", modules, ".txt", sep=""),
                                 weighted = TRUE,
                                 threshold = 0.5,
                                 nodeNames = modProbes,
                                 altNodeNames = modGenes,
                                 nodeAttr = moduleColors[inModule])
}