#############################relate modules to external clinical triats######################################

# Define numbers of genes and samples

nGenes = ncol(datExpr0)

nSamples = nrow(datExpr0)

moduleTraitCor = cor(MEs, datTraits, use = "p")

moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nSamples)

sizeGrWindow(10,6)

#pdf(file="8_Module-trait relationships.pdf",width=10,height=6)

# Will display correlations and their p-values

textMatrix = paste(signif(moduleTraitCor, 2), "\n(",

                   signif(moduleTraitPvalue, 1), ")", sep = "")

dim(textMatrix) = dim(moduleTraitCor)

par(mar = c(6, 8.5, 3, 3))

# Display the correlation values within a heatmap plot

labeledHeatmap(Matrix = moduleTraitCor,

               xLabels = names(datTraits),

               yLabels = names(MEs),

               ySymbols = names(MEs),

               colorLabels = FALSE,

               colors = greenWhiteRed(50),

               textMatrix = textMatrix,

               setStdMargins = FALSE,

               cex.text = 0.5,

               zlim = c(-1,1),

               main = paste("Module-trait relationships"))

#dev.off()