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# Plots the kME values of genes in two groups of expression data for each module in an inputted color vector
kMEcomparisonScatterplot <- function (datExpr1, datExpr2, colorh, inA=NULL, inB=NULL,
MEsA=NULL, MEsB=NULL, nameA="A", nameB="B", plotAll=FALSE, noGrey=TRUE, maxPlot=1000,
pch=19,
fileName = if (plotAll) paste("kME_correlations_between_",nameA,"_and_",nameB,"_all.pdf",sep="") else
paste("kME_correlations_between_",nameA,"_and_",nameB,"_inMod.pdf",sep=""),
...){
# First, get the data
if (is.null(dim(datExpr1))) {
write ("Error: datExpr1 must be a matrix",""); return(0)
}
if (is.null(datExpr2)){
datA = datExpr1[inA,]
datB = datExpr1[inB,]
if ((is.null(dim(datA)))|(is.null(dim(datB)))) {
write ("Error: Check input for inA and inB.",""); return(0)
}
} else {
if (is.null(dim(datExpr2))) {
write ("Error: datExpr2 must be a matrix",""); return(0)
}
datA = datExpr1
datB = datExpr2
}
if ((dim(datA)[2]!=length(colorh))|(dim(datB)[2]!=length(colorh))){
write ("Error: Both sets of input data and color vector must all have same length.",""); return(0)
}
if(is.null(MEsA))
MEsA = (moduleEigengenes(datA, colors=as.character(colorh), excludeGrey=noGrey))$eigengenes
if(is.null(MEsB))
MEsB = (moduleEigengenes(datB, colors=as.character(colorh), excludeGrey=noGrey))$eigengenes
mods = substring(names(MEsA),3)
kMEsA = as.data.frame(cor(datA,MEsA,use="p"))
kMEsB = as.data.frame(cor(datB,MEsB,use="p"))
# Second, make the plots
xlab = paste("kME values in",nameA)
ylab = paste("kME values in",nameB)
printFlush(paste("Plotting kME scatterplots into file", fileName));
if (plotAll){
pdf(file=fileName)
numPlot = min(maxPlot,length(colorh));
these = sample(1:length(colorh),numPlot)
for (i in 1:length(mods)){
plotCol = mods[i]; if(mods[i]=="white") plotCol="black"
verboseScatterplot(kMEsA[these,i],kMEsB[these,i],main=mods[i],
xlab=xlab,ylab=ylab,pch=pch,col=plotCol,...)
}
dev.off()
return("DONE - Plotted All")
}
pdf(file=fileName)
for (i in 1:length(mods)){
these = colorh==mods[i]
plotCol = mods[i]; if(mods[i]=="white") plotCol="black"
verboseScatterplot(kMEsA[these,i],kMEsB[these,i],main=mods[i],
xlab=xlab,ylab=ylab,pch=pch,col=plotCol,...)
}
dev.off()
return("DONE - Plotted only in module")
}
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