Nothing
PCplot <-
function(out,ug="unguided",type="1v2",npcs,...){
# out - output of gPCA.batchdetect
# ug - "guided" or "unguided" principal components plots?
# type - "1v2" plots the first PC versus the second PC;
# "comp" compares all PCs up to the value of npc with density plots on the diagonal
# npcs - number of principal components comparisons to plot for type "comp"
if (type=="1v2") {
par(mfrow=c(1,1))
if (ug=="unguided") {
plot(out$PCu[,1],out$PCu[,2],col=rainbow(out$b)[out$batch],pch=out$batch,
xlab=expression(PC[1]),ylab=expression(PC[2]),...)
} else {
plot(out$PCg[,1],out$PCg[,2],col=rainbow(out$b)[out$batch],pch=out$batch,
xlab=expression(PC[1]),ylab=expression(PC[2]),...)
}
} else {
if (ug=="unguided"){
par(mfrow=c(npcs,npcs))
for (i in 1:npcs){
for (j in 1:npcs){
if (i==j){
plot(density(out$PCu[,i]),main="",xlab="")
} else {
plot(out$PCu[,i],out$PCu[,j],col=rainbow(out$b)[out$batch],pch=out$batch,
xlab=as.expression(substitute(paste(PC[subi]),list(subi=i))),
ylab=as.expression(substitute(paste(PC[subj]),list(subj=j))),...)
}
}
}
} else {
par(mfrow=c(npcs,npcs))
for (i in 1:npcs){
for (j in 1:npcs){
if (i==j){
plot(density(out$PCg[,i]),main="",xlab="")
} else {
plot(out$PCg[,i],out$PCg[,j],col=rainbow(out$b)[out$batch],pch=out$batch,
xlab=as.expression(substitute(paste(PC[subi]),list(subi=i))),
ylab=as.expression(substitute(paste(PC[subj]),list(subj=j))),...)
}
}
}
}
}
}
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