Question

I can use Plot function. Could use plot to get the pca results. But not sure how to label these points according to my datapoints which are rownames(Sample) numbered 1 to 90

Sample<-read.table(file.choose(),header=F,sep="\t")
Sample.scaled<-data.frame(apply(Sample_2XY,2,scale))
Sample_scaled.2<-data.frame(t(na.omit(t(Sample_2XY.scaled))))

pca.Sample<-prcomp(Sample_2XY.scaled.2,retx=TRUE)

pdf("Sample_plot.pdf")
plot(pca.Sample$x)
dev.off()

Answer 1

Here is a simple way of doing it, with plotting the first two components:

plot( pca.Sample$x[,1], pca.Sample$x[,2] )
text( pca.Sample$x[,1], pca.Sample$x[,2], rownames( Sample ), pos= 3 )

By the way, you can use your regular device to see the plots on the go, and then copy the contents of that device to PDF:

dev.copy2pdf( file= "something.pdf" )