The meaning of units on the axes of a PCA plot

Question

I've used the R packages DESeq2 and ggplot2 and the following code

vsd <- varianceStabilizingTransformation(dds)
data <- plotPCA(vsd, intgroup=c("condition"), returnData=TRUE)
percentVar <- round(100 * attr(data, "percentVar"))
plotPCA <- ggplot(data, aes(PC1, PC2, color=condition)) +
geom_point(size=3) +
  xlab(paste0("PC1: ",percentVar[1],"% variance")) +
  ylab(paste0("PC2: ",percentVar[2],"% variance")) +
  geom_text(aes(label=names),hjust=0.25, vjust=-0.5, show_guide = F)
ggsave("PCA.pdf", plot = plotPCA)

to produce the following PCA plot:

I know the axes are the principal components but I am confused by the units displayed. I thought the axes of a PCA plot are unit-less. But then I did image search on Google for "PCA plot" and saw tons of plots displaying units on their axes. Does anyone know what is the meaning of these units?

Answer 1

It seems the question has been answered here - the units are, apparently, the raw component scores. Which makes sense, actually.

Answer 2

The principal components are linear combinations of the original variables. If the original variables have different units, then it will not give meaning to give units to the PCA axes. But in the very special case that all the original variables have the same unit, then the principal component will have that same unit.

Can you reference some specific example you have seen with units on the principal components?