#run PCA
pca.results <- prcomp(t(expression))

#vector of colors
cols <- as.character(indata$Annotation)
cols[cols=="K"] <- 'red'
cols[cols=="LG"] <- 'lightgreen'
cols[cols=="G"] <- 'darkgreen'

#plot it
plot(pca.results$x[,1], pca.results$x[,2], col=cols)