Adding ellipses to a principal component analysis (PCA) plot

Question

I am having trouble adding grouping variable ellipses on top of an individual site PCA factor plot which also includes PCA variable factor arrows.

My code:

Answer 1

Here's a ggplot solution, using the nice ggbiplot library. An obvious improvement over plot are the labels on this one.

library(devtools) # don't forget to install Rtools first
install_github("vqv/ggbiplot")

library(ggbiplot)
data.class <- data[,1]
data.pca <- prcomp(data[,2:9], scale. = TRUE)
g <- ggbiplot(data.pca, obs.scale = 1, var.scale = 1, 
              groups = data.class, ellipse = TRUE, circle = TRUE)
g <- g + scale_color_discrete(name = '')
g <- g + theme(legend.direction = 'horizontal', 
              legend.position = 'top')
print(g)