Short PCA example with FactoMineR and ggplot2 in R

pca.R

#Copyright (c) 2012 Bruno Vieira [http://bmpvieira.com]
#License: CC BY
#Short PCA example with FactoMineR and ggplot2 in R

library(FactoMineR)
library(ggplot2)
data = read.table("data.tsv", head=T, row.names=1)
pca = PCA(data[,2:ncol(data)], scale.unit=T, graph=F)
PC1 = pca$ind$coord[,1]
PC2 = pca$ind$coord[,2]
plotdata = data.frame(cbind(group=data[,1],PC1,PC2))
plotdata$group = factor(plotdata$group)
plot = ggplot(plotdata, aes(PC1, PC2)) + 
geom_text(aes(label=rownames(plotdata)), size=2.5, hjust=0.5, vjust=-0.5) + 
geom_point(aes(colour=group))
print(plot)