#Biplot of the PCA on transformed species data (scaling 1)
windows()
plot(spe.h.pca)
windows()
biplot(spe.h.pca)
windows()
plot(spe.h.pca, scaling=1, type="none", # scaling 1 = distance biplot : 
                                        # distances among objects in the biplot approximate their Euclidean distances
                                        # but angles among descriptor vectors DO NOT reflect their correlation
     xlab = c("PC1 (%)", round((spe.h.pca$CA$eig[1]/sum(spe.h.pca$CA$eig))*100,2)), #this comes from the summary
     ylab = c("PC2 (%)", round((spe.h.pca$CA$eig[2]/sum(spe.h.pca$CA$eig))*100,2)))
points(scores(spe.h.pca, display="sites", choices=c(1,2), scaling=1),
       pch=21, col="black", bg="steelblue", cex=1.2)
text(scores(spe.h.pca, display="species", choices=c(1), scaling=1),
     scores(spe.h.pca, display="species", choices=c(2), scaling=1),
     labels=rownames(scores(spe.h.pca, display="species", scaling=1)),
     col="red", cex=0.8)