3D plots that POP!

#Produce 3D anaglyphs in R using the 'anaglyph' package
library(anaglyph)
library(vegan)


species<-data(varespec) #example data from vegan package 
NMDS<-metaMDS(varespec, k=3) #where k equal the number of dimensions 
sites <- scores(NMDS, display = "sites") #run NMDS 

x<-sites[,1] #assign each dimension or axis to an object 
y<-sites[,2]
z<-sites[,3]

anaglyph.plot(x, y, z, left = "red", right = "cyan", depth = "med", style = "pop-out", pch=20, xlab="Axis 1", ylab="Axis 2")

#Produce a 3D plot using 'ordiplot3d' function 

ordination<-ordiplot3d(NMDS, display = "sites", choices = 1:3, xlab="Axis 1", ylab="Axis 2", zlab="Axis 3", type="n") #make cyan 3D ordination 
points(ordination, "points", pch=20, col="cyan")
dev.copy2eps() #save as .eps and rename "cyan"


ordination<-ordiplot3d(NMDS, display = "sites", choices = 1:3, xlab="Axis 1", ylab="Axis 2", zlab="Axis3", type="n")#make cyan 3D ordination 
points(ordination, "points", pch=20, col="red")

dev.copy2eps() #save as .eps and rename "red"