Online Trick

library(vegan)
library(vegan)
data(dune)
sol <- metaMDS(dune)
 
# use ordipointlabel -
# here is an example where I added cex according to species frequencies:
plot(sol, type = "n")
cex.lab = colSums(dune > 0) / nrow(dune) + 1
col.lab = rgb(0.2, 0.5, 0.4, alpha = 0.6)
ordipointlabel(sol, displ = "sp", col = col.lab, cex = cex.lab)
 
 
# you could also use pointLabel() from maptools package:
library(maptools)
x = as.vector(sol$species[,1])
y = as.vector(sol$species[,2])
w = row.names(sol$species)
 
plot(sol, type = "n")
points(sol, displ = "species", cex = 1, pch = 4, col = 3)
pointLabel(x, y, w, col = col.lab, cex = cex.lab)

library(vegan)

### data on 35 species of Oribatid mites
### data description at: http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/mite.html
data(mite)

### ...and environmental variables
data(mite.env)

### the factor which you wish to use for labeling the displayed sites
### in the ordination diagramm:
fac<-mite.env$Topo
sol<-metaMDS(mite)

windows(9,5)
par(mfrow=c(1,2))

### graph with "spider":
plot(sol,type="n")
points(sol, display = "sites", cex=0.65, select=which(fac=="Hummock"),
       pch = 21,col="black", bg="black")
points(sol, display = "sites", cex=0.65, select=which(fac=="Blanket"),
       pch = 21,col="black", bg="white")
ordihull(sol,group=fac,show.groups="Hummock")
ordihull(sol,group=fac,show.groups="Blanket",lty=3)
orditorp(sol, dis = "sp", pcex=0,air=0.85,col="grey35",cex=0.8 ,font=3)

### graph with "hull":
plot(sol,type="n")
points(sol, display = "sites", cex=0.65, select=which(fac=="Hummock"),
       pch = 21,col="black", bg="black")
points(sol, display = "sites", cex=0.65, select=which(fac=="Blanket"),
       pch = 21,col="black", bg="white")
ordispider(sol,group=fac,show.groups="Hummock")
ordispider(sol,group=fac,show.groups="Blanket",lty=3)
orditorp(sol, dis = "sp", pcex=0,air=0.85,col="grey35",cex=0.8 ,font=3)