Avoid Overplotting of Text in Ordination Diagram

June 25, 2012

(This article was first published on theBioBucket*, and kindly contributed to R-bloggers)

Referring to a recent posting on r-sig-eco mailing list I'll add this example to theBioBucket:

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)