Avoid Overplotting of Text in Ordination Diagram

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)

A Word Cloud with Spatial Meaning

..Some time ago I did a word cloud for representing a Google Scholar search result. Tal Galili pointed me at a post by Drew Conway that expanded on the topic of word clouds lacking spatial meaning. In fact the spatial ordering of words in a word cloud is arbitrary and meaningless..

As I am an ecologist, I soon came to the idea that text could be treated as a multivariate data set - assuming that words can be treated as species and sentences being similar to samples. So, presuming that it makes sense to put sentences and words in a cross-table as I similarly would do with a species / samples matrix, it may also be sensible to analyze such a matrix by ordination-methods for multivariate data, mostly used by ecologist recently. I chose NMDS ordination, as it is robust and quite easy to compute with R-package {vegan}.

Custom Labels for Ordination Diagram

Here is how you do custom labels, hull, spider in a vegan ordination diagram: