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:

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:
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)

To leave a comment for the author, please follow the link and comment on their blog: theBioBucket*.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)