On Sun, 2011-05-22 at 12:15 +1000, Andrew Halford wrote: > Hi Dave, > > I used the indval function from the package labdsv (your package Dave, I > believe) and confirmed these results with output from the indicspecies > package. I want to use all the species to construct the PCA ordination but > only want to show the species vectors for those 27 species identified as > significant group discriminators. > > Andy
If you really want to do this Canoco-esque type of thing then it is easy, but you need to build the plot up yourself. Here is an exmaple: ## load packages and example data require(vegan) require(labdsv) data(dune) data(dune.env) ## Indicators of Management type set.seed(38) inds <- with(dune.env, indval(dune, Management)) ## ordinate dune.pca <- rda(dune, scale = TRUE) ## exract scores you want to plot presume species and sites dune.site <- scores(dune.pca, display = "sites", scaling = 3) dune.spp <- scores(dune.pca, display = "species", scaling = 3)[inds$pval <= 0.05, ] ## plot plot(dune.pca, display = c("sites","species"), type = "n", scaling = 3) points(dune.site) arrows(0, 0, dune.spp[,1], dune.spp[,2], col = "red", length = 0.05) lab.xloc <- dune.spp[,1] * 1.2 lab.yloc <- dune.spp[,2] * 1.2 text(lab.xloc, lab.yloc, rownames(dune.spp), col = "red", cex = 0.8) The placement of the labels is crude and can be improved, but not in a mailing list post. HTH G > On Sun, May 22, 2011 at 1:19 AM, Dave Roberts < > dvr...@ecology.msu.montana.edu> wrote: > > > On 05/20/2011 11:54 PM, Andrew Halford wrote: > > > >> Hi All, > >> > >> I have done a IndVal analysis on a dataset which has identified 27 species > >> out of 57 as being significant arbiters of site differences. What I want > >> to > >> do is a PCA biplot (data is hellinger transformed prior to this) with only > >> these 27 species on the ordination, not all 57, How can I control the > >> species I want displayed? > >> > >> cheers > >> > >> Andy > >> > > > > -- > > Andrew, > > > > We need a little more information. Which IndVal function did you use? > > It should return a vector of p-values you can use as a mask [p-val <= > > 0.05,] on your taxon matrix. But are you saying you want to use all 57 in > > constructing the PCA and only identify 27, or that you only want to use > > those 27 in the construction of the PCA? > > > > Dave Roberts > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology