Gavin and Jari, thank you very much. Actually, I am interested in both, sites and species. I have 3000 species (tropical forest trees) and I am trying to read the txt file with read.table. I tried also read.delim, but I don't know how to bring the sites names in the plot. I guess now I have the answer, using text(). What happened if I have a txt file like this: site Abarema adenophora Abarema macradenia Abatia parviflora Abelmoschus esculentus Abelmoschus moschatus General Viejo 1 1 1 1 1 Rio Pacuar 0 0 0 0 0 Las Brisas 0 0 0 1 1 San Pedro 0 0 0 1 1 Rio Convento 0 0 0 1 1 What will be the way to keep blank spaces for sites and species. I know that species will be unnecessary in this case because I have too many and I cannot show them in the plot, but just to learn for another time. Best, Manuel On 01/04/2011 03:16 a.m., Gavin Simpson wrote: > On Fri, 2011-04-01 at 07:01 +0300, Jari Oksanen wrote: >> On 31/03/11 23:18 PM, "Manuel Spínola" wrote: >> >>> Dear list members, >>> >>> I would like to include sites names with blank spaces in an ordiplot for >>> an nmds (in vegan). >>> How I do that? >>> >> Manuel, >> >> Like Gav wrote, R indeed is a bit patronizing and doesn't let you to use >> dimension names with blank. > It does. I made the species labels in my examples *not* have spaces in > them because Manuel said only his site names had spaces. The following > works just fine: > > require(vegan) > set.seed(1) > dat<- data.frame(matrix(runif(100), ncol = 10)) > names(dat)<- paste("Spp", 1:10) > rownames(dat)<- paste("Site", 1:10) > mod<- metaMDS(dat) > plot(mod, type = "text") > >> R only wants to protect you from trouble. > Indeed - it is a pain to look at `Spp 1` now, for example, as everything > needs to be quoted: > > R> dat$`Spp 1` > [1] 0.26550866 0.37212390 0.57285336 0.90820779 0.20168193 0.89838968 > [7] 0.94467527 0.66079779 0.62911404 0.06178627 > > One issue that might catch people out is that R doesn't let you read > data in with spaces in the colnames (unless read.table()'s check.names = > FALSE is set) - spaces get replaced with `.`. > > However, the only constraint on rownames is that they be non-missing and > non-duplicated. Both sets of names need to be syntactically valid but > spaces are fine. > > Hence one can always change the row/colnames to suit just before > plotting so one doesn't need to resort to extra plotting calls to > achieve the desired result. That said, one usually will need extra calls > to ordiplot functions as ordinations are complex beasts to plot so > drawing the points with custom text labels is no real hardship either. > > Either approach works. > > G > >> However, vegan lets you use any names in text() function for metaMDS: just >> list those names as a vector of quoted text in 'labels' argument to >> text.metaMDS(). The names given in 'labels' can have blanks, or even be al >> blanks as long as they are quoted. The length of the 'labels' must match the >> number of items plotted. >> >> All vegan text() functions for ordination plots should have the 'labels' >> argument. I cannot guarantee that all of them have, but you can always >> report missing cases to us. The text() for metaMDS() certainly has 'labels' >> as you can see if you read the help page ?metaMDS (which may not be a bad >> idea). >> >> Cheers, Jari Oksanen >> >> _______________________________________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspinola@una.ac.cr mspinola10@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Personal website: Lobito de río Institutional website: ICOMVIS [[alternative HTML version deleted]]