[R-sig-eco] Sites names with spaces in ordiplot
Gavin Simpson
gavin.simpson at ucl.ac.uk
Fri Apr 1 13:29:58 CEST 2011
On Fri, 2011-04-01 at 05:14 -0600, Manuel Spínola wrote:
> 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().
I mentioned this in my last email - the one you are replying to. The
issue is that R will check the species (variable) names on input and
remove spaces, replacing them with a `.`. But you *can* control whether
it does this or not using check.names = FALSE.
For example. Here is a simple CSV file:
,"Spp 1","Spp 2","Spp 3"
"Site 1",1,4,7
"Site 2",2,5,8
"Site 3",3,6,9
with spaces in both the species and site names.
We read it in via:
dat <- read.csv("spp.csv", row.names = 1, check.names = FALSE)
dat
And it gives us:
Spp 1 Spp 2 Spp 3
Site 1 1 4 7
Site 2 2 5 8
Site 3 3 6 9
So it *has* preserved the spaces in the species names and it hasn't
touched the row names.
We can ordinate this with out any problems:
require(vegan)
mod <- metaMDS(dat)
plot(mod, type = "text")
Ok, that is a pretty pointless plot but it works.
Does that help?
G
> 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"<mspinola10 at gmail.com>
> 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 at 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 at una.ac.cr
> mspinola10 at gmail.com
> Teléfono: (506) 2277-3598
> Fax: (506) 2237-7036
> Personal website: Lobito de río
> <https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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