[R] label plotting on nmds diagram

[Gavin Simpson]

On Wed, 2007-11-14 at 11:22 -0300, Antonio Olinto wrote:
> Hi,
> 
> I'm using nmds command (library vegan) to analyze some fishing data.

I doubt it - there is no nmds command. Do you mean metaMDS() ? This uses
isoMDS() from package MASS with some extra features.

> 
> I'd like to plot not only points, but also the names of species and stations in
> a specified position.
> 
> I used the command
> text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds
> $points),pos=3,cex=0.5)
> 
> But the labels are sometimes overlapped.
> 
> Is there any way to use identify, or a similar command, to plot the row names in
> a given position? Identify would be perfect but it indicates the row number and
> I'd like to have the row name given in nmds$points.

Have a look at ?orditorp in vegan for an alternative approach, but yes
you can use identify, but you have to capture the output of the plot
call and use that in your identify call:

require(vegan)
data(varespec)
mod <- cca(varespec)
mod.plt <- plot(mod, display = "species", type = "p")
identify(mod.plt)

See ?identify.ordiplot for more info.

HTH

> 
> Many thanks,
> 
> Antonio Olinto
> Sao Paulo Fisheries Institute
> Brasil
> 
> 
> 
> 
> 
> 
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> 
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