[R] label plotting on nmds diagram

[Antonio Olinto]

Hi Gavin, thanks for your message.

You are right. The function nmds is from library labdsv and not from vegan. My
mistake.

Well, that's what I did:

library(vegan)
library(labdsv)
nms.euc <- nmds(dis.euc,4)
initial  value 13.457832 
iter   5 value 8.589716
iter  10 value 7.989993
iter  15 value 7.734503
iter  20 value 7.539719
iter  25 value 7.438721
final  value 7.397254 
converged

plot(nms.euc)
text(nms.euc$points[,1],nms.euc$points[,2],labels=row.names(nms.euc$points),pos=4,cex=0.7)
# got overwritten labels

identify(plot(nms.euc))
numeric(0)

It seems that ordiplot is not suitable to nmds but only to cca and rda.

But you understood exactly what I want. Your example showed for cca what I want
for nmds plot. 

Best regards,

Antonio


Citando Gavin Simpson <gavin.simpson em ucl.ac.uk>:

> 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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