[R-sig-eco] returning site and species coordinates in NMDS using vegan

[Sven Adler (2)]

Hi Lauren,
type
?plot
or ?par
and you will find several possibilities to change the view of your plot (most of them works in plot.cca to! It is a little bit tricky, but once you understood it, it will be much more easier and faster to build very nice plots in R as if you want to do the same in EXCEL or Power Point ( Power Point: Export the Graph as emf file to Power Point, with a dubble click on the graph you can change whatever you want to change, or use text fields) – and if you save the code for the plot, changes in the future can be done much more faster, as if you have to do all these things in other programs. 
http://addictedtor.free.fr/graphiques/ here you can find several ideas (with the R code) how flexible R graphics are 
Sven 
________________________________________
Von: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org]" im Auftrag von "Gavin Simpson [gavin.simpson at ucl.ac.uk]
Gesendet: Dienstag, 20. September 2011 23:45
Bis: L Quinn
Cc: r-sig-ecology at r-project.org
Betreff: Re: [R-sig-eco] returning site and species coordinates in NMDS using vegan

On Tue, 2011-09-20 at 20:54 +0000, L Quinn wrote:
> Hi,
> I am running a simple NMDS as outlined by Jari Oksanen in vegantutor, e.g.
> spp.dist<-vegdist(spp)spp.mds<-metaMDS(spp,trace=FALSE)spp.mds
> I am able to plot the results (species nicely overlaying sites) using
> plot(spp.mds,display="species",type="t",family="sans",font=2,xlim=c(-0.4,0.4),ylim=c(-0.4,0.4))# and points(env.mds,display="sites")
> However, try as I might, I am not able to make this figure look pretty enough in R to satisfy journal editors/reviewers. I want to redraw the results in Excel, but I don't know how to extract species and site coordinates from spp.mds. I see that I can do this using isoMDS in MASS, but I'd prefer to use vegan. Perhaps I'm missing something obvious, but I haven't been able to find it anywhere so far. How does one go about extracting those coordinates?
> Thanks in advance.
> Lauren

Why don't you tell use what you want to do to produce a plot that will
meet the reviewers/editors requirements? That way we can help you with R
code to do the plot as I am 100% certain you won't be able to do a
better job with Excel.

Yes, I am that confident! I've published umpteen papers using vegan
plots, that with a bit of crafting haven't had any problems getting past
reviewers/editors of the ecological/environmental journals I have
published in.

G

--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 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 at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology