---------- Forwarded message ----------
From: Gian Maria Niccolò Benucci <gian.benucci@gmail.com>
Date: 2010/5/22
Subject: Re: [R-sig-eco] Graphical parameters in metaMDS
To: Jari Oksanen <jari.oksanen@oulu.fi>


Jari,

Sorry, in the future I will spcify the pakages where the functions are and
then I'll post the query.

Anyway, I tried your code, as you suggested:

> plot(NMS.2.new, type = "n")
> with(env.table, points(NMS.2.new, pch=as.numeric(Host)), pch=1.5,
col=blue)
> with(env.table, legend("topleft",
leg=levels(Host),pch=seq_along(length(Host))))

But:
- the "pch" and the "col" commands do not make any dimensional change of
points on the graph (I treid using different pch values)
- the legent is print in the left top but the symbols are the same for the
two host I have in the env.table, (two open circles) instead of the open
circles and the open triangles I had into the graph.

I'll try to study better the functions you suggested me and I will post the
new code if I find a solution that works well.
Thank you very very much,


G.



2010/5/22 Jari Oksanen <jari.oksanen@oulu.fi>

On 21/05/10 20:49 PM, "Gian Maria Niccolò Benucci" <gian.benucci@gmail.com>
> wrote:
>
> > Hi all,
> >
> > I would ask about graphical parameters in metaMDS plots. I have this
> code:
> >
> >> metaMDS(data.ectomyco, distance="bray", k=2, trymax=100,
> autotransform=F)
> > -> NMS.2
> >> plot(NMS.2, type="n")
> >> ordisymbol(NMS.2, env.table, "Host", legend=T)
> >
> > My question is:
> > How could I enlarge the points symbols of the sites? is there a functions
> as
> > "pch=0.7" that I can use as when I plot points symbols in other other
> graphs
> > (i.g. rankabundance curves). I need to plot different symbols for
> different
> > "Host" I have in the environmental table and these symbols are too small
> to
> > fit in the paper column.
> > Any help will be surely appreciated, many thank you in advance...
> >
> Gian,
>
> I know the function metaMDS (because I wrote it), but I have no idea about
> ordisymbols -- except that I've been thinking to write a function with that
> name. I know is that you can use vegan function points() for the task. the
> points() function accepts all usual graphical arguments, including pch,
> cex,
> col etc. However, it doesn't have legend argument,  but you msut supply it
> separately. Neither does it know 'env.table'. Looking at your code above, I
> guess (but this is guessing: I don't know ordisymbols) the same effect can
> be reached with
>
> plot(NMS.2, type = "n")
> with(env.table, points(NMS.2, pch=as.numeric(Host)) ## add pch, col etc...
> with(env.table, legend("topleft", leg=levels(Host),
> pch=seq_along(length(Host)))
>
> Of course, all of this is completely untested.
>
> Cheers, Jari Oksanen
>
> PS. When you ask for the advice on non-standard commands defined only in
> packages, you should tell us what are the packages involved. In this case,
> metaMDS and ordisymbol are in different packages so that you need extra
> care
> in their interface, and you should also express this in your query.
>
>


-- 
Gian Maria Niccolò Benucci
Ph.D. Candidate
Department of Applied Biology - University of Perugia
Borgo XX Giugno, 74
I-06121 - Perugia, ITALY
Tel: +39.0755856433
Fax: +39.0755856069
Email: gian.benucci@gmail.com



-- 
Gian Maria Niccolò Benucci
Ph.D. Candidate
Department of Applied Biology - University of Perugia
Borgo XX Giugno, 74
I-06121 - Perugia, ITALY
Tel: +39.0755856433
Fax: +39.0755856069
Email: gian.benucci@gmail.com

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