[R] envfit vector labels with ordiplot3d

[Gavin Simpson]

On Mon, 2011-09-12 at 03:24 -0700, Briony wrote:
> Thank you very much for the suggestion. And while I'm here, thank you for
> vegan and the documentation that goes with it.
> 
> >Function ordiplot3d uses scatterplot3d, and it returns also all
> >scatterplot3d items, like functions xyz.converter and points3d that
> >can be used for tuning labels.
> 
> I tried ordilabel(pl$arrows) but the labels only seem to be in two
> dimensions.

It *really* does help to read the documentation for functions. Like most
of the functions in vegan that extract information from ordinations,
ordilabel() extracts information for "axes" 1 and 2 only, by default.

Does

ordilabel(pl$arrows, choices = 1:3)

work for you?

G

> >With ordixyplot I can see no other choice than that you edit the
> >function and preferably contribute your edited function to vegan
> >(and will be credited with the function help).
> 
> I'm not a skilled enough user of R to edit the ordixyplot function - so I'll
> pass on that invitation to anyone else who reads this thread?
> 
> Thanks again,
> Briony 
> 
> Briony <brionynorton <at> gmail.com> writes:
> 
> >
> > Hi R experts,
> >
> > I'm looking for some help with plotting vectors from envfit in vegan, onto
> > a
> > 3d plot using ordiplot3d. So far I have
> >
> > data.mds <- metaMDS(data, k=3,trace = FALSE)
> > vect_data<-envfit(data.mds,vegdata[,3:21],choices=1:3,permu=9999)
> > ordiplot3d(data.mds,envfit=vect_data)
> > ordixyplot(data.mds,pch=pts,envfit=vect_data)
> >
> > (my data's not really called data, I thought it might be easier to
> > communicate this way)
> >
> > These display the vectors as arrows, but what I would really like is for
> > the
> > arrows to be labelled, like what comes up automatically in ordirgl or with
> > a
> > 2D ordiplot.
> >
> > I've gone through the help and tried everything I can work out, but I must
> > be missing something important, because nothing's worked so far. I would
> > be
> > happy to use ordixyplot and show a series of 2D plots, but I can't get
> > labels on those arrows either.
> >
> > Any pointers in the right direction would be gratefully received.
> > Briony
> 
> Briony,
> 
> There really is no way to do this automatically, but if someone fixes the
> functions, we are happy to incorporate those changes in vegan.
> 
> You may be able to achieve something like that with ordiplot3d, but I am
> not sure it looks completely satisfactory. Function ordiplot3d returns
> invisibly the plotting object which contains, among other items. the
> coordinates of arrow heads in the  flattened graph. So this could work:
> 
> pl <- ordiplot3d(data.mds,envfit=vect_data)
> ordilabel(pl$arrows)
> 
> Function ordiplot3d uses scatterplot3d, and it returns also all
> scatterplot3d items, like functions xyz.converter and points3d that
> can be used for tuning labels.
> 
> With ordixyplot I can see no other choice than that you edit the
> function and preferably contribute your edited function to vegan
> (and will be credited with the function help).
> 
> Cheers, Jari Oksanen
> 
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