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 > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- > View this message in context: > http://r.789695.n4.nabble.com/envfit-vector-labels-with-ordiplot3d-tp3800669p3807015.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
