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$arrows, choices = 1:3) work for you? G Thanks for the suggestion. Unfortunately that didn't work - it returned an error (Error in scores.default(x, choices = choices, display = display, ...) : subscript out of bounds). The ordilabel help says "ordilabel(x, display, labels, choices = c(1, 2)..." which seems to suggest the function might not allow a third axis at the moment? Cheers, Briony On Tue, Sep 13, 2011 at 2:53 AM, Gavin Simpson [via R] < ml-node+s789695n3807984...@n4.nabble.com> wrote: > On Mon, 2011-09-12 at 03:24 -0700, Briony wrote: > > Thank you very much for the suggestion. And while I'm here, thank you for > > > vegan and the documentation that goes with it. > > > > >Function ordiplot3d uses scatterplot3d, and it returns also all > > >scatterplot3d items, like functions xyz.converter and points3d that > > >can be used for tuning labels. > > > > I tried ordilabel(pl$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. > > > > ______________________________________________ > > [hidden email] > > <http://user/SendEmail.jtp?type=node&node=3807984&i=0>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 > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=3807984&i=1>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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/envfit-vector-labels-with-ordiplot3d-tp3800669p3807984.html > To unsubscribe from envfit vector labels with ordiplot3d, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3800669&code=YnJpb255bm9ydG9uQGdtYWlsLmNvbXwzODAwNjY5fC0xODk1MTY2Mjk2>. > > -- View this message in context: http://r.789695.n4.nabble.com/envfit-vector-labels-with-ordiplot3d-tp3800669p3809900.html Sent from the R help mailing list archive at Nabble.com. 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