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I'm trying to produce biplots from constrained ordinations (dbRDA to be exact) and I would like to re-scale the lengths of the vector arrows. plot and ordiplot commands in vegan automatically scale the constraint vector arrows to fit the figure and therefore truncates the biplot score axis. An example:

library("vegan")
data(varechem)
data(varespec)
ord <- capscale(varespec ~ ., data = varechem) 
plot(ord)

The biplot score axis for the vector arrows for the constraints are truncated (i.e. the full range from -1 to 1 is not shown) and cannot be read (particularly difficult for the right-hand side axis). Whereas scaling the CAP axis is of course easy using ylim and xlim I have yet to find a solution for re-scaling the constraints. I'm sure the answer is a very simple one, but I'm relatively new to vegan and haven't managed to figure it out after two days of trying.

Cheers,
-Aapo

Gavin Simpson
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AKa
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  • As these are just direction ins space and the interpretation is the *relative* magnitude (between constraints) in those directions, I'm struggling to see what you gain by doing this other than making it harder to see the relationships between variables or samples in the plot? – Gavin Simpson Oct 10 '14 at 21:49
  • Well, to be honest I'm not all excited about doing that either, but it was a referee request. I figured it might not harm if I fulfill the request although it does not seem totally sensible. Anyways, if it turns out to be too big of a task I think it is not difficult to talk my way out of doing that. However, in general, I think it is interesting to know which aspects of the ordination can be modified (nice blog posts in your blog on the topic by the way). – AKa Oct 11 '14 at 07:08

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