[R-sig-eco] ordipointlabel with shortened names

[Gavin Simpson]

Resending as I had some mail trouble yesterday and don't see this one to
have gone through. See in-line below...

On Tue, 2013-06-18 at 12:58 -0700, Kevin McCluney wrote:
> Hi,
> 
> I've been trying to use ordipointlabel() to add taxa names to an nmds
> (metaMDS) graph in VEGAN.  I can add the full names from the database, but I
> would like to use the shortened names I created using make.cepnames().  I've
> tried:
> 
> pl3v2 <- ordipointlabel(mds, dis="sp", add = TRUE, lab=shnam)

I'm afraid this is not possible yet - the labels are hard coded from the
species scores. Hence I suggest you do

names(foo) <- make.cepnames(names(foo))

where foo is your data frame. Then refit the NMDS.

I'll see about allowing the passing in of labels but it won't happen for
a few weeks.

HTH

G

> But I get the following error message:
> 
> Error in text.default(lab, labels = labels, col = col, cex = cex, font =
> font,  : 
>   graphical parameter "lab" has the wrong length
> In addition: Warning message:
> In text.default(lab, labels = labels, col = col, cex = cex, font = font,  :
>   NAs introduced by coercion
> 
> I've also tried "labels" instead of "lab" and I get:
> 
> Error in text.default(lab, labels = labels, col = col, cex = cex, font =
> font,  : 
>   formal argument "labels" matched by multiple actual arguments
> 
> I guess this function doesn't yet work like orditorp?  Can anyone think of a
> workaround?
> 
> I've tried orditkplot:
> 
> orditkplot(pl3v2, dis = "sp")
> 
> But I get this error:
> 
> Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class =
> "tclObj") : 
>   [tcl] bad screen distance "-NaN".
> 
> I've also tried using identify(), but I have a few taxa that are literally
> right on top of each other and try as I might, I can't get all of the taxa
> that are on top of each other to show up.
> 
> Any help would be appreciated.  Thanks!
> 
> Kevin E. McCluney, PhD
> Post-doctoral Research Scholar
> Department of Entomology
> North Carolina State University
> 
> 
> 
> --
> View this message in context: http://r-sig-ecology.471788.n2.nabble.com/ordipointlabel-with-shortened-names-tp7578224.html
> Sent from the r-sig-ecology mailing list archive at Nabble.com.
> 
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-- 
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
523 Research and Innovation Centre          [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada


-- 
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
523 Research and Innovation Centre          [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada