[R] plot betadisper, change of pch

[David Winsemius]

On May 9, 2012, at 6:20 AM, Albin Blaschka wrote:

>
> Hello!
>
> After performing an analysis with betadisper, package vegan I would  
> like to plot the results - so far, so good. But I would also like to  
> "tune" a little bit the plotting characters, as '+' and 'x' are a  
> little to similar...
>
> My (boiled down) code:
>
> [See session info at the bottom of the mail, vegan is vegan_2.0-3]
>
> mod <- betadisper(mydata, mygroups, type='median')
> syms <- c(rep(1:4, each = 16))
> modplot <- plot(mod, axes = c(1,2), main='', pch=syms)
>
> I get the error message (roughly translated from german):
> "formal argument 'pch' fits to more given arguments"
> [formales Argument "pch" passt zu mehreren gegebenen Argumenten]
>
> What do I have to change?

In such an instance you generally need to get the code of a possibly  
hidden function named "plot.<class-returned-by-betadisp>" where you  
get the class by running:

class(mod)  # then type
plot.<that-result>  # and if that fails
getAnywhere(plot.<that-result>)

Then go in and either add a 'pch' argument or change the hardcoded  
values in the function body.

As it turns out you can see the function without even loading vegan  
just by doing this:

vegan:::plot.betadisper

'pch' appears a couple of times and it is colliding with your values  
in the points() calls. The function should probably be written so that  
it can accept a 'pch' argument.

-- 
David.


>
> Thank you in advance!
> Albin
>
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=de_AT.UTF-8       LC_NUMERIC=C  
> LC_TIME=de_AT.UTF-8        LC_COLLATE=de_AT.UTF-8
> [5] LC_MONETARY=de_AT.UTF-8    LC_MESSAGES=de_AT.UTF-8     
> LC_PAPER=C                LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C  
> LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rgl_0.92.798      reshape_0.8.4     plyr_1.7.1         
> MASS_7.3-16     vegan_2.0-3       permute_0.7-0     RPostgreSQL_0.3-2
> [8] DBI_0.2-5
>
> loaded via a namespace (and not attached):
> [1] grid_2.15.0    lattice_0.20-6 tools_2.15.0
>
>
> -- 
> | Albin Blaschka, Mag.rer.nat.
> | Etrichstrasse 26, A-5020 Salzburg
> | * www.albinblaschka.info * www.thinkanimal.info *
> | - It's hard to live in the mountains, hard but not hopeless!
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius, MD
West Hartford, CT