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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David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
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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.
