[R] plot betadisper, change of pch

[Uwe Ligges]

Runnig the examples from ?betadisper and adding a pch statement gives:

 >      plot(mod, pch=2)
Error in plot.xy(xy.coords(x, y), type = type, ...) :
   formal argument "pch" matched by multiple actual arguments

 > traceback()
5: plot.xy(xy.coords(x, y), type = type, ...)
4: points.default(g$centroids, pch = 16, cex = 1, col = "red", ...)
3: points(g$centroids, pch = 16, cex = 1, col = "red", ...)
2: plot.betadisper(mod, pch = 2)
1: plot(mod, pch = 2)

This shows that the author hardcoded the pch in the code, hence you can 
only change it by changing the code - or send a feature request to the 
vegan maintainer (ideally including a patch, CCing).

Best,
Uwe Ligges



On 09.05.2012 12:20, 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?
>
> 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
>
>