[BioC] topGO: full-length descriptions in graph output
James W. MacDonald
jmacdon at uw.edu
Thu Sep 13 19:34:24 CEST 2012
On 9/13/2012 4:29 AM, Frank Schwach [guest] wrote:
> does anybody know if there is any way in the topGO package to force full-length descriptions of the GO terms to be printed in the graph? By default, only about 20 characters of the descriptions are printed.
If you look at the help page for showSigOfNodes(), there is an argument
.NO.CHAR that is listed as an internal function. This controls the
number of characters that are shown in the graph, and defaults to 20.
You can bump that up to whatever value you see fit, but note that it
*is* listed as an internal function, so you are stepping into the deep
end of the pool - if things don't work the way you want, it will likely
be up to you to figure out why and fix it.
> Thanks for your help!
> -- output of sessionInfo():
> R version 2.11.1 (2010-05-31)
>  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>  LC_MONETARY=C LC_MESSAGES=C
>  LC_PAPER=en_GB.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  topGO_1.16.2 SparseM_0.85 GO.db_2.4.1
>  RSQLite_0.9-1 DBI_0.2-5 AnnotationDbi_1.10.1
>  Biobase_2.8.0 graph_1.26.0
> loaded via a namespace (and not attached):
>  grid_2.11.1 lattice_0.18-8 tools_2.11.1
> Sent via the guest posting facility at bioconductor.org.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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