[BioC] two-line labels in GO graphs

[Marc Carlson]

Robert Castelo wrote:
> dear list,
>
> i would like to produce a GO graph where the labels of the nodes are
> formed by the GO identifier and the GO term and these two pieces of
> information appear in two different lines within the node, in order to
> draw nodes somewhat narrower than if i have these two pieces in one
> single line.
>
> the following code does the job putting GO ID and GO term in the same
> line separated by one space character:
>
> library(GOstats)
> library(Rgraphviz)
>
> goterms <- eapply(GOTERM,Term)
> g <- GOGraph("GO:0016265",GOBPPARENTS)
> g <- removeNode("all",g)
> mt <- match(nodes(g),names(goterms))
> nodattr <- makeNodeAttrs(g,label=paste(nodes(g),goterms[mt],sep=" "),
>                          shape="ellipse",fillcolor="#f2f2f2",
>                          fixedsize=FALSE)
> plot(g,nodeAttrs=nodattr)
>
>
> if i replace the space character " " by "\n" in the 'sep' parameter of
> the 'makeNodeAttrs' function, i do not get the desired behavior, it just
> shows the GO ID.
>
> anyone has tried this or has an idea how it could be done ?
>
>
>
> my sessionInfo():
>
> R version 2.6.0 (2007-10-03) 
> x86_64-unknown-linux-gnu 
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils
> datasets 
> [8] methods   base     
>
> other attached packages:
>  [1] Rgraphviz_1.16.0    GOstats_2.4.0       Category_2.4.0     
>  [4] genefilter_1.16.0   survival_2.32       RBGL_1.14.0        
>  [7] annotate_1.16.1     xtable_1.5-2        GO.db_2.0.2        
> [10] AnnotationDbi_1.0.6 RSQLite_0.6-4       DBI_0.2-4          
> [13] Biobase_1.16.1      graph_1.16.1       
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.9  rcompgen_0.1-15
>
>
> thanks!!
> robert.
>
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>   

First of all thanks for pointing this out. I have looked into why this
was happening and have found the cause to be the source files that come
from ftp.geneontology.org . As you observed, the error appears to only
affect the direct term to term association mapping for this one term. I
have notified them of the error and I anticipate that it will probably
be cleaned up very soon.

Marc