[BioC] two-line labels in GO graphs

[Marc Carlson]

Marc Carlson wrote:
> 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
>
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>
>   
Oops sorry, I responded to the wrong email with this post. Please ignore
this. How embarrassing. :P

Marc