[BioC] two-line labels in GO graphs

[Robert Castelo]

hi Florian,

thanks for your answer, could you point out to me how can i install this
latest Rgraphviz devel version? (i've googled "Rgraphviz devel" but i
couldn't identify anything meaninful to me)

thanks!
robert.

On Thu, 2008-03-13 at 12:27 -0700, Florian Hahne wrote:
> Hi Robert,
> For some strange reason, graphviz strips the linebreaks from the  
> labels when it returns things, however it uses them when computing the  
> graph layout. In the latest Rgraphviz devel version we introduced a  
> slightly revised interface for graph plotting and you might want to  
> take a look at the new vignette there.
> 
> Basically, what you want to do is set the labels in the nodeRenderInfo  
> slot of your graph object and plot that using layoutGraph and  
> renderGraph
> 
> nodeRenderInfo(g) <- list(label=yourLabels)
> 
> g <- layoutGraph(g)
> renderGraph(g)
> 
> This should keep the linebreaks
> 
> Cheers,
> Florian
> 
> On 13.03.2008, at 09:00, Marc Carlson <mcarlson at fhcrc.org> 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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> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
> > 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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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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>