[R] makeGOGraph node spacing

[Ben Bolker]

Loren Engrav wrote:
> 
> Greetings
> 
> Am newbie using MacOS10.4.10
> R version 2.6.0 Patched (2007-11-09 r43408)
> Gostats 2.4.0
> RGraphviz 1.16.0
> Xcode X11 1.1.3 - XFree86 4.4.0
> 
> I want to make an induced GO tree from 1019 genes so I did
> 
>> x <- scan(file="GeneIDsToBioconductor2.txt", sep=",")
> Read 1019 items
>> xc <- as.character(x)
>> xctree <- makeGOGraph(xc, Ontology="BP", removeRoot=FALSE)
> 
> Then I did
>> plot (xctree)
> 
> And it produces the tree but
> 1) the nodes are so close together that the GO term labels overlap, I
> moved
> them around with Illustrator but that was painful and we have several more
> trees to do, and
> 2) it produced bizillions of warnings like
> 1: In arrows(head_from[1], head_from[2], head_to[1], head_to[2],  ... :
>   zero-length arrow is of indeterminate angle and so skipped
> 
> Then I did
>> plot (xctree, attrs=list(node=list(shape="box", nodesep=1)))
> 
> This yielded only 2 warnings
> 1: In arrows(head_from[1], head_from[2], head_to[1], head_to[2], col =
> edgeColor,  : zero-length arrow is of indeterminate angle and so skipped
> 
> But the tree has not changed, still overlapping node labels
> 
> three questions please
> 1) are the warnings related to content and I need worry about them or are
> they just graphical and I need not
> 2) is there a way to spread out the nodes to prevent label overlap
> 3) if the process cut warnings to 2, why no change in the graph
> 
> 

   You might have better luck with this on the Bioconductor mailing list ...

  Ben Bolker

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