[R] makeGOGraph node spacing

[Loren Engrav]

Thank you
I will move it over


> From: Ben Bolker <bolker at ufl.edu>
> Date: Sun, 18 Nov 2007 08:05:15 -0800 (PST)
> To: <r-help at r-project.org>
> Subject: Re: [R] makeGOGraph node spacing
> 
> 
> 
> 
> 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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