[BioC] makeGOGraph internode distance

[Loren Engrav]

Greetings

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

Thank you

Loren Engrav, MD
Univ Washington
Seattle