Thank you I will move it over
> From: Ben Bolker <[EMAIL PROTECTED]> > Date: Sun, 18 Nov 2007 08:05:15 -0800 (PST) > To: <r-help@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 > > -- > View this message in context: > http://www.nabble.com/makeGOGraph-node-spacing-tf4828913.html#a13820491 > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
