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 Thank you Loren Engrav, MD Univ Washington Seattle I sent this 9 and 3hrs ago but somehow failed Perhaps it was the pdf attachment so I removed that and tried again The pdf of the graph can be seen at <http://homepage.mac.com/engrav> Click on the Filesharing arrow and download the pdf I apologize if this shows up 3 times ______________________________________________ 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.
