[BioC] Rgraphviz rendering

[Bornman, Daniel M]

Dear BioC,

I am rendering my own graph of gene ontology terms from my own 2 column
matrix of nodes and nodes they are connected to, respectively.  I am
using the {graph} package command, ftM2graphNEL.  Everything is working
well and the results are very presentable until I try to manipulate
attributes. If I plot the graph with the plot() method in {Rgrapgviz}
with the graph object as the ONLY argument (everything else set as
default), the graph is drawn in a very readable form and resembles any
GO graph you see in the Bioconductor literature with "all" nodes
eventually leading to the root node.  

However, when I change an attribute, say the fillcolor of the nodes
using plot(myGraph, attrs = list(node = list(fillcolor = "yellow"))),
the graph is rendered in a not-so readable format.  It looks like all
the nodes at each "generation" are flattened and separated into distinct
rows.  Regardless, does anyone know why my graph is being rendered
differently after I set attributes?


Thanks,
Daniel Bornman
Battelle Memorial Institute
505 King Ave
Columbus, OH 43201
614.424.3229