[BioC] help with rendering layers in Rgraphviz

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Wed Jun 13 06:42:36 CEST 2007

On Jun 12, 2007, at 11:20 AM, Mark W Kimpel wrote:

> I am using Rgraphviz in "neato" mode to layout a graph with about 500
> nodes and 1500 edges. Rgraphviz first renders the nodes and then the
> edges, meaning that I have a lot of edges overlapping with nodes. I
> would like to put the edges behind the nodes to avoid this.
> In reviewing documentation of both Graphviz and Rgraphviz, I do not
> think using the "no overlap" option would work with a graph of this
> size. Being able to see each and every edge is also not important  
> for my
> application, so I am wondering if I can use layers to render the edges
> in a layer behind the nodes.
> Will this work? If not, any other suggestions? If it will, could an
> expert supply me with some sample code to render edges and nodes in
> separate layers? I could not find any in the documentation I reviewed.

In the code for Rgraphviz we just use Graphviz to layout the graph,  
ie. we get the (x,y) positions of the nodes and the function forms of  
the lines. Having those (and some other parameters we also need) we  
render (draw) the graph using standard R functions. So I doubt that  
Graphviz has any option that will affect this from the point of view  
of Rgraphviz. You could export the graph in dot format and then use  
the command line version of Graphviz to actually render (draw) the  
Or you could try and hack the R code as you please. That should not  
be terrible hard in fact. You can get the relevant code by
R> getMethod("plot", "Ragraph")

(Ragraph is the name of the object after we retrieve it from Graphviz  
layout routine).


> Thanks,
> Mark
> -- 
> ---
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
> 15032 Hunter Court, Westfield, IN  46074
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> (317) 663-0513 Home (no voice mail please)
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