[BioC] Ensuring two graphs have the same layout in Rgraphviz

[Wolfgang Huber]

 > I'm also now interested in controlling the appearance of the nodes. It
 > would seem that you can have a constant node size, with the label font
 > size determined by the size of the node; or a variable node size, with
 > the label font size determined by attributes.  I would like a
 > combination, ie a consistent node size, but font size determined by
 > attributes, and overlapping the node shape edges where needed.
 >
 > Michael



Hi Michael,

unfortunately I don't think this can be done with the current 
implementation, see the body of

    setMethod("plot", "Ragraph", ...

in 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rgraphviz/R/graph.R
(user: readonly, password: readonly). The code there is rather 
straightforward and simplistic, maybe if you are adventurous give it a 
try to improve it. If you think your changes would be of general use, 
you'd want to coordinate this with the maintainer Li Long who is 
currently refactoring much of the package, including this part (see also 
section 8 of the package vignette).

  Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


> 
> 
> From: tc.fhcrc at gmail.com [mailto:tc.fhcrc at gmail.com] On Behalf Of Tony
> Chiang
> Sent: 29 January 2007 12:59
> To: michael watson (IAH-C)
> Cc: Bioconductor Mail List
> Subject: Re: [BioC] Ensuring two graphs have the same layout in
> Rgraphviz
> 
> 
> Hi Michael,
> 
> I don't know the exact answer to your question, but I do have a hack
> solution. If you plot all the edges for both graphs, but make a subset
> of the edges in graph 1 white (or what ever background color you use)
> and then the complement of those edges in graph 2 white, you will get
> two graphs with seemingly different 
> edges with the same layout. If there are any better solutions, I would
> be interested to hear them as well.
> 
> Cheers,
> --TC
> 
> 
> On 1/29/07, michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> wrote: 
> 
> 	Hi
> 	
> 	Sorry for the obvious question, I read the PDFs and tried to
> figure it
> 	out but couldn't.  I want to show two graphs, they have the same
> nodes
> 	but different edges.  I want the nodes to stay in the same place
> for the 
> 	two graphs, but obviously the edges will change.  How do I
> ensure the
> 	nodes stay in the same place for both graphs?
> 	
> 	Many thanks
> 	Mick
> 	
> 	The information contained in this message may be\ confident...{{dropped}}
> 
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