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

[michael watson (IAH-C)]

Figured out that the breaks were due to extra edges I had defined as
having color "white".  This is why Mondays are bad. 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of michael
watson (IAH-C)
Sent: 29 January 2007 14:30
To: Tony Chiang
Cc: Bioconductor Mail List
Subject: Re: [BioC] Ensuring two graphs have the same layout in
Rgraphviz

No problems.
 
I think this may be more of a problem with my set up than with
Rgraphviz, but we will see.  I have a graph object, which I created
using some data and code.  I have also set the colors for the edges.
Example 1 produces this:
 
http://coxpress.sourceforge.net/g277network.jpg  (broken edges at the
top left node, and in the center)
 
Example 2 produces this:
 
http://coxpress.sourceforge.net/g2772network.jpg
 
Now, I've looked at these in Internet Explorer, Irfanview and Adobe and
some of the edges are broken all of them.  Of course, this could just be
my set up.  How do they look to you?
 
Code:
# example1

attr <- getDefaultAttrs()

attr$node$shape="ellipse"

attr$node$fixedsize=TRUE

attr$node$height=0.3

attr$node$width=0.3

 

jpeg("g277network.jpg", height=1000, width=1000, quality=100)

plot(graph,"neato", edgeAttrs = eAttr, attrs=attr)

dev.off()

 

# example2

attr <- getDefaultAttrs()

attr$node$shape="ellipse"

attr$node$fixedsize=TRUE

attr$node$height=0.3

attr$node$width=0.3

 

jpeg("g2772network.jpg", height=1000, width=1000, quality=100)

par(lwd=2)

plot(graph,"neato", edgeAttrs = eAttr, attrs=attr)

dev.off()

 


________________________________

From: tc.fhcrc at gmail.com [mailto:tc.fhcrc at gmail.com] On Behalf Of Tony
Chiang
Sent: 29 January 2007 14:13
To: michael watson (IAH-C)
Cc: Bioconductor Mail List
Subject: Re: [BioC] Ensuring two graphs have the same layout in
Rgraphviz


Hi Mick,

I don't think I have ever produced a graph where the edges and nodes
were broken. But send the code and let me see if I or anyone else can
reproduce this type of behaviour. I am going to copy the bioconductor
list because if this turns out to be an error, then it would be nice to
have this online so the list would also know. Hope that is ok with you. 

Cheers,
--TC


On 1/29/07, michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> wrote: 

	Hi Tony
	 
	Just briefly taking this off the list as I am not sure if this
is a problem just with my graphics card or if it is the package.  The
plots and images (both from jpeg() and bmp()) produced by Rgraphviz are
not the best quality on my PC, with some edges and nodes appearing
broken.
	 
	Do you get this too, or is it just that my graphics card is not
good enough?
	 
	Thanks
	Mick
	
	
________________________________

	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
		
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confidentia...{{dropped}} 
		
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