I am generating some complex graph output using Rgraphviz:
plot(graphNEL object) and it is too cluttered to easily decipher on
screen. Saving the screen output to postscript does not help. What
seems like it might work would be outputting directly to a .ps file
after setting options(papersize=customLargeSize).
Can this be accomplished. If so, how? If not, is there a better option
to accomplish what I need to do?
Thanks,
Mark
Mark W. Kimpel MD
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Official Business Address:
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Department of Psychiatry
Indiana University School of Medicine
Biotechnology, Research, & Training Center
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(317) 490-5129 Home, Work, & Mobile
1-(317)-536-2730 FAX
Hi Mark,
"Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes:
> I am generating some complex graph output using Rgraphviz:
> plot(graphNEL object) and it is too cluttered to easily decipher on
> screen. Saving the screen output to postscript does not help. What
> seems like it might work would be outputting directly to a .ps file
> after setting options(papersize=customLargeSize).
>
> Can this be accomplished. If so, how?
It looks like the postscript device accepts paper="special" in which
case the paper size can be defined using widght and height. I haven't
tried this, but it sounds like what you want.
> If not, is there a better option to accomplish what I need to do?
It depends on what you need to do :-)
Laying out large graphs in a readable fashion is difficult. If there
is a part of the graph that you want to emphasize, you may be able to
improve the display by varying the node sizes. You can also take a
look at the subgraph plotting in Rgraphviz. This essentially gives
a hint to the layout algorithms that a subgraph is important.
Hope that helps some.
+ seth
"Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes:
> Seth,
>
> I am a novice at manipulating options in R and working with output
> devices.
>
> Assuming I want to set my postscript paper size as Width= 15" and
> Height= 15", what code would set the option for this?
>
> Also, how to I get the plot method for Rgraphviz to output to
postscript
> instead of screen?
Warning: untested code ahead
I think it would look something like this:
## a graphNEL instance you want to plot
g
## setup the postscript device. All plot commands will be
## sent to this device until you call dev.off().
postscript(file="bigGraphPlot.ps", paper="special",
width=15, height=15)
## do the plot, you should not see anything on screen
plot(g)
## close the graphics device
dev.off()
You might also want to try the pdf() device.
On Tue, 2006-06-06 at 14:00 -0700, Seth Falcon wrote:
> "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes:
>
> > Seth,
> >
> > I am a novice at manipulating options in R and working with output
> > devices.
> >
> > Assuming I want to set my postscript paper size as Width= 15" and
> > Height= 15", what code would set the option for this?
> >
> > Also, how to I get the plot method for Rgraphviz to output to
postscript
> > instead of screen?
>
> Warning: untested code ahead
>
> I think it would look something like this:
>
> ## a graphNEL instance you want to plot
> g
>
> ## setup the postscript device. All plot commands will be
> ## sent to this device until you call dev.off().
> postscript(file="bigGraphPlot.ps", paper="special",
> width=15, height=15)
> ## do the plot, you should not see anything on screen
> plot(g)
> ## close the graphics device
> dev.off()
>
>
> You might also want to try the pdf() device.
I've personally had success with:
pdf("foo.pdf", width=24, height=36) ### width/height whatever you want
plot(g)
dev.off()
for large networks of genes (also a graphNEL object). Even if you
don't
print it out, the layout is much easier to read when opened on-screen.
--Jake
Seth,
I am a novice at manipulating options in R and working with output
devices.
Assuming I want to set my postscript paper size as Width= 15" and
Height= 15", what code would set the option for this?
Also, how to I get the plot method for Rgraphviz to output to
postscript
instead of screen?
Mark
Mark W. Kimpel MD
(317) 490-5129 Home, Work, & Mobile
1-(317)-536-2730 FAX
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth
Falcon
Sent: Tuesday, June 06, 2006 4:03 PM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] help with large Rgraphviz output
Hi Mark,
"Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes:
> I am generating some complex graph output using Rgraphviz:
> plot(graphNEL object) and it is too cluttered to easily decipher on
> screen. Saving the screen output to postscript does not help. What
> seems like it might work would be outputting directly to a .ps file
> after setting options(papersize=customLargeSize).
>
> Can this be accomplished. If so, how?
It looks like the postscript device accepts paper="special" in which
case the paper size can be defined using widght and height. I haven't
tried this, but it sounds like what you want.
> If not, is there a better option to accomplish what I need to do?
It depends on what you need to do :-)
Laying out large graphs in a readable fashion is difficult. If there
is a part of the graph that you want to emphasize, you may be able to
improve the display by varying the node sizes. You can also take a
look at the subgraph plotting in Rgraphviz. This essentially gives
a hint to the layout algorithms that a subgraph is important.
Hope that helps some.
+ seth
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