[BioC] help with large Rgraphviz output

Kimpel, Mark William mkimpel at iupui.edu
Tue Jun 6 22:27:07 CEST 2006


I am a novice at manipulating options in R and working with output

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 W. Kimpel MD 


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-----Original Message-----
From: bioconductor-bounces at 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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