[BioC] Help: Slow Loading pdfs Produced by 'plot'

Seth Falcon sfalcon at fhcrc.org
Wed Jun 20 10:55:03 CEST 2007

"M. Jankowski" <mjankowski at gmail.com> writes:
> y = Subset(x,rectangleGate("FSC.H",c(52,2000), "SSC.H",=c(52,2000)))
> plot(y)
> #This also looks fine but the resulting *.pdf or figure must be
> massive. It takes a full minute, albeit on my 4 year old computer, to
> load the *.pdf. This problem occurs whether or not I run the code in
> Sweave or on the command line.
> Where and how do I change the settings to adjust how large the *.pdf's
> get (assuming size is the problem)? There is a ton of data on the
> plot, is there some way to generate a pdf that looks the same but
> takes up much less space/loading time?

You can take two approaches to produce graphics with a smaller output
file size:

  1. Plot fewer points.

  2. Switch to a bitmap rather than vector based graphics format
     (e.g. jpg, png).

For approach (1), you might consider a function like smoothScatter
(should be in the geneplotter package).

For approach (2), see the help pages for the relevant graphics

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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