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

Byron Ellis byron.ellis at gmail.com
Wed Jun 20 11:48:32 CEST 2007

Actually, the standard plot for flowCore already uses smoothScatter so
that's already been done. The same is also true of flowViz (although
you can turn it off in flowViz) and neither should be producing
particularly massive pdfs. If the data are not HIPPA restricted it
might be interesting to see if there's something pathological about
your data (aside from the disease of course...) that might explain it
and let us perhaps track down a plotting bug.

Failing that, Seth's first suggestion is also relevant and can be
accomplished using (what else) but a sampleFilter(). This is just
another filter, like rectangleGate, that returns a small subset of the
data. You may need to use flowCore:::sampleFilter rather than just
sampleFilter due to an oversight in the NAMESPACE file, but it is
available in all versions of flowCore. Just give it a number of events
and you're off to the races (it can be used in Subset commands just
like rectangleGate).

On 6/20/07, Seth Falcon <sfalcon at fhcrc.org> wrote:
> "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
> devices.
> + seth
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> http://bioconductor.org
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Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian

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