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

[M. Jankowski]

Before I ask my question I just want to say how impressed I am with R,
Bioconductor, the packages, and the helpful community here!

Ok, on to the question. I run this code with the command "R CMD SWEAVE *.Snw":
> library("flowCore")
> x <- read.FCS("/home/mdj/data/yifacs2/NL7_PHA03_1.fcs", transformation = FALSE,
+ alter.names = TRUE)
> print(summary(x))
#This looks just fine but does not look pretty in text format.

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?

Thanks again in advance. Let me know if there is a better place for me
to ask this question.

Thanks!
Matt