[R] Size of plots in pdf files#can it be smaller?

[Henrik Bengtsson]

Hi,

I've got a trial version of a thinScatter() function that
(down-)samples 2d-scatter plots while preserving the empirical density
distribution.  You can grab it by:

source("http://www.braju.com/R/hbLite.R");
hbLite("scatterPlots");

Example from example(thinScatter):

library("scatterPlots");

# Sample scatter data
n <- 10e3
x <- rnorm(n=n)
y <- rnorm(n=n)
xy <- cbind(x=x, y=sin(x)+y/5)

layout(matrix(1:4, nrow=2, byrow=TRUE))
par(mar=c(5,4,2,1))

# Plot data
plot(xy, pch=1)

# Thin scatter data by subsampling
rhos <- c(1/3, 1/4, 1/6)
for (kk in seq(along=rhos)) {
  xy2 <- thinScatter(xy, size=rhos[kk])
  points(xy2, pch=1, col=kk+1)
  title <- paste(sprintf("%.1f%%", 100*c(1, rhos)), collapse=", ")
  mtext(side=3, line=0, paste("Densities:", title))
}

for (kk in seq(along=rhos)) {
  xy2 <- thinScatter(xy, size=rhos[kk])
  plot(xy2, pch=1, col=kk+1)
  mtext(side=3, line=0, sprintf("Density: %.1f%% [n=%d]",
100*rhos[kk], nrow(xy2)))
}

If the mailing list allows it, a PNG is attached.

/Henrik

On Mon, Sep 7, 2009 at 1:50 PM, Philipp Pagel<p.pagel at wzw.tum.de> wrote:
>> I have to produce arrangements of 25 simple plots of the type
>> plot(x,y,pch=".") where there are typically on the order of 20000
>> points.
>> So, overall, I have about 500000 points. When I use the pdf device,
>> I get file sizes (on a Windows machine) of about 10 MB.
>> When I then zip the files, I'm down to about 0.5MB, so the original
>> pdf files were created with a lot of 'air'.
>> I'm wondering why the pdf files are so large and whether there is an
>> alternative to produce them smaller. Any ideas?
>
> As far as I know, R cannot directly produce compressed pdf files. You
> could postprocess your plots. E.g. pdftk is quite conveniant:
>
> pdftk foo.pdf cat output foo2.pdf compress
>
> Maybe in a loop if many files are involved.
>
> cu
>        Philipp
>
> --
> Dr. Philipp Pagel
> Lehrstuhl für Genomorientierte Bioinformatik
> Technische Universität München
> Wissenschaftszentrum Weihenstephan
> 85350 Freising, Germany
> http://webclu.bio.wzw.tum.de/~pagel/
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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