R help - Jul 2012 - Thinning Lattice Plot

Is there an easy way to "thin" a lattice plot? I often create plots
from
large data sets, and use the "pdf" command to save them to a file, but
the
resulting files can be huge, because every point in the underlying dataset
is rendered in the plot, even though it isn't possible to see that much
detail.

For example:

require(Hmisc)
x <- rnorm(1e6)

pdf("test.pdf")
Ecdf(x)
dev.off()

The resulting pdf files is 31MB. Is there any easy way to get a smaller pdf
file without having to manually prune the dataset?

Thanks.

- Elliot

-- 
Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
134 Mount Auburn Street | Cambridge, MA | 02138
Phone: (617) 503-4619 | Email: elliot.bernstein@fdopartners.com

	[[alternative HTML version deleted]]

On Jul 30, 2012, at 2:13 PM, Elliot Joel Bernstein wrote:
> Is there an easy way to "thin" a lattice plot? I often create
plots
> from
> large data sets, and use the "pdf" command to save them to a
file,
> but the
> resulting files can be huge, because every point in the underlying  
> dataset
> is rendered in the plot, even though it isn't possible to see that  
> much
> detail.
>
> For example:
>
> require(Hmisc)
> x <- rnorm(1e6)
>
> pdf("test.pdf")
> Ecdf(x)
> dev.off()
>
> The resulting pdf files is 31MB. Is there any easy way to get a  
> smaller pdf
> file without having to manually prune the dataset?
There are plotting routines that display the density of distributions.  
I use hexbin fairly frequently but that is for 2d plots.  If you  
wanted the ECDF of a 1d vector, you could use cumsum() on the output  
of hist() or quantile() with suitable arguments to their parameters to  
control the degree of aggregation. Either of these yields an 8KB file  
on my machine.

 > pdf("test.pdf")
 > xyplot( cumsum(hist(x, plot=F)$intensities) ~ hist(x, plot=F) 
$breaks )
 > dev.off()
quartz
      2

 > pdf("test.pdf")
 > xyplot( (0:100)/100 ~ quantile(x, prob=(0:100)/100)  )
 > dev.off()
quartz
      2


>
> Thanks.
>
> - Elliot
>
> -- 
> Elliot Joel Bernstein, Ph.D. | Research Associate | FDO Partners, LLC
> 134 Mount Auburn Street | Cambridge, MA | 02138
> Phone: (617) 503-4619 | Email: elliot.bernstein at fdopartners.com
>
David Winsemius, MD
Alameda, CA, USA

On Tue, Jul 31, 2012 at 2:43 AM, Elliot Joel Bernstein
<elliot.bernstein at fdopartners.com> wrote:
> Is there an easy way to "thin" a lattice plot? I often create
plots from
> large data sets, and use the "pdf" command to save them to a
file, but the
> resulting files can be huge, because every point in the underlying dataset
> is rendered in the plot, even though it isn't possible to see that much
> detail.
>
> For example:
>
> require(Hmisc)
> x <- rnorm(1e6)
>
> pdf("test.pdf")
> Ecdf(x)
> dev.off()
(This is not a lattice plot, BTW.)
> The resulting pdf files is 31MB.
Hmm, for me it's 192K. Perhaps you have not bothered to update R recently.
> Is there any easy way to get a smaller pdf
> file without having to manually prune the dataset?
In general, as David noted, you need to do some sort of data
summarization; great if tools are available to that, otherwise
yourself. In this case, for example, it seems reasonable to do

Ecdf(quantile(x, probs = ppoints(500, a=1)))

If you don't like to do this yourself, ecdfplot() in latticeExtra will allow

library(latticeExtra)
ecdfplot(x, f.value = ppoints(500, a=1))

-Deepayan