Re: [R] heavy graphs
Georg Ehret wrote:
Dear R community,I am creating large graphs with hundreds of
thousands of datapoints. My usual way for output was pdf, but now I am
getting file sizes of 30Mb that do not open well (or at all) in Adobe. Is
there a way to reduce the resolution or get rid of overlaying datapoints?
Any other idea is also warmly welcome!
Hi Georg,
As others have noted, bitmapped graphics will handle overlaid points
better than pdf. You might be able to use the count.overplot function
that clumps together points and prints the number of points rather than
the points themselves. However, with that many points, you might finish
up with a jumble of numbers.
Another possibility is to bin the points and print a color matrix that
represents the number of points in each bin.
# not a very elegant function, the example runs pretty slowly
bin.points-function(x,y,nxbins,nybins) {
binmat-matrix(0,nrow=nybins,ncol=nxbins)
xrange-range(x)
yrange-range(y)
xinc-diff(xrange)/nxbins
yinc-diff(yrange)/nybins
for(row in 1:nybins) {
for(col in 1:nxbins) {
binmat[row,col]-
sum((x = xrange+xinc*(row-1)) (x xrange+xinc*row)
(y = yrange+yinc*(col-1)) (y yrange+yinc*col))
if(col==nxbins)
binmat[row,col]-binmat[row,col] + sum((x == xrange[2])
(y = yrange+yinc*(col-1)) (y yrange+yinc*col))
}
if(row==nybins)
binmat[row,col]-binmat[row,col] + sum((y == yrange[2])
(x = xrange+xinc*(row-1)) (x xrange+xinc*row))
}
return(binmat)
}
binmat-bin.points(rnorm(10),rnorm(10),20,20)
require(plotrix)
color2D.matplot(binmat,show.legend=TRUE)
Jim
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Re: [R] heavy graphs
It's probably best to choose a different format like PNG or jpeg. -roger On Tue, Apr 15, 2008 at 5:22 PM, Georg Ehret [EMAIL PROTECTED] wrote: Dear R community,I am creating large graphs with hundreds of thousands of datapoints. My usual way for output was pdf, but now I am getting file sizes of 30Mb that do not open well (or at all) in Adobe. Is there a way to reduce the resolution or get rid of overlaying datapoints? Any other idea is also warmly welcome! Thank you and wishing you a good day! Georg. ** Georg Ehret Johns Hopkins Baltimore - US [[alternative HTML version deleted]] __ R-help@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. -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@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.
Re: [R] heavy graphs
But you also might have the additional problem that too many data points just produce an incoherent solid blob, no matter the format. Lots of folks have written about this. Check out JCGS and computer graphics literature for ideas. Also,this is one arena where fancy, dynamic, interactive software (maybe xgobi) might be useful. Maybe not (too much data). Finally, canonical answer: **appropriately** sample and plot only the sample data. The key is in defining appropriately,of course. -- Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Roger Peng Sent: Tuesday, April 15, 2008 2:34 PM To: Georg Ehret Cc: r-help Subject: Re: [R] heavy graphs It's probably best to choose a different format like PNG or jpeg. -roger On Tue, Apr 15, 2008 at 5:22 PM, Georg Ehret [EMAIL PROTECTED] wrote: Dear R community,I am creating large graphs with hundreds of thousands of datapoints. My usual way for output was pdf, but now I am getting file sizes of 30Mb that do not open well (or at all) in Adobe. Is there a way to reduce the resolution or get rid of overlaying datapoints? Any other idea is also warmly welcome! Thank you and wishing you a good day! Georg. ** Georg Ehret Johns Hopkins Baltimore - US [[alternative HTML version deleted]] __ R-help@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. -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@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. __ R-help@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.
Re: [R] heavy graphs
On 15/04/2008 5:22 PM, Georg Ehret wrote: Dear R community,I am creating large graphs with hundreds of thousands of datapoints. My usual way for output was pdf, but now I am getting file sizes of 30Mb that do not open well (or at all) in Adobe. Is there a way to reduce the resolution or get rid of overlaying datapoints? Any other idea is also warmly welcome! A hexbin plot might be an alternative. This is implemented in the hexbin package on Bioconductor. Duncan Murdoch __ R-help@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.
Re: [R] heavy graphs
Look at the hexbin package (bioconductor I think). -Original Message- From: Georg Ehret [EMAIL PROTECTED] To: r-help [EMAIL PROTECTED] Sent: 4/15/08 3:23 PM Subject: [R] heavy graphs Dear R community,I am creating large graphs with hundreds of thousands of datapoints. My usual way for output was pdf, but now I am getting file sizes of 30Mb that do not open well (or at all) in Adobe. Is there a way to reduce the resolution or get rid of overlaying datapoints? Any other idea is also warmly welcome! Thank you and wishing you a good day! Georg. ** Georg Ehret Johns Hopkins Baltimore - US [[alternative HTML version deleted]] __ R-help@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. __ R-help@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.
