[R] pairs

Prof Brian Ripley ripley at stats.ox.ac.uk
Thu Jan 9 09:45:03 CET 2003

Sounds like the problem is in your X server and not in R.  I've seen this
with Xfree (and don't use that myself on Linux).

1) I suggest you try a postscript() device, and convert later if you need
to.  Expect a very large file size.

2) Don't plot all the points.  You say you have a `very large dataset'. In
statistics, we give numbers, not vague descriptions.  However, with what
that means to me (many millions of rows) a scatterplot of a very large
dataset is going to be mainly black at least in places.  (We've
experienced that with 1.4 million points, for example.) That's not a good
way to display the data.  Either use a density plot, or if you are
interested in outliers, thin the centre.  We did this by estimating a
density phat, then randomly selecting points with probability min(1,
const/phat(x))  for a suitable `const'.

On Thu, 9 Jan 2003, J C wrote:

> Hello,
> I'm fairly new to R so please excuse me if I am asking something obvious.
> I have looked in the FAQ, Introduction, and help pages, and searched the
> archives, but I don't know much about graphics yet.
> I'm running Red Hat Linux 2.14.18  on a machine blessed with dual 1.5 Xeon
> processors and 3.7GB of RAM. I have a very large dataset with 27 variables,
> and in exploring the data I want to take snapshots using pairs(). The lower
> matrix and diagonal are filled with other graphics. (Please don't suggest
> that I cut down the variable number! This is in fact the trimmed-down,
> must-have set of variables.)
> Of course, even with all that memory, I get a crash about 2/3 of the way
> through. This is one of those cases where it's hard to troubleshoot since
> everything works fine for small datasets.  It is tantalizing because the
> process takes over two hours to display most of the figure before the
> freeze happens.
> However, it seems to me that the crash is more related to the kind of
> graphics device that I'm using and the size of the device.For instance, if
> I'm using X11 it crashes slower than using png, and right now I'm trying
> bitmap to produce a png file (it hasn't crashed after a half hour now, but
> there's always time for that later.)  The plot also gets further along if I
> set a small area for the device, but of course then the plots are
> ridiculously tiny and hard to interpret.  I have 729 little plots, and I'd
> be satisfied if they were at least .75 inches on each side... about 21 in.
> square altogether.
> What can I do to increase the chances that I'll be able to produce a
> viewable, printable image?
> Suppose that bitmap works-- can I raise the resolution up from 72 without
> fear?
> Thanks,
> Jean
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Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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