Wayne,
Try the iplot command in iPlots. You can then vary both the
pointsize and the transparency of your scatterplot interactively and
decide which scatterplot conveys the information best. Sometimes
it's helpful to use more than one scatterplot when presenting your
results.
(I must admit to being very surprised that jittering and sunflower
plots have been suggested for a dataset of 5000 points. Do those who
mentioned these methods have examples on that scale where they are
effective?)
Antony Unwin
Professor of Computer-Oriented Statistics and Data Analysis,
University of Augsburg,
Germany
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