Duncan Murdoch wrote: > On 18/12/2007 7:31 AM, Antony Unwin wrote: >> 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?) > > Sure. The original post said there were about 50-60 unique locations. > This plot: > > x <- rbinom(5000, 20, 0.15) > y <- rbinom(5000, 20, 0.15) > plot(x,y) > > has a few more unique locations; tune those probabilities if you want it > closer. Due to the overlap, the distribution is very unclear. But this > plot > > plot(jitter(x), jitter(y))
Another alternative is smoothscatter() in the geneplotter package from Bioconductor, which does a pretty reasonable job with these example data. Best, Jim > > makes the distribution quite clear. > > I wouldn't use the default pch if I had 50000 points, but with pch=".", > it's not so bad even in that case. > > 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. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ______________________________________________ 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.
