Just a note, Base graphics does support transparency as long as the device plotting to supports it.
-- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Dennis Murphy > Sent: Thursday, March 31, 2011 1:36 AM > To: Samuel Dennis > Cc: R-help@r-project.org > Subject: Re: [R] Graph many points without hiding some > > Hi: > > I can think of a couple: (1) size reduction of the points; (2) alpha > transparency; (3) (1) + (2) > > >From your original plot in base graphics, I reduced cex to 0.2 and it > didn't > look too bad: > > plot(rnorm(x,mean=19),rnorm(x),col=3,xlim=c(16,24), cex = 0.2) > points(rnorm(x,mean=20),rnorm(x),col=1, cex = 0.2) > points(rnorm(x,mean=21),rnorm(x),col=2, cex = 0.2) > > AFAIK, base graphics doesn't have alpha transparency available, but the > ggplot2 package does. One approach is to adjust the alpha transparency > on > default size points; another is to combine reduced point size with > alpha > transparency. Here is your example rehashed for ggplot2. > > require(ggplot2) > d <- data.frame(x1 = rnorm(10000, mean = 19), x2 = rnorm(10000, mean = > 20), > x3 = rnorm(10000, mean = 21), x = rnorm(10000)) > # Basically stacking x1 - x3, creating two new vars named variable and > value > dm <- melt(d, id = 'x') # from reshape package, loads with ggplot2 > # Alpha transparency is set to a low level with default point size, > # but the colors in the legend are muted by the level of transparency > ggplot(dm, aes(x = x, y = value, colour = variable)) + theme_bw() + > geom_point(alpha = 0.05) + > scale_colour_manual(values = c('x1' = 'black', > 'x2' = 'red', 'x3' = 'green')) > > # A tradeoff is to reduce the point size and increase alpha a bit, but > these > changes will > # also be reflected in the legend. > > ggplot(dm, aes(x = x, y = value, colour = variable)) + theme_bw() + > geom_point(alpha = 0.15, size = 1) + > scale_colour_manual(values = c('x1' = 'black', > 'x2' = 'red', 'x3' = 'green')) > > You may well find the legend to be useless for this example, so to get > rid > of it, > > ggplot(dm, aes(x = x, y = value, colour = variable)) + theme_bw() + > geom_point(alpha = 0.15, size = 1) + > scale_colour_manual(values = c('x1' = 'black', > 'x2' = 'red', 'x3' = 'green')) + > opts(legend.position = 'none') > > The nice thing about the ggplot2 graph is that you can adjust the point > size > and alpha transparency to your tastes. The default point size is 2 and > the > default alpha = 1 (no transparency). > > HTH, > Dennis > > On Wed, Mar 30, 2011 at 10:04 PM, Samuel Dennis <sjdenn...@gmail.com> > wrote: > > > I have a very large dataset with three variables that I need to graph > using > > a scatterplot. However I find that the first variable gets masked by > the > > other two, so the graph looks entirely different depending on the > order of > > variables. Does anyone have any suggestions how to manage this? > > > > This code is an illustration of what I am dealing with: > > > > x <- 10000 > > plot(rnorm(x,mean=20),rnorm(x),col=1,xlim=c(16,24)) > > points(rnorm(x,mean=21),rnorm(x),col=2) > > points(rnorm(x,mean=19),rnorm(x),col=3) > > > > gives an entirely different looking graph to: > > > > x <- 10000 > > plot(rnorm(x,mean=19),rnorm(x),col=3,xlim=c(16,24)) > > points(rnorm(x,mean=20),rnorm(x),col=1) > > points(rnorm(x,mean=21),rnorm(x),col=2) > > > > despite being identical in all respects except for the order in which > the > > variables are plotted. > > > > I have tried using pch=".", however the colours are very difficult to > > discern. I have experimented with a number of other symbols with no > real > > solution. > > > > The only way that appears to work is to iterate the plot with a for > loop, > > and progressively add a few numbers from each variable, as below. > However > > although I can do this simply with random numbers as I have done > here, this > > is an extremely cumbersome method to use with real datasets. > > > > plot(1,1,xlim=c(16,24),ylim=c(-4,4),col="white") > > x <- 100 > > for (i in 1:100) { > > points(rnorm(x,mean=19),rnorm(x),col=3) > > points(rnorm(x,mean=20),rnorm(x),col=1) > > points(rnorm(x,mean=21),rnorm(x),col=2) > > } > > > > Is there some function in R that could solve this through > automatically > > iterating my data as above, using transparent symbols, or something > else? > > Is > > there some other way of solving this issue that I haven't thought of? > > > > Thankyou, > > > > Samuel Dennis > > > > [[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. > > > > [[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.
