This example of how to use the `smoothScatter()`

function from the Bioconductor
*geneplotter* package was posted to
Andrew
Gelman’s blog by Gregor Gorjanc. The blog entry provides links to other resources
for plotting large data sets.

## Load BioConductor package "geneplotter", which requires ## annotate, Biobase, and RColorBrewer. library( package = "geneplotter" ) options( device = "X11" ) if ( interactive() ) { ## Create a matrix where the first 5000 points are centered on [0,0] ## and the second 5000 points are centered on [3,3]. x1 <- matrix( rnorm( 1e4, mean = 0, sd = 1.0 ), ncol = 2 ) x2 <- matrix( rnorm( 1e4, mean = 3, sd = 1.5 ), ncol = 2 ) x <- rbind( x1, x2 ) ## The quartz device draws these figures poorly, so use the X11 device. ## Use layout to set up a figure with four plots. X11() layout( matrix( 1:4, ncol = 2, byrow = TRUE ) ) ## Demonstrate four styles of smooth scatter plots. ## Example 1: smoothScatter( x, nrpoints = 0 ) ## Example 2: smoothScatter( x ) ## Example 3: smoothScatter( x, nrpoints = Inf, colramp = colorRampPalette( RColorBrewer::brewer.pal( 9, "YlOrRd" ) ), bandwidth = 40 ) ## Example 4: colors <- densCols( x ) plot( x, col = colors, pch = 20 ) }

The output is:

Four examples of smooth scatter plots