like this:
library(rgl)
open3d()
x <- sort(rnorm(1000))
y <- rnorm(1000)
z <- rnorm(1000) + atan2(x,y)
plot3d(x, y, z, col=rainbow(1000))
open3d()
x <- sort(rnorm(20))
y <- rnorm(20)
z <- rnorm(20) + atan2(x,y)
plot3d(x, y, z, col=rainbow(20))
The key here is calling open3d
before the second plot to open a new "device"