plot3d() produces a 3d plot that I can twist around and rotate. But when I call plot3d() again, the previous plot goes away and is replaced by this
An alternative to have "two 3d plots opened at once" is using mfrow3d from library("rgl"). It works the same way as par("mfrow") in classic R.
The following adapted code (from here) produces two side-by-side 3D plots (2 columns) in one window:
library(rgl)
mfrow3d(1, 2)
x <- sort(rnorm(1000))
y <- rnorm(1000)
z <- rnorm(1000) + atan2(x,y)
plot3d(x, y, z, col=rainbow(1000))
x <- sort(rnorm(20))
y <- rnorm(20)
z <- rnorm(20) + atan2(x,y)
plot3d(x, y, z, col=rainbow(20))