This works fine.

x <- sort(rnorm(1000))
y <- rnorm(1000)
z <- rnorm(1000) + atan2(x, y)
plot3d(x, y, z, col = rainbow(1000))

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This one also works.

open3d()

## wgl 
##   2

spheres3d(x, y, z, col = rainbow(1000))

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