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There is an example in ?plot3d if you are talking about plotting points in a 3d space and colouring them: <pre><code>x <- sort(rnorm(1000)) y <- rnorm(1000) z <- rnorm(1000) + atan2(x,y) plot3d(x, y, z, col=rainbow(1000)) </code></pre> But if you mean to colour the points by a 4th variable, say a grouping variable, then we can modify the example above to do this by creating a grouping variable <pre><code>grp <- gl(5, 200) ## 5 groups 200 members each ## now select the colours we want cols <- 1:5 ## Now plot plot3d(x, y, z, col=cols[grp]) </code></pre> <hr> OK, is this more what you want? <pre><code>X <- 1:10 Y <- 1:10 ## Z is now a 100 row object of X,Y combinations Z <- expand.grid(X = X, Y = Y) ## Add in Z1, which is the 3rd variable ## X,Y,Z1 define the surface, which we colour according to ## 4th variable Z2 Z <- within(Z, { Z1 <- 1.2 + (1.4 * X) + (-1.9 * Y) Z2 <- 1.2 + (1.4 * X) - (1.2 * X^2) + (1.9 * Y) + (-1.3 * Y^2) Z3 <- 1.2 + (1.4 * X) + (-1.9 * Y) + (-X^2) + (-Y^2)}) ## show the data head(Z) ## Set-up the rgl device with(Z, plot3d(X, Y, Z1, type = "n")) ## Need a scale for Z2 to display as colours ## Here I choose 10 equally spaced colours from a palette cols <- heat.colors(10) ## Break Z2 into 10 equal regions cuts <- with(Z, cut(Z2, breaks = 10)) ## Add in the surface, colouring by Z2 with(Z, surface3d(1:10,1:10, matrix(Z1, ncol = 10), color = cols[cuts], back = "fill")) with(Z, points3d(X, Y, Z1, size = 5)) ## show grid X,Y,Z1 </code></pre> Here's a modification where the plane surface <code>Z1</code> is curved (<code>Z3</code>). <pre><code>## Set-up the rgl device plotting Z3, a curved surface with(Z, plot3d(X, Y, Z3, type = "n")) with(Z, surface3d(1:10,1:10, matrix(Z3, ncol = 10), color = cols[cuts], back = "fill")) </code></pre> The detail of what I did to get <code>Z2</code> probably doesn't matter, but I tried to get something like the graph you linked to. If I've still not got what you want, can you edit your Q with some example data and give us a better idea of what you want? HTH
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