How to plot log transformed data in rgl 3d plot?

Question

I do a 3d plot with the rgl package and I want to use a log transformed z axes. What I do is:

# Dummy data. x <- seq(1, 2, length = 10); y <- seq(1, 3, length = 10) z <- outer(x, y, function(x, y) x + exp(y)); z <- log(z) # Plot. rgl::persp3d(x, y, z, col= "white") rgl::surface3d(x, y, z, front = "lines")

The 3d object looks as I expect. But I want the z labels not to say the log values, instead I want it to show the raw values, i.e. where the 3 is there should be a 20 (since exp(3) is approx. 20). So I am looking for some equivalent to ggplot2::scale_y_continuous(trans= "log10") as discussed here. How to do this with the rgl package?

user2554330 · Accepted Answer · 2024-11-16 17:17:44Z

One way is to tell persp3d() to skip the axes, then use calls like axes3d(), box3d(), axis3d() or bbox3d()to draw them where you want them. For example,

library(rgl) x <- seq(1, 2, length = 10); y <- seq(1, 3, length = 10) z <- outer(x, y, function(x, y) x + exp(y)); z <- log10(z) # Plot. open3d() persp3d(x, y, z, col= "white", polygon_offset = 1) surface3d(x, y, z, front = "lines") zticks <- pretty(z) zlabels <- signif(10^zticks, 2) axes3d(zat = zticks, zlab = zlabels)

The help page for the latest version (1.3.14) shows a slightly simpler way using axes3d().

Looks nice but for some reason the labels appear on another box side than the axes name. I would like the labels to be at the same place as the axes name but have no idea how to set this
You can use axes3d(zat = zticks, zlab = zlabels) for a better solution. I forgot that axes3d() accepts most of the arguments of bbox3d(). Don't say axes=FALSE in the persp3d() call if you want to keep the box.

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