3D plot in R using persp3D - Axis issues - r

Question

I have a matrix (m) and I'm trying to plot a 3D representation of that matrix.
> dput(head(m))
structure(c(21930, 21844, 21758, 21672, 21586, 21500, 22016,
21930, 21844, 21758, 21672, 21586, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(6L, 26L), .Dimnames = list(
NULL, c("freq.min", "freq.max", "X0", "X1", "X2", "X3", "X4",
"X5", "X6", "X7", "X8", "X9", "X10", "X11", "X12", "X13",
"X14", "X15", "X16", "X17", "X18", "X19", "X20", "X21", "X22",
"X23")))
I managed to plot a 3D surface plot, but both the axes and the axis labels are incorrect. Note that the 3D surface plot below uses the entire matrix rather than just the header, which I only include here as the dput for brevity.
persp3D(z = m[,3:26], col = "lightgrey", shade = 0.5, ticktype = "detailed", axes=T)
Let's start with the axes themselves: the axis that goes from X0 to X23 should be the X axis of the matrix (column names), but here it is regarded as the Y axis. The Y axis, regarded here as the X axis, ranges from 0 to 22016 in 256 intervals of 86.
I've spent the last many hours scouring the internet for answers on how to change the axis labels, but have not succeeded. From what I understand, if I turn off the axis argument in persp3D (axes=F) I can then customize the axis in a subsequent line, like so:
axis3d(edge= 'y+-', at =seq(0,23,by=1) ,
labels = seq(0,23,by=1))
However, a RGL device pops up, and only the axis is plotted without the actual plot itself, which stays unchanged in the built-in R graphics device.
How do I successfully change the axes?

Answer 1

Does this what you're looking for?
clab <- 0:23
rlab <- seq(0, 21586, 86)
cnum <- length(clab)
rnum <- length(rlab)
m <- matrix(
c(runif(0.5*cnum*rnum)-1, runif(0.5*cnum*rnum)+1),
rnum, cnum,
dimnames = list(rlab, clab))
library(rgl)
plot3d(
clab, rlab, t(m),
type="n",
aspect = c(100, 200, 20),
xlab = "x", ylab = "y", zlab = "z",
sub = "Grab me and rotate me!"
)
surface3d(
clab, rlab, t(m),
color = c("black", "white"),
alpha = 0.5,
add = TRUE
)
To change the axis you can interchange x and y and transpose z with t().
As a side note: I wrote two functions to transform 3D point cloud data from tall to wide format and vice versa: recexcavAAR::spatialwide and recexcavAAR::spatiallong. I find them quite useful to go back and forth between plotting and analysis. Maybe they're useful for you.
Edit:
Alternative solution with single call to persp3d
clab <- 0:23
rlab <- seq(0, 21586, 86)
cnum <- length(clab)
rnum <- length(rlab)
m <- matrix(
c(runif(0.5*cnum*rnum)-1, runif(0.5*cnum*rnum)+1),
rnum, cnum,
dimnames = list(rlab, clab))
library(rgl)
persp3d(
clab, rlab, t(m),
color = c("black", "white"),
alpha = 0.5,
aspect = c(100, 200, 20),
xlab = "x", ylab = "y", zlab = "z",
sub = "Grab me and rotate me!"
)