R rgl distance between axis ticks and tick labels

Question

I am plotting some point data using plot3d(). I would like to bring my y axis tick labels a little closer to my y axis tick marks.

The best way I can think of doing this is to

1) plot the data first, without drawing the axes

2) call on axis3d() to draw the y axis and tick marks but suppress labels from being drawn.

3) query the current position of each tick mark in 3D space. Store positions in a vector.

4) use mtext3d() to add labels at positions based on an adjustment to the vector

I am having a problem at step 3. I don't know how to query the position of each tick mark. par3d() allows you to query a number of graphical parameters, is there something similar I can use to get the position each y axis tick?

Am I approaching this wrong? Probably.

Here is an example piece of code, without text added for y axis labels....

require(rgl)
x <- rnorm(5)
y <- rnorm(5)
z <- rnorm(5)
open3d()
plot3d(x,y,z,axes=F,xlab="",ylab="",zlab="")
par3d(ignoreExtent=TRUE)
par3d(FOV=0)
par3d(userMatrix=rotationMatrix(0,1,0,0))
axis3d('y',nticks=5,labels = FALSE)
par3d(zoom=1)
par3d(windowRect=c(580,60,1380,900))

Answer 1

One way to do this is to explicitely define the tick locations before drawing the axis, instead of querying them after drawing the axis. Then you can use the line= option of mtext3d to control the distance of the tick labels from the axis like this:

require(rgl)
rgl.close()
x <- rnorm(5)
y <- rnorm(5)
z <- rnorm(5)
open3d()
plot3d(x,y,z,axes=F,xlab="",ylab="",zlab="")
par3d(ignoreExtent=TRUE)
par3d(FOV=0)
par3d(userMatrix=rotationMatrix(0,1,0,0))
par3d(zoom=1)
par3d(windowRect=c(580,60,1380,900))

# and here is the trick:
my.ticks <- pretty(y, n=5)
axis3d('y', at=my.ticks, labels=rep("", 5))
mtext3d(paste(my.ticks), at=my.ticks, edge='y', line=.6)

Answer 2

I found that the easiest way to control both the label position and tick length in axis3d is to rewrite the function with a couple of extra parameters ticksize and lab_dist added which can be used to overwrite the default values embedded in the function. The default values of ticksize = 0.05 , and lab_dist = 3 reproduce the behaviour of the original axis3d .

To get smaller ticks and closer labels, you can then call it with eg

axis3('y', nticks=5, labels = FALSE, ticksize = 0.03, lab_dist = 2)

The new function looks like this:

axis3 <- function (edge, at = NULL, labels = TRUE, tick = TRUE, line = 0, 
          pos = NULL, nticks = 5, ticksize = 0.05, lab_dist = 3, ...) 
{
  save <- par3d(skipRedraw = TRUE, ignoreExtent = TRUE)
  on.exit(par3d(save))
  ranges <- rgl:::.getRanges()
  edge <- c(strsplit(edge, "")[[1]], "-", "-")[1:3]
  coord <- match(toupper(edge[1]), c("X", "Y", "Z"))
  if (coord == 2) 
    edge[1] <- edge[2]
  else if (coord == 3) 
    edge[1:2] <- edge[2:3]
  range <- ranges[[coord]]
  if (is.null(at)) {
    at <- pretty(range, nticks)
    at <- at[at >= range[1] & at <= range[2]]
  }
  if (is.logical(labels)) {
    if (labels) 
      labels <- format(at)
    else labels <- NA
  }
  mpos <- matrix(NA, 3, length(at))
  if (edge[1] == "+") 
    mpos[1, ] <- ranges$x[2]
  else mpos[1, ] <- ranges$x[1]
  if (edge[2] == "+") 
    mpos[2, ] <- ranges$y[2]
  else mpos[2, ] <- ranges$y[1]
  if (edge[3] == "+") 
    mpos[3, ] <- ranges$z[2]
  else mpos[3, ] <- ranges$z[1]
  ticksize <- ticksize * (mpos[, 1] - c(mean(ranges$x), mean(ranges$y), 
                                    mean(ranges$z)))
  ticksize[coord] <- 0
  if (!is.null(pos)) 
    mpos <- matrix(pos, 3, length(at))
  mpos[coord, ] <- at
  x <- c(mpos[1, 1], mpos[1, length(at)])
  y <- c(mpos[2, 1], mpos[2, length(at)])
  z <- c(mpos[3, 1], mpos[3, length(at)])
  if (tick) {
    x <- c(x, as.double(rbind(mpos[1, ], mpos[1, ] + ticksize[1])))
    y <- c(y, as.double(rbind(mpos[2, ], mpos[2, ] + ticksize[2])))
    z <- c(z, as.double(rbind(mpos[3, ], mpos[3, ] + ticksize[3])))
  }
  result <- c(ticks = segments3d(x, y, z, ...))
  if (!all(is.na(labels))) 
    result <- c(result, labels = text3d(mpos[1, ] + lab_dist * ticksize[1], 
                                        mpos[2, ] + lab_dist * ticksize[2], 
                                        mpos[3, ] + lab_dist * ticksize[3], 
                                        labels, ...))
  lowlevel(result)
}