Thursday, March 20, 2014

Custom tick labels in R perspective plots

In R, the persp() is a built-in function to create surface plots. The basic usage is straightforward: create a matrix of values

# plot a 10x10 matrix of random values in the range -100..100:
persp( matrix(runif(100, min=-100, max=100), nrow=10, ncol=10) )

All well and good, until it's time to prepare the plots for presentation -- and suddenly it becomes apparent that plots created with persp() do not work well with axis(), text(), mtext(), par(), and other standard graphics device functions.

The trans3d documentation refers the reader to the persp documentation for examples; those examples are too convoluted to serve any useful educational purpose. A quick note to documentation writers: always include an example showing the simplest possible use of your function on trivial data sets (usually the array of integers from 1 to 10, or sin(x) if a function is required). Do not use only edge cases and exciting demos as examples.

The discussion that follows will demonstrate how to construct a perspective plot with custom labels using persp() and trans3d(). The data to be plotted is a 10x10 matrix of values in the range -100:100.


The first thing to understand is that persp() does not just draw a plot; it also returns a perspective matrix (or pmat) which can be used to translate 3-dimensional coordinates to the 2-dimensional coordinate system used in the image of the plot.

The function that performs this translation is trans3d(). Its arguments are the x, y, and z coordinates to be translated, followed by the pmat. The return value is a list with two elements: x and y, the two-dimensional coordinates in the image.

If one of the x, y, and z arguments is a vector, then the vector is considered to be a line at the other two coordinates. Thus, a line along the X axis from (0, 10, 10) to (10, 10, 10) would be translated using trans3d(0:10, 10, 10, pmat); a line along the Y axis from (0, 3, 10) to (0, 7, 10) would be translated using trans3d(0, 3:7, 10, pmat).


Enough background; time for an example.


Basic Perspective Plot

First, some definitions of the data ranges to keep things clear:

x.axis <- 1:10
min.x <- 1
max.x <- 10
y.axis <- 1:10
min.y <- 1
max.y <- 10
z.axis <- seq(-100, 100, by=25)
min.z <- -100
max.z <- 100

Pay particular attention to z.axis: in addition to specifying the range of each axis, the *.axis variables also specify the tick marks of each axis.

Next, a draw the initial perspective plot, saving the pmat:

pmat <- persp( x=x.axis, y=y.axis,
               matrix(runif(100, min=-100, max=100), nrow=10, ncol=10), 
               xlab='', ylab='', zlab='', 
               ticktype='detailed', box=FALSE, axes=FALSE, 
               mar=c(10, 1, 0, 2), expand=0.25,
               col='green', shade=0.25, theta=40, phi=30 )

Note the theta (rotation along the vertical axis) and phi (rotation along the horizontal axis) parameters. It is useful to play with these a bit, as different data sets will require different viewing angles. The r ("eyepoint distance") and d ("perspective strength") parameters provide further control of the view. Note also that box and axes parameters are FALSE: we will be drawing our own axes.


Drawing the Axes

In this plot, the X axis will be drawn at min.y and min.z (left side of Y, bottom of Z), Y at max.x and min.z (right side of X, bottom of Z), and Z at min.x and min.y (left side of X, left side of Y).

These parameters are passed to trans3d() to calculate the coordinates of a line at each axis, as described previously. The translated coordinates can be passed directly to lines().

lines(trans3d(x.axis, min.y, min.z, pmat) , col="black")
lines(trans3d(max.x, y.axis, min.z, pmat) , col="black")
lines(trans3d(min.x, min.y, z.axis, pmat) , col="black")


Drawing Tick Marks

Adding tick marks requires calculating the position of a second line, parallel to the axis, and using segments() to draw ticks that span the distance between the axis and the second line. The basic procedure is as follows:

tick.start <- trans3d(x.axis, min.y, min.z, pmat)
tick.end <- trans3d(x.axis, (min.y - 0.20), min.z, pmat)
segments(tick.start$x, tick.start$y, tick.end$x, tick.end$y)

Note the (min.y - 0.20) in the calculation of tick.end. This places the second line, parallel to the X axis, at the position -0.20 on the Y axis (i.e., into negative/unplotted space).

The tick marks on the Y and Z axes can be handled similarly:

tick.start <- trans3d(max.x, y.axis, min.z, pmat)
tick.end <- trans3d(max.x + 0.20, y.axis, min.z, pmat)
segments(tick.start$x, tick.start$y, tick.end$x, tick.end$y)

tick.start <- trans3d(min.x, min.y, z.axis, pmat)
tick.end <- trans3d(min.x, (min.y - 0.20), z.axis, pmat)
segments(tick.start$x, tick.start$y, tick.end$x, tick.end$y)


Adding Tick Mark Labels

The final step is to label the ticks on each axis. Once again, the procedure is to calculate the position of a line, parallel to the axis, at the position where the labels are to be displayed:

labels <- c('first', 'second', 'third', 'fourth', 'fifth', 'sixth', 'seventh', 'eighth', 'ninth', 'tenth')
label.pos <- trans3d(x.axis, (min.y - 0.25), min.z, pmat)
text(label.pos$x, label.pos$y, labels=labels, adj=c(0, NA), srt=270, cex=0.5)

The adj=c(0, NA) expression is used to left-justify the labels, the srt=270 expression is used to rotate the labels 270°, and the cex=0.5 expression is used to scale the label text to 75% of its original size.

The labels on the Y and Z axes are produced similarly:

labels <- c('alpha', 'beta', 'gamma', 'delta', 'epsilon', 'zeta', 'eta', 'theta', 'iota', 'kappa')
label.pos <- trans3d((max.x + 0.25), y.axis, min.z, pmat)
text(label.pos$x, label.pos$y, labels=labels, adj=c(0, NA), cex=0.5)

labels <- as.character(z.axis)
label.pos <- trans3d(min.x, (min.y - 0.5), z.axis, pmat)
text(label.pos$x, label.pos$y, labels=labels, adj=c(1, NA), cex=0.5)

Note that the Y and Z axis tick labels do not need to be rotated.


The Final Product



6 comments:

  1. Hello,

    Thank you for this code, I found it extremely helpful. I spent hours trying to figure out how to add annotation to axis ticks.

    I wonder if we can package in a nice way for better flexibility!!

    ReplyDelete
  2. Also, in the pmat function, you used , and "' just after persp, a typo!!

    ReplyDelete
    Replies
    1. Yeah, took me ages to figure out so I thought it worth documenting.

      Thanks for the typo -- blogger tries to fix source code for you, inevitably breaking stuff. Hopefully it's fixed now.

      Delete
  3. Hi !

    Just a message to thank you a lot for your post !
    It saved me because i was looking for some code to print persp plots with no values on the z-axis.
    I used trans3D as you described to get draw something like i want from a persp graph with no box and no axes;
    I spent hours to manage this !!

    P.S, forgive my english, i'm french so my sentences could seem strange :p

    ReplyDelete
  4. can you give example with rsm

    ReplyDelete
  5. reading this in 2017. thank you so much!

    ReplyDelete