Using RGL in pkgdown web sites

Duncan Murdoch

Source: vignettes/pkgdown.Rmd

What is the problem?

pkgdown is an R package that makes it easy to build a web site for your package. However, the previous version 1.6.1 on CRAN didn’t work so well for packages whose examples use RGL or other packages like leaflet that use htmlwidgets. This document described changes that support both of these. The changes are now incorporated into pkgdown 2.0.0, so everything but user instructions has been removed.

Using `RGL in examples.

If you use RGL in example code, they should appear automatically in examples. The RGL output is set up to mimic what would happen in a knitr document that uses

setupKnitr(autoprint = TRUE)

i.e. the output RGL commands will automatically be included in the display. Low-level changes will be collected into a single display:

# Show regression plane with z as dependent variable
library(rgl)
open3d()
## null 
##    3
x <- rnorm(100)
y <- rnorm(100)
z <- 0.2*x - 0.3*y + rnorm(100, sd = 0.3)
fit <- lm(z ~ x + y)

plot3d(x, y, z, type = "s", col = "red", size = 1)

# No plot here, because of the planes3d() call below

coefs <- coef(fit)
a <- coefs["x"]
b <- coefs["y"]
c <- -1
d <- coefs["(Intercept)"]
planes3d(a, b, c, d, alpha = 0.5)

Specifying the size of figures

By default, pkgdown generates standard plots which are wider than they are high (according to the golden ratio). Often RGL plots look better with equal width and height, since the contents may be rotated by the user.

To specify the size of plots in pkgdown, you use the figures entry in _pkgdown.yml. The defaults are similar to

figures:
  dev: ragg::agg_png
  dpi: 96
  dev.args: []
  fig.ext: png
  fig.width: 7
  fig.height: ~
  fig.retina: 2
  fig.asp: 1.618
  bg: NA
  other.parameters: []

By default RGL uses these parameters as well, but allows you to override any of fig.width, fig.height and fig.asp by specifying an rgl entry in other.parameters. For example:

figures:
  fig.width: 5
  other.parameters:
    rgl:
      fig.asp: 1

This will make all plots have a width of 5 inches and will make RGL plots square.