Control dot border colors in phytools dotTree

A phytools user recently asked if it was possible to control the outline color of dots in the the dotTree function for plotting discrete or continuous character data as dots adjacent to the tips of the phylogeny.

#rstats help! anyone know an argument that governs the dot outline color in phytools::dotTree()?
I want to set it to white or transparent please. ping @phytools_liam .https://t.co/fmsTkTEyBf pic.twitter.com/Cmk1rDi0rI

— Hedvig (@Laserhedvig) June 5, 2023

The answer was no; however, I have now pushed an update to allow this, which can be obtained by updating phytools from GitHub.

Here’s a very quick demo.

Load phytools:

library(phytools)

Load some test data.

data(sunfish.data)
data(sunfish.tree)

Create the plot using default border settings.

cols<-setNames(viridisLite::viridis(n=2),
    levels(sunfish.data[[1]]))
dotTree(sunfish.tree,sunfish.data[,1,drop=FALSE],ftype="i",
  colors=cols,fsize=0.7)

OK, now let’s make some adjustments based on the new options available to us.

dotTree(sunfish.tree,sunfish.data[,1,drop=FALSE],ftype="i",
  colors=cols,fsize=0.7,border="blue")

More commonly, I imagine, users might like to do away with the border altogether. This can be accomplished by setting it to "transparent" (or to the background color of the plot, for that matter) as follows. Note that in this case the plotted size of our dots will seem to shrink, so I added the function argument cex.dot to account for that.

dotTree(sunfish.tree,sunfish.data[,1,drop=FALSE],ftype="i",
  colors=cols,fsize=0.7,border="transparent",cex.dot=1.1)

Excellent!

The same set of arguments also works for continuous character data. For example:

data("anoletree")
data("anole.data")
dotTree(anoletree,anole.data,fsize=0.5,border="transparent",cex.dot=1.5,
  length=20,standardize=TRUE,colors=palette()[2],labels=TRUE)

That’s all for now.