There have been some user-reported issues with the phytools dependency plotrix that I'm still trying to figure out.
Basically, folks have reported (and I have experienced) plotting trees using
dotTree and obtaining a result that looks something like this:
Obviously, this is no good.
While I figure this out what I'd recommend is installing the previous version of plotrix, which can be done from source in a new R session as follows:
install.packages( "https://cran.r-project.org/src/contrib/Archive/plotrix/plotrix_3.6-1.tar.gz", type="source")
The problem that remains is that if a newer version of phytools is installed from GitHub, the dependency packages will also be updated if a newer version can be found - except in our case, we don't want that! To avoid it, just do the following:
Note that to do this you should still first ensure that all the other phytools dependencies are installed & up-to-date!
I also added another small update to the internally used function
phylogram, which in turn affects mostly
plot.cophylo. This update
pts to be used instead of as a logical, to specify the
relative point size of the plotted points at the tips of the tree. This
value should be specified relative to
1 being the default, which
is in turn determined by the plotted edge widths!
Here's a quick demo:
library(phytools) dotTree(tree,X) ## the default
dotTree(tree,X,pts=FALSE) ## turned off
dotTree(tree,X,pts=0.7) ## smaller
dotTree(tree,X,pts=1.5) ## larger)
dotTree(tree,X,pts=1.2,lwd=2) ## different lwd
You get the idea.