I just created a new interactive version of the phytools function
phylo.toBackbone, which creates a backbone phylogeny in which some
clades are represented as triangles. This tree can then we plotted with an
plot method for the object class
Most of the code changes can be seen
The updates are kind of hacky - principally because the original version of this
appears to have been coded by me in 2013.
In previous versions of this function (e.g., 1, 2) the user had to supply the backbone tree as input along with a translation table. This is still possible, or course; however the current version allows the user to collapse clades into triangles by clicking on the fully plotted tree. This should be a nice feature for some users.
Obviously, interactive mode is kind of difficult to demonstrate - consequently I have embedded a screenshot video of a demo at the bottom. The following is just an illustration of the product. Remember for publication to save to PDF (or another line art format) to avoid aliasing, particularly on the edges of the triangles.
##  '0.5.38'
## ## Backbone phylogenetic tree with 15 subtrees and 14 resolved internal nodes. ## ## Labels: t40, t10, t27, t13, t39, ... ## Diversities: 1, 1, 1, 1, 1, ...
plot(obj) ## defaults
cols ## color some of the clades
## Clade 1 Clade 2 Clade 4 ## "black" "red" "green3"
par(cex=0.8) ## change font size par(font=3) ## change font type plot(obj,col=cols,vscale=0.7)
Here is the interactive demo:
No puedo ver el video, dice que es un video privado.ReplyDelete
Thank you Liam!ReplyDelete
I have an issue with this function phylo.toBackbone. When I click on 'click to stop' after having named all collapsed clades, it doesn't recognize my click as a stop signal. It thinks I've selected the closest to the stop-box node. So I have no way to stop it...
I'm using Mac by the way, maybe, this is the issue?