Mapping a continuous trait onto the branches of a phylogeny using variable edge widths: Part IV

A couple of days ago I posted some code showing how to plot a right- (or left-) facing phylogram with polygons for branches.

As of this afternoon, I have just pushed these new functions to the phytools GitHub page. This update can be obtained by downloading & installing phytools directly from GitHub using devtools.

library(devtools)
install_github("liamrevell/phytools")

Beyond what I showed yesterday, the major feature that I added was the option to turn on borders around our polygons, and the option to plot the vertical lines connecting edges as simple lines (that is, without width).

Here's an example:

data(sunfish.tree)
data(sunfish.data)
buccal.length<-setNames(sunfish.data$buccal.length,
    rownames(sunfish.data))
bl.object<-edge.widthMap(sunfish.tree,buccal.length)
plot(bl.object,fsize=0.9,max.width=0.8,
    legend="relative buccal length",
    color=palette()[4],min.width=0.05,border="black",
    lwd=3)

Alright, for fun let's simulate some data for two characters & apply it to facing trees:

tree<-pbtree(n=40)
X<-sim.corrs(tree,vcv=matrix(c(1,0.7,0.7,1),2,2))
par(mfrow=c(1,2))
plot(edge.widthMap(tree,X[,1]),color=palette()[2],
    lwd=4,direction="rightwards",max.width=0.8,
    ftype="off",legend="trait x",border="black")
plot(edge.widthMap(tree,X[,2]),color=palette()[4],
    lwd=4,direction="leftwards",max.width=0.8,
    ftype="off",legend="trait y",border="black")

Lastly, let's see what it looks like when we plot the vertical lines connecting edges in the plotted tree as simple lines (rather than as polygons) as was suggested in a response to my first post on this subject:

That's really neat. Thanks! Also, is it possible to only vary the width of real branches ( those defined by branch length) so you don't end up with what looks like a bunch of polytomies?

— Roi Maor (@Roi_Maor) July 15, 2020

data(mammal.tree)
data(mammal.data)
lnHomeRange<-setNames(log(mammal.data$homeRange),
    rownames(mammal.data))
homeRange.fit<-edge.widthMap(mammal.tree,lnHomeRange)
homeRange.fit

## Object of class "edge.widthMap" containing:
## (1) Phylogenetic tree with 49 tips and 48 internal nodes.
## (2) Vector of node values for a mapped quantitative
##     trait.

plot(homeRange.fit,vertical.as.polygon=FALSE,
    border="black",max.width=0.8,lwd=2,
    color=palette()[4],legend="log(home range size)")