*I want to plot vertical lines indicating various time points on my tree. . . . Is there an easy way to do this in R. . . ?*

The answer turns out to be that yes - it is relatively easy to do this using the base function lines. Let's try:

First, let's use pbtree to simulate a tree and plot.phylo to plot it:

> tree<-pbtree(n=30,scale=100)

> x<-plot(tree)

Ok, now, the dimensions of the plotted area in plot.phylo are 0 to the tree height (plus some extra space for the labels) on the horizontal axis; and 1 through the number of tips (here 30) on the vertical axis. In case we didn't know this already, it is also returned silently by plot.phylo. Here, we have stored this in x:

> x

$type

[1] "phylogram"

...

$x.lim

[1] 0.0000 108.3092

$y.lim

[1] 1 30

...

$Nnode

[1] 29

Now let's add lines at 25, 50, and 75 (time units) above the root:

> # with our plotting window still open

> lines(x=c(25,25),y=c(1,30),lwd=2)

> lines(x=c(50,50),y=c(1,30),lwd=2)

> lines(x=c(75,75),y=c(1,30),lwd=2)

> lines(x=c(75,75),y=c(-10,30),lwd=2)

(Note that all three lines are the same height - if they seem different that is an optical illusion!) Note that we can extend the lines a little bit beyond the dimensions given (say, in this case, using: lines(x=c(50,50),y=c(-10,40),lwd=2), for instance); however we cannot extend them to the edges of the plotting window unless we use: plot.phylo(...,no.margin=TRUE). Without the margin, what we did above would look as follows:

> x<-plot(tree,no.margin=TRUE)

> lines(x=c(25,25),y=c(-10,40),lwd=2)

> lines(x=c(50,50),y=c(-10,40),lwd=2)

> lines(x=c(75,75),y=c(-10,40),lwd=2)

We can do pretty much the same thing using phytools plotTree or plotSimmap, except that we need to keep in mind that these functions automatically rescale the horizontal plotting area (including labels) to unit length. To find the total height of the rescaled tree, we need to subtract the font size × the maximum string width of the tip labels from 1. So, in the case of plotSimmap, we would do:

> # simulate a character history

> tree<-sim.history(tree,Q=matrix(c(-1/20,1/20,1/20,-1/20),2,2))

> # set colors for plotting

> cols<-c("red","blue"); names(cols)<-c(1,2)

> # plot tree

> f<-1 # font size

> plotSimmap(tree,cols,pts=F,fsize=f)

> # add lines

> h<-1-f*max(strwidth(tree$tip.label))

> lines(x=c(0.25*h,0.25*h),y=c(-10,40),lwd=2)

> lines(x=c(0.5*h,0.5*h),y=c(-10,40),lwd=2)

> lines(x=c(0.75*h,0.75*h),y=c(-10,40),lwd=2)

Fot fun, let's combine this with make.era.map:

> tree<-make.era.map(tree,c(0,25,50,75,100))

> plotSimmap(tree,lwd=3,pts=F)

> h<-1-max(strwidth(tree$tip.label))

> lines(x=c(0.25*h,0.25*h),y=c(-10,40),lwd=3,col="red")

> lines(x=c(0.5*h,0.5*h),y=c(-10,40),lwd=3,col="green")

> lines(x=c(0.75*h,0.75*h),y=c(-10,40),lwd=3,col="blue")

Pretty cool.