A quick & easy trick to flip the x ("time") axis on a lineages through time plot

Here's a quick & easy trick to flip the direction of the x-axis (to show time running backwards from the present day into the past) on a lineages-through-time (LTT) plot.

To start, I'll load phytools and read a tree from file. (Here I'm using a tree of darters from Near et al. 2011.)

library(phytools)
tree<-read.tree(file=
    "http://www.phytools.org/Rbook/9/etheostoma_percina_chrono.tre")

Next, I'll compute my "ltt" object without graphing it using phytools::ltt.

obj<-ltt(tree,plot=FALSE)
obj

## Object of class "ltt" containing:
## 
## (1) A phylogenetic tree with 201 tips and 198 internal
##     nodes.
## 
## (2) Vectors containing the number of lineages (ltt) and
##     branching times (times) on the tree.
## 
## (3) A value for Pybus & Harvey's "gamma" statistic of
##     gamma = NA, p-value = NA.

(The γ statistic shows up as NA because our tree has polytomies – but for graphing the LTT we don't need to worry about that.)

Finally, I'll graph the "ltt" object, without showing the axes, I'll add, first, the vertical (y) axis – and then I'll flip the directionality of the x axis before adding it too.

plot(obj,log="y",log.lineages=FALSE,bty="n",axes=FALSE,
    xlab="time (mybp)")
axis(2)
h<-axTicks(1)
par(usr=c(par()$usr[2:1],par()$usr[3:4]))
axis(1,h[length(h):1])

Cool. It works!