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
## 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!