A phytools user recently asked the following:
“I am currently using the
ltt95 function on a
"multiPhylo" object. I would like to known if there is a
solution to reverse the time axis from the root of the tree to
Indeed this is not too difficult.
already returns an object of class
"ltt95" invisibly. This
object is basically a matrix containing the plotted data for x and
y in columns, with a few different attributes to tell the S3 plotting
method for objects of its class how to handle the matrix. So if we were naive
as to the functionality of our plotting method, we could just manipulate the
contents of that matrix to get the plot that we wanted. phytools makes things
even easier, however, as there is an argument
xaxis in the
plotting method for objects of class
"ltt95" that automates this
all for us.
Here's how we can use it to control the direction of x in various ways:
## load phytools library(phytools)
## Loading required package: ape ## Loading required package: maps
## simulate some trees trees<-pbtree(n=100,scale=50,nsim=100) ## now create a standard ltt95 plot obj<-ltt95(trees,log=TRUE)
## OK - now if we want to simply flip the values on x ## so that they should "time before present" plot(obj,xaxis="flipped")
## we can also plot time before present as "negative time" plot(obj,xaxis="negative")
Well, that's really it.
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