branch.length.diff - visualize how terminal branch lengths differ between two sets of phylogenies

The code for this function can be found here.

The arguments to pass to the function are:

• multiPhy - An object of class multiPhylo
• multiPhy1 - An object of class multiPhylo
• plot.top - Plot only the terminal taxa that show the most variation in branch length? Can take a numeric argument specifying how many tips to plot.
• show.top - Allows addition of a legend to the plot showing the mean absolute branch length difference for the top n tips. Can take a numeric argument.
• marPar - A numeric vector of length 4 specifying the plotting margins.
• taxon.label.cex - A numeric vector of length 1 specifying the size of the taxon labels
• pt.cex - A numeric argument specifying size of the plotted points
• bar.width - numeric value for the width of the bar lines
• label.horiz - logical: should the taxon names be plotted horizontally?

I will demonstrate thie plotting function using two posterior sets of phylogenies that were constructedd with and without topological constraints respectively. In doing so, we can see which taxa have their branch lengths affected the most through specification of topological constraints.

library(ape)

# The function
source("branch.length.diff.R")

# The data
multiPhy <- read.nexus("set1.nex")

multiPhy1 <- read.nexus("set2.nex")

A standard use of the function

branch.length.diff(multiPhy, multiPhy1)

Add a legend showing the five highest values

branch.length.diff(multiPhy, multiPhy1, show.top = 5)

Alternatively, only plot the five highest values

branch.length.diff(multiPhy, multiPhy1, plot.top = 5, 
                   pt.cex = 2, bar.width = 2, label.horiz = TRUE, taxon.label.cex = 0.7)