plot.shared.nodes

This function compares phylogenies to identify topological similarities. Let’s start by loading required libraries, and then visualize a set of example phylogenies.

library(ape)
library(phytools)
library(dplyr)

phy.set <- readRDS("phy.list.RDS")
par(mfrow=c(1,3))
plot(phy.set[[1]], cex=2)
plot(phy.set[[2]], cex=2)
plot(phy.set[[3]], cex=2)

We want to compare how the topology of the phylogenies on the center and right compare against the topology on the left. This function always assumes that the target topology of interest is the first entry in the list of trees. The function itself only takes a few arguments:

• phy.list: A list or multiPhylo containing the phylogenies of interest
• pie.cols: A character vector the same length as the number of phylogenies being compared against the target phylogeny (in this example n = 2)
• cex: numeric vector length 1 corresponding to the size of the pies being plotted
• ...: Optional arguments to be passed to plot.phylo

Let’s load the function, and define our parameters for plotting

source("plot.shared.nodes.R")

pie.cols <- c("#1b9e77", "#d95f02")

cex <- 2

Now we can visualize the plot, and add a legend.

par(mai = c(.5,.1,.1,.1))
plot.shared.nodes(phy.set, pie.cols, cex)
axisPhylo()
legend(x = 0, 
       y = 1.75, 
       legend = c("Present in comparison 1",
                                   "Present in comparison 2"), 
       fill = pie.cols, border = "black",
       cex = .8)