Make HPD node plot- Add probability density information into phylogenies

Updated Nov 2nd 2015: Function re-written to be much more stable, and added additional functionality

The supporting files are the function code, phylogeny, and species group information.

There are two functions provided, with a few dependent packages:

library(phyloch)
## Loading required package: ape
## Loading required package: colorspace
## Loading required package: XML
library(ape)
library(phytools)
## Loading required package: maps
## 
##  # ATTENTION: maps v3.0 has an updated 'world' map.        #
##  # Many country borders and names have changed since 1990. #
##  # Type '?world' or 'news(package="maps")'. See README_v3. #
library(strap)
## Loading required package: geoscale

First we must load the file containing the functions to be used, the example phylogeny, and the species group information.

source("make_HPD_node_plot.R")
phy <- read.nexus("example.phylo.nex")
load("species_group_info.RData")

Next, we will generate some data to be plotted onto our phylogeny:

# This function requires that "node", "min" and "max" appear in the column names in some form
age_data <- as.data.frame(matrix(NA, ncol=3, nrow=3))
colnames(age_data) <- c("Genus", "Minimum", "Maximum")
age_data[1,] <- c("Genus_A", 20 ,35 )
age_data[2,] <- c("Genus_B", 17, 28)
age_data[3,] <- c("Genus_C", 22, 35)

age_data[,2] <- as.numeric(age_data[,2])
age_data[,3] <- as.numeric(age_data[,3])

age_data
##     Genus Minimum Maximum
## 1 Genus_A      20      35
## 2 Genus_B      17      28
## 3 Genus_C      22      35

The first function provided (find.nodes) will identify the most recent common ancestor for each specified group. The nodes identified are where the age data will subsequently be plotted.

find.nodes requires:

* data: A `data.frame` containing the minimum, and and maximum ages, as well as the corresponding species group names
* phy: An object of class `phylo`
* spp_group_list: An object of class `list` where the names match the group names in `data`, and each element contains species found in `phy$tip.label`
* colname: A vector of class `character` and length 1. Specify the column name in `data` that correponds to the species group data

Using the previously defined age data, and loaded species group data:

age.data.inc.nodes <- find.nodes(age_data, phy, species_group_info, colname = "Genus")

Now we have a data.frame with our age data, and the corresponding node in the phylogeny

age.data.inc.nodes
##     Genus Minimum Maximum Node
## 1 Genus_A      20      35   23
## 2 Genus_B      17      28   31
## 3 Genus_C      22      35   29

The previously generated data can now be used to generate our plot:

make_HPD_node_plot(phy=phy, data=age.data.inc.nodes, line.width=5, node.col = "lightblue",line.col = "red",node.pch=21, node.cex=2)