This function will plot discrete data at the tips of a non-ultrametric phylogeny The supporting data are: function code, phylogeny, and data.
The arguments to pass to the function are: * phy - A phylogeny of class phylo * data - A data.frame where the data to be plotted is contained * plot.data - The name of the column in the data.frame to be plotted * pch - numeric value for the plotting symbol to be used * cols - character string specifying the colors to be used in plotting. There must be one color for every unique plot.data value * cex - Size of the symbols
First load the example data provided
data <- read.csv("data.csv")
require(ape)
phy <- read.nexus("phy.nex")
source("add.tip.icons.R")In this first example, we will plot the Location data. Here, there are three states to be plotted (1, 2 & 3), which will be represented by the colors red, blue & green in that order.
add.tip.icons(phy, data, grouping="Species", plot.data = "Location", cex=3)
Changing pch changes the plotting symbol. When a value above 20 is used, the specified colors wil change the background color (as above). When the pch value is 20 or lower, the overall color of the symbol will be changed (see ?pch for more information), for example:
add.tip.icons(phy, data, cex=3, pch=15)
Next, we will plot the size data. Now there are five states present, meaning that additional colors must be specified.
add.tip.icons(phy, data, grouping = "Species", plot.data="Size", cols=rainbow(5), cex=3)