About this page…

This page describes the use of TreeBreaker as a R package. If you would prefer to use TreeBreaker as a standalone application, see here.

Installation

The package can be installed in R using the command:

devtools::install_github('ansariazim/treeBreaker')

You should then be able to load the package with:

library(treeBreaker)

Analysis

Analysis can be performed using the command:

res=treeBreaker('testData/testTree.newick','testData/phenoTestFile.txt','out')

The first argument is the name of a Newick file containing the tree to analyse, the second argument is the name of a tab separated file containing the phenotype data, and the third argument is the name of a file in which to store the results.

Exploring the results

Once the analysis has finished running, results can be displayed as follows:

plot(res)

plot(res,'trace')

plot(res,'states')

plot(res,'correlation')