| SigTree-package {SigTree} | R Documentation |
Determine significantly responsive branches in phylogenetic trees
Description
SigTree is a package of functions to determine significant response of branches of phylogenetic trees and produce colored plots both in R and (via exported .tre file) FigTree.
plotSigTree takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values and determines the significance of the branches (as families of p-values) and plots the tree with colored branches (corresponding to families) according to the level of significance of the branch. export.inherit produces a CSV file (or data frame) with the p-values for all branches as well as which tips belong to which branches. export.figtree exports a .tre file that can be opened in FigTree that produces a colored plot (with colors according to the significance of corresponding branches) with p-value annotations.
Details
| Package: | SigTree |
| Type: | Package |
| Version: | 1.10.6 |
| Date: | 2017-09-29 |
| License: | GPL-3 |
For more information, see the documentation for
plotSigTree, export.inherit, and export.figtree.
To access the tutorial document for this package, type in R: vignette("SigTree")
Author(s)
John R. Stevens and Todd R. Jones
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
References
Stevens J.R., Jones T.R., Lefevre M., Ganesan B., and Weimer B.C. (2017) "SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree." Computational and Structural Biotechnology Journal 15:372-378.
Jones T.R. (2012) "SigTree: An Automated Meta-Analytic Approach to Find Significant Branches in a Phylogenetic Tree" (2012). MS Thesis, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/etd/1314
FigTree is available at http://tree.bio.ed.ac.uk/software/figtree/.