SigTree: Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

Takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values, and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to their levels of significance. Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches. Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to their significance of corresponding groups of p-values) with p-value annotations.

Author
John R. Stevens and Todd R. Jones
Date of publication
2016-02-06 11:07:46
Maintainer
John R. Stevens <john.r.stevens@usu.edu>
License
GPL-3
Version
1.10.3

View on CRAN

Man pages

export.figtree
Function to export a 'NEXUS' file that can be opened in...
export.inherit
Function to produce a CSV file with the p-value for each...
plotSigTree
Function to plot the phylogenetic tree in R with branches...
SigTree.other
SigTree Other Functions
SigTree-package
Determine significantly responsive branches in phylogenetic...

Files in this package

SigTree
SigTree/inst
SigTree/inst/sample
SigTree/inst/sample/sample.csv
SigTree/inst/sample/sample.tre
SigTree/inst/sample/singletonsample.tre
SigTree/inst/CITATION
SigTree/inst/doc
SigTree/inst/doc/SigTree.Rnw
SigTree/inst/doc/SigTree.R
SigTree/inst/doc/SigTree.pdf
SigTree/src
SigTree/src/SigTree.c
SigTree/NAMESPACE
SigTree/NEWS
SigTree/R
SigTree/R/SigTree.other.R
SigTree/R/export.inherit.R
SigTree/R/plotSigTree.R
SigTree/R/export.figtree.R
SigTree/vignettes
SigTree/vignettes/sigsampleFigTree.jpg
SigTree/vignettes/SigTree.Rnw
SigTree/MD5
SigTree/build
SigTree/build/vignette.rds
SigTree/DESCRIPTION
SigTree/man
SigTree/man/SigTree.other.Rd
SigTree/man/export.figtree.Rd
SigTree/man/plotSigTree.Rd
SigTree/man/export.inherit.Rd
SigTree/man/SigTree-package.Rd