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SigTree (version 1.10.6)

Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

Description

Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.

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Version

Install

install.packages('SigTree')

Monthly Downloads

39

Version

1.10.6

License

GPL-3

Maintainer

John Stevens

Last Published

October 2nd, 2017

Functions in SigTree (1.10.6)

adonis.tree

Function to perform adonis test of independence on p-values from tests of multiple OTUs.
export.figtree

Function to export a NEXUS file that can be opened in FigTree to produce a plot of the phylogenetic tree with branches colored according to significance of families of p-values
export.inherit

Function to produce a CSV file with the p-value for each branch as well as a list of all of the tips in each branch's family
p2.p1

Function to convert two-tailed p-values to one-tailed, for use by other SigTree functions.
SigTree-package

Determine significantly responsive branches in phylogenetic trees
SigTree.other

SigTree Other Functions
plotSigTree

Function to plot the phylogenetic tree in R with branches (tips) colored according to significance of families of p-values (tips' p-values)