export.figtree takes tree and unsorted.pvalues and produces a NEXUS file that can FigTree can subsequently open. The p-values for each branch (family of tips) are computed and the branches are colored accordingly. It computes the p-values based on arguments involving p-value adjustment (for multiple hypothesis testing) and either Stouffer's or Fisher's p-value combination method. There are arguments that allow for the customization of the p-value cutoff ranges as well as the colors to be used in the coloring of the branches. There is also an option to include annotations for each edge that contain the p-value for the corresponding branch.
● Data Source:
CranContrib
● Keywords: tree
● Alias: export.figtree
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plotSigTree
(Package: SigTree) :
Function to plot the phylogenetic tree in R with branches (tips) colored according to significance of families of p-values (tips' p-values)
plotSigTree takes tree and unsorted.pvalues and computes p-values for each branch (family of tips) and colors the corresponding descendant branches. It computes the p-values based on arguments involving p-value adjustment (for multiple hypothesis testing) and either Stouffer's or Fisher's p-value combination method. There are arguments that allow for the customization of the p-value cutoff ranges as well as the colors to be used in the coloring of the branches.
● Data Source:
CranContrib
● Keywords: dplot, tree
● Alias: plotSigTree
●
4 images
export.inherit takes tree and unsorted.pvalues and produces a CSV file (or data frame) with p-values for each branch (including tips) as well as a list of all of the tips that belong to each branch's family (i.e., all of the tips that are descendants of the branch). The p-values are computed based on arguments involving p-value adjustment (for multiple hypothesis testing) and either Stouffer's or Fisher's p-value combination method.
● Data Source:
CranContrib
● Keywords: tree
● Alias: export.inherit
●
0 images
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 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.
● Data Source:
CranContrib
● Keywords: dplot, tree
● Alias: SigTree, SigTree-package
●
0 images
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