SigTree.other: SigTree Other Functions

Description

Internal functions used by the main functions of SigTree (plotSigTree, export.figtree, and export.inherit):


`num.edges`	determine the number of edges in `tree`
`num.tips`	determine the number of tips in `tree`
`num.internal.nodes`	determine the number of nodes in `tree`
`num.total.nodes`	determine the number of total nodes (internal + tips) in `tree`
`srt.pvalues`	sort `unsorted.pvalues` by tip labels (column 1) to be in same order as tip labels in `tree`
`stouffers`	perform Stouffer's Method on a vector of p-values; return one p-value
`fishers`	perform Fisher's Method on a vector of p-values; return one p-value
`index.matrix`	create matrix to identify the descendants/tips (rows) belonging to each node/family (column)
`p.p2.ADJ.p1`	convert 1-sided p-values to 2-sided, perform p-value adjustment (for multiple-hypothesis
	testing), and convert back to 1-sided
`result`	calculate p-values for each node/edge branch
`tip.colors`	determine coloring of each tip
`edge.colors`	determine coloring of each edge
`plotphylo2`	(based on `ape` package's `plot.phylo` function); plots `tree` while allowing for different
	edge coloring (root edge when `type="fan"`, and different colors for each half of the
	"perpendicular-to-the-root" edges). Prior to package version 1.2, `plot.phylo` was used instead.
	Beginning in package version 1.3 (to attain CRAN compatibility), includes .C calls to copies of four
	`ape` .C functions (copied with credit under `ape`'s GPL license).
`circularplot2`	(based on `ape` package's `circular.plot` function) called by `phyloplot2` when `type="fan"`
`hartung`	perform Hartung's Method on a vector of p-values; return one p-value

Arguments

Details

It is assumed that each internal node has exactly two descendants. It is also assumed that each internal node has a lower number than each of its ancestors (excluding tips).

To access the tutorial document for this package (including this function), type in R: vignette("SigTree")

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" MS Thesis, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/etd/1314