SigTree.other {SigTree}

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

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")

Note

Extensive discussion of methods developed for this package are available in Jones (2012). In that reference, (and prior to package version number 1.1), the srt.pvalues function was named sort.pvalues (the name change was made to resolve S3 class issues), and plotphylo2 was not available.

Author(s)

John R. Stevens and Todd R. Jones

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