plot: Plot Phylogenies with Significant OTU

In POSTm: Phylogeny-Guided OTU-Specific Association Test for Microbiome Data

Plot Phylogenies with Significant OTU

Description

Plot phylogenetic tree on the current graphical device as defined by package ape with tip labels highlighted to show the significant OTU.

Usage

## S3 method for class 'POST'
plot(x, ..., siglevel = 0.05, method = "none", alpha = 0.05, subTree = TRUE)

Arguments

x	A POST object. The value object returned by post(). Note that a tree of class "phylo" must have been provided to the original analysis.
...	Additional arguments to be passed to plot.phylo.
siglevel	A numeric object. The significance level; OTU's with (adjusted or raw) p-values below this level will be highlighted. Default is 0.05.
method	A character object. Must be one of {"holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "TSBH", "none"}, where 'none' indicates the raw POST p-values. "TSBH" is the two-stage Benjamini & Hochberg procedure. See ?stats::p.adjust for descriptions of all other possible values.
alpha	A numeric object. A nominal type I error rate, or a vector of error rates, used for estimating the number of true null hypotheses in the two-stage Benjamini & Hochberg procedure ("TSBH"). Default is 0.05. Ignored if method is not TSBH.
subTree	A logical object. If TRUE, only the OTU used in the analysis are included in the plot.

Value

No return value, called to produce graphical elements.

Examples

data("POSTmData")

y <- as.integer(x = metadata[,"GC"] == "BV")
X <- metadata[,"mRace"]

result <- post(y = y, 
               X = X, 
               OTU = otu[,1:20], 
               tree = otutree,
               cValues = seq(0,0.05,by=0.01))

plot(x = result)

POSTm documentation built on May 29, 2024, 9:24 a.m.