plot {POSTm}

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)