compbiasPlot: plot the compositional bias for the sub-taxinomic rank

In manta: Microbial Assemblage Normalized Transcript Analysis

Description

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Usage

compbiasPlot(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')), meta.lev='phylum',  meta.lev.lim=nrow(x$meta.sum[[meta.lev]]), breaks=10, xlim=c(0,.5), type='box', col=NULL, ...)

Arguments

x	a MANTA object.
pair	named vector of the pair of conditions of interest
meta.lev	the taxinomic rank to plot.
meta.lev.lim	the taxinomic rank for diversity measure.
breaks	breaks for the histogram.
xlim	x axis limits.
type	type of plot.
col	colors
...	additional params.

Value

a compositional bias plot

See Also

DGEList, manta

Examples

manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
load(manta.path)
			
compbiasPlot(x, meta.lev='genus_sp')

manta documentation built on Oct. 31, 2019, 3:03 a.m.