metagenomeSeq (version 1.14.0)

plotOTU: Basic plot function of the raw or normalized data.

Description

This function plots the abundance of a particular OTU by class. The function uses the estimated posterior probabilities to make technical zeros transparent.

Usage

plotOTU(obj, otu, classIndex, log = TRUE, norm = TRUE, jitter.factor = 1, pch = 21, labs = TRUE, xlab = NULL, ylab = NULL, jitter = TRUE, ...)

Arguments

obj

A MRexperiment object with count data.

otu

The row number/OTU to plot.

classIndex

A list of the samples in their respective groups.

log

Whether or not to log2 transform the counts - if MRexperiment object.

norm

Whether or not to normalize the counts - if MRexperiment object.

jitter.factor

Factor value for jitter.

pch

Standard pch value for the plot command.

labs

Whether to include group labels or not. (TRUE/FALSE)

xlab

xlabel for the plot.

ylab

ylabel for the plot.

jitter

Boolean to jitter the count data or not.

...

Additional plot arguments.

Value

Plotted values

See Also

cumNorm

Examples

data(mouseData)
classIndex=list(controls=which(pData(mouseData)$diet=="BK"))
classIndex$cases=which(pData(mouseData)$diet=="Western")
# you can specify whether or not to normalize, and to what level
plotOTU(mouseData,otu=9083,classIndex,norm=FALSE,main="9083 feature abundances")