metagenomeSeq (version 1.14.0)

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

Description

This function plots the abundance of a particular OTU by class. The function is the typical manhattan plot of the abundances.

Usage

plotFeature(obj, otuIndex, classIndex, col = "black", sort = TRUE, sortby = NULL, norm = TRUE, log = TRUE, sl = 1000, ...)

Arguments

obj

A MRexperiment object with count data.

otuIndex

The row to plot

classIndex

A list of the samples in their respective groups.

col

A vector to color samples by.

sort

Boolean, sort or not.

sortby

Default is sort by library size, alternative vector for sorting

norm

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

log

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

sl

Scaling factor - if MRexperiment and norm=TRUE.

...

Additional plot arguments.

Value

counts and classindex

See Also

cumNorm

Examples

data(mouseData)
classIndex=list(Western=which(pData(mouseData)$diet=="Western"))
classIndex$BK=which(pData(mouseData)$diet=="BK")
otuIndex = 8770

par(mfrow=c(2,1))
dates = pData(mouseData)$date
plotFeature(mouseData,norm=FALSE,log=FALSE,otuIndex,classIndex,
col=dates,sortby=dates,ylab="Raw reads")