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

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

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")

HCBravoLab/metagenomeSeq documentation built on Dec. 20, 2024, 4:06 p.m.