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Last data update: 2014.03.03

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

plotOTU

R Documentation

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

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(metagenomeSeq)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/metagenomeSeq/plotOTU.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotOTU
> ### Title: Basic plot function of the raw or normalized data.
> ### Aliases: plotOTU
> 
> ### ** 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")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>