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Last data update: 2014.03.03

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

plotGenus

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

plotGenus(obj, otuIndex, classIndex, norm = TRUE, log = TRUE,
  no = 1:length(otuIndex), labs = TRUE, xlab = NULL, ylab = NULL,
  jitter = TRUE, jitter.factor = 1, pch = 21, ...)

Arguments

`obj`	An MRexperiment object with count data.
`otuIndex`	A list of the otus with the same annotation.
`classIndex`	A list of the samples in their respective groups.
`norm`	Whether or not to normalize the counts - if MRexperiment object.
`log`	Whether or not to log2 transform the counts - if MRexperiment object.
`no`	Which of the otuIndex to plot.
`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.
`jitter.factor`	Factor value for jitter
`pch`	Standard pch value for the plot command.
`...`	Additional plot arguments.

Value

plotted data

Examples


data(mouseData)
classIndex=list(controls=which(pData(mouseData)$diet=="BK"))
classIndex$cases=which(pData(mouseData)$diet=="Western")
otuIndex = grep("Strep",fData(mouseData)$family)
otuIndex=otuIndex[order(rowSums(MRcounts(mouseData)[otuIndex,]),decreasing=TRUE)]
plotGenus(mouseData,otuIndex,classIndex,no=1:2,xaxt="n",norm=FALSE,ylab="Strep normalized log(cpt)")

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/plotGenus.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGenus
> ### Title: Basic plot function of the raw or normalized data.
> ### Aliases: genusPlot plotGenus
> 
> ### ** Examples
> 
> 
> data(mouseData)
> classIndex=list(controls=which(pData(mouseData)$diet=="BK"))
> classIndex$cases=which(pData(mouseData)$diet=="Western")
> otuIndex = grep("Strep",fData(mouseData)$family)
> otuIndex=otuIndex[order(rowSums(MRcounts(mouseData)[otuIndex,]),decreasing=TRUE)]
> plotGenus(mouseData,otuIndex,classIndex,no=1:2,xaxt="n",norm=FALSE,ylab="Strep normalized log(cpt)")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>