Function to construct the classic MA plots from a dataset

Description

Note that a ggplot2 object is returned, which can be modified programatically.

The default operation is to construct a reference array be averaging all probes across the whole datasets, and then making an MA plot by comparing each array to this reference. A log2 transformation is performed, but this can be turned-off by setting do.log=FALSE.

Alternatively, a SampleGroup may be specified. This is a character string that should match a column in the phenoData for the object. Then, the resulting MA plot will contain all pairwise comparisons between samples belonging to the same group. A list of ggplot objects is returned, each item in the list being a different group.

Details

Densities are computed using the 'hexbin' package

Value

A list of ggplot2 objects is returned.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){
data(exampleSummaryData)
rawdata <- channel(exampleSummaryData, "G")
 mas <- plotMA(rawdata,do.log=FALSE)
mas
##Smoothed lines can be added
mas + geom_smooth(col="red")
##Added lines on the y axis
mas + geom_hline(yintercept=c(-1.5,1.5),col="red")
##Changing the color scale
mas + scale_fill_gradient2(low="yellow",mid="orange",high="red")

mas <- plotMA(rawdata,do.log=FALSE,SampleGroup="SampleFac")
mas[[1]]
mas[[2]]

}

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)

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> library(beadarray)
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: ggplot2
Welcome to beadarray version 2.22.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarray/maplots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMA-methods
> ### Title: Function to construct the classic MA plots from a dataset
> ### Aliases: plotMA,ExpressionSetIllumina-method
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ data(exampleSummaryData)
+ rawdata <- channel(exampleSummaryData, "G")
+  mas <- plotMA(rawdata,do.log=FALSE)
+ mas
+ ##Smoothed lines can be added
+ mas + geom_smooth(col="red")
+ ##Added lines on the y axis
+ mas + geom_hline(yintercept=c(-1.5,1.5),col="red")
+ ##Changing the color scale
+ mas + scale_fill_gradient2(low="yellow",mid="orange",high="red")
+ 
+ mas <- plotMA(rawdata,do.log=FALSE,SampleGroup="SampleFac")
+ mas[[1]]
+ mas[[2]]
+ 
+ }
Loading required package: beadarrayExampleData
No sample factor specified. Comparing to reference array
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>