plotMA-methods {beadarray} | R Documentation |
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.
Densities are computed using the 'hexbin' package
A list of ggplot2 objects is returned.
Mark Dunning
if(require(beadarrayExampleData)){ library(ggplot2) 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") ## Not run: mas[[1]] mas[[2]] ## End(Not run) }