DESeq2 (version 1.10.0)

plotMA: MA-plot from base means and log fold changes

Description

A simple helper function that makes a so-called "MA-plot", i.e. a scatter plot of log2 fold changes (on the y-axis) versus the mean of normalized counts (on the x-axis).

Usage

"plotMA"(object, alpha = 0.1, main = "", ylim, ...)
"plotMA"(object, alpha, main = "", ylim, MLE = FALSE, ...)

Arguments

object

a DESeqResults object produced by results; or a DESeqDataSet processed by DESeq, or the individual functions nbinomWaldTest or nbinomLRT

alpha

the significance level for thresholding adjusted p-values

main

optional title for the plot

ylim

optional y limits

...

further arguments passed to plotMA if object is DESeqResults or to results if object is DESeqDataSet

MLE

whether to plot the MLE (unshrunken estimates), defaults to FALSE. Requires that results was run with addMLE=TRUE. Note that the MLE will be plotted regardless of this argument, if DESeq() was run with betaPrior=FALSE.

Details

This function is essentially two lines of code: building a data.frame and passing this to the plotMA method for data.frame from the geneplotter package. The code of this function can be seen with: getMethod("plotMA","DESeqDataSet") If users wish to modify the graphical parameters of the plot, it is recommended to build the data.frame in the same manner and call plotMA.

Examples

dds <- makeExampleDESeqDataSet()
dds <- DESeq(dds)
plotMA(dds)
res <- results(dds)
plotMA(res)