DESeq2 (version 1.12.3)

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 = "", xlab = "mean of normalized counts", ylim, MLE = FALSE, ...)
"plotMA"(object, alpha, main = "", xlab = "mean of normalized counts", 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

xlab

optional defaults to "mean of normalized counts"

ylim

optional y limits

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.

...

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

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)