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

In mikelove/DESeq2: Differential gene expression analysis based on the negative binomial distribution

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

## S4 method for signature 'DESeqDataSet'
plotMA(
  object,
  alpha = 0.1,
  main = "",
  xlab = "mean of normalized counts",
  ylim,
  colNonSig = "gray60",
  colSig = "blue",
  colLine = "grey40",
  returnData = FALSE,
  MLE = FALSE,
  ...
)

## S4 method for signature 'DESeqResults'
plotMA(
  object,
  alpha,
  main = "",
  xlab = "mean of normalized counts",
  ylim,
  colNonSig = "gray60",
  colSig = "blue",
  colLine = "grey40",
  returnData = FALSE,
  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
colNonSig	color to use for non-significant data points
colSig	color to use for significant data points
colLine	color to use for the horizontal (y=0) line
returnData	logical, whether to return the data.frame used for plotting
MLE	if betaPrior=TRUE was used, 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. See lfcShrink for examples on how to plot shrunken log2 fold changes.
...	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, now copied from the geneplotter package. The code was modified in version 1.28 to change from red to blue points for better visibility for users with color-blindness. The original plots can still be made via the use of returnData=TRUE and passing the resulting data.frame directly to geneplotter::plotMA. The code of this function can be seen with: getMethod("plotMA","DESeqDataSet") If the object contains a column svalue then these will be used for coloring the points (with a default alpha=0.005).

Author(s)

Michael Love

Examples

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

mikelove/DESeq2 documentation built on July 25, 2024, 11:11 p.m.