plotMA {DESeq2} | R Documentation

## 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` 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)

[Package DESeq2 version 1.27.31 Index]