plotMA3by2 {limma} | R Documentation

## Write MA-Plots to Files

### Description

Write MA-plots to files in PNG format, six plots to a file in a 3 by 2 grid arrangement.

### Usage

    plotMA3by2(MA, prefix="MA", path=NULL, main=colnames(MA), zero.weights=FALSE, common.lim=TRUE, device="png", ...)

### Arguments

`MA` | an `MAList` or `RGList` object, or any list with components `M` containing log-ratios and `A` containing average intensities
`prefix` | character string giving prefix to attach to file names
`path` | character string specifying directory for output files
`main` | character vector giving titles for plots
`zero.weights` | logical, should points with non-positive weights be plotted
`common.lim` | logical, should all plots on a page use the same axis limits
`device` | device driver for the plot. Choices are `"png"`, `"jpeg"`, `"pdf"`, `"postscript"`.
`...` | any other arguments are passed to `plotMA`

### Details

This function writes a series of graphic files to disk. Each file contains six MA-plots in three rows and two columns. The layout is optimized for A4-sized paper.

The graph format can be `"png"` or `"jpeg"`, which are screen-resolution formats, or `"pdf"` or `"postscript"`, which are loss-less formats. `"png"` is not available on every R platform. Note that `"pdf"` or `"postscript"` may produce very large files.

### Value

No value is returned, but one or more files are written to the working directory. The number of files is determined by the number of columns of `MA`.

### Author(s)

Gordon Smyth

### See Also

An overview of diagnostic functions available in LIMMA is given in 09.Diagnostics.

[Package limma version 2.18.3 Index]