limma: plotma3by2 – R documentation

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limma

plotma3by2

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

Arguments

`object`	an `MAList`, `RGList`, `EListRaw` or `EList` object, or a matrix containing log-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 object.

Author(s)

Gordon Smyth