limma (version 3.22.7)

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

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.

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.

See Also

plotMA

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