metaseqR (version 1.12.2)

diagplot.pairs: Massive X-Y, M-D correlation plots

Description

This function uses the read counts matrix to create pairwise correlation plots. The upper diagonal of the final image contains simple scatterplots of each sample against each other (log2 scale) while the lower diagonal contains mean-difference plots for the same samples (log2 scale). This type of diagnostic plot may not be interpretable for more than 10 samples.

Usage

diagplot.pairs(x, output = "x11", path = NULL, ...)

Arguments

x

the read counts matrix or data frame.

output

one or more R plotting device to direct the plot result to. Supported mechanisms: "x11" (default), "png", "jpg", "bmp", "pdf" or "ps".

path

the path to create output files.

...

further arguments to be passed to plot devices, such as parameter from par.

Value

• The filename of the pairwise comparisons plot produced if it's a file.

Examples

require(DESeq)
data.matrix <- counts(makeExampleCountDataSet())
diagplot.pairs(data.matrix)