R: plot intensities using 'pairs'

pairs.AffyBatch {affy}

R Documentation

plot intensities using 'pairs'

Description

Plot intensities using the function 'pairs'

Usage

## S3 method for class 'AffyBatch'
pairs(x, panel=points, ..., transfo=I, main=NULL, oma=NULL,
                  font.main = par("font.main"),
                  cex.main = par("cex.main"), cex.labels = NULL, 
                  lower.panel=panel, upper.panel=NULL, diag.panel=NULL,
                  font.labels = 1, row1attop = TRUE, gap = 1)

Arguments

`x`	an `AffyBatch` object.
`panel`	a function to produce a plot (see `pairs`).
`...`	extra parameters for the 'panel' function.
`transfo`	a function to transform the intensity values before generating the plot. 'log' and 'log2' are popular choices.
`main`	title for the plot
`oma`	see 'oma' in `par`.
`font.main`	see `pairs`.
`cex.main`	see `pairs`.
`cex.labels`	see `pairs`.
`lower.panel`	a function to produce the plots in the lower triangle (see `pairs`).
`upper.panel`	a function to produce the plots in the upper triangle (see `pairs`).
`diag.panel`	a function to produce the plots in the diagonal (see `pairs`).
`font.labels`	see `pairs`.
`row1attop`	see `pairs`.
`gap`	see `pairs`.

Details

Plots with several chips can represent zillions of points. They require a lot of memory and can be very slow to be displayed. You may want to try to split of the plots, or to plot them in a device like 'png' or 'jpeg'.

[Package affy version 1.56.0 Index]