pairs.AffyBatch: plot intensities using 'pairs'

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

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'.

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.