lumi (version 2.24.0)

pairs-methods: Pair plot of an ExpressionSet object

Description

Creating pairs plot of sample intensities in an ExpressionSet object

Usage

"pairs"(x, ..., smoothScatter = FALSE, logMode = TRUE, subset = 5000, fold=2, dotColor=1, 
	highlight = NULL, highlightColor = 2, main = NULL, checkTransform = TRUE)

Arguments

x

a ExpressionSet object

...

optional arguments to pairs.

smoothScatter

whether use smoothScatter function to plot points

logMode

whether plot the data in log2 scale

subset

subset of rows used to plot. It can be an index vector, or the length of a random subset

fold

The fold-change threshold used to estimate the number of probes having high fold-changes

dotColor

color of points in the scatter plot

highlight

the subset dots need to be highlighted

highlightColor

the color for those highlighted dots

main

title of the plot

checkTransform

whether to check the data is log2-transformed or not

Details

To increase the plot efficiency, by default, we only plot RANDOMLY selected subset of points (based on parameter "subset"). If users want to plot all the points, they can set the parameter "subset = NULL". When smoothScatter is set as TRUE, the subsetting will be suppressed because smoothScatter function has good plot efficiency for large number of points.

See Also

LumiBatch-class, pairs

Examples

## load example data
data(example.lumi)

pairs(example.lumi)

pairs(example.lumi, smoothScatter=TRUE)