pairs-methods {lumi}R Documentation

Pair plot of an ExpressionSet object

Description

Creating pairs plot of sample intensities in an ExpressionSet object

Usage

## S4 method for signature 'ExpressionSet':
pairs(x, ..., smoothScatter = FALSE, logMode = TRUE, subset = 5000, main = NULL)

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
main title of the plot

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)

if (require(geneplotter))
        pairs(example.lumi, smoothScatter=TRUE)

[Package lumi version 1.8.3 Index]