pairs-methods: Pair plot of an ExpressionSet object

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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, 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)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.