plotDensities {limma} | R Documentation

## Plot Expression Densities

### Description

Plot the density of expression values for multiple arrays on the same plot.

### Usage

    ## S3 method for class 'RGList'
    plotDensities(object, log=TRUE, group=NULL, col=NULL, main="RG Densities",
                  bc.method="subtract", ...)
    ## S3 method for class 'MAList'
    plotDensities(object, log=TRUE, group=NULL, col=NULL, main="RG Densities", ...)
    ## S3 method for class 'EListRaw'
    plotDensities(object, log=TRUE, bc.method="subtract", ...)
    ## S3 method for class 'EList'
    plotDensities(object, log=TRUE, ...)
    ## Default S3 method:
    plotDensities(object, group=NULL, col=NULL, main=NULL, legend="topleft", ...)

### Arguments

`object` | an `RGList`, `MAList`, `EListRaw` or `EList` object containing expression data. Or any data object that can be coerced to a matrix.
`log` | logical, should densities be plotted on the log2 scale?
`group` | optional vector or factor classifying the arrays into groups. Should be same length as `ncol(object)`.
`col` | optional vector of colors of the same length as the number of groups.
`main` | the main title for the plot.
`bc.method` | background subtraction method passed to `backgroundCorrect`.
`legend` | character string giving position to place legend. See `legend` for possible values. Can also be logical, with `FALSE` meaning no legend.
`...` | other arguments are passed to `plotDensities.default` or `density`.

### Details

This function is useful to display and contrast the distribution of expression values on different arrays. It can for example be used to display the effects of between-array normalization. See the section on between-array normalization in the LIMMA User's Guide.

### Value

A plot is created on the current graphics device.

### Author(s)

Natalie Thorne and Gordon Smyth

### See Also

An overview of diagnostic plots in LIMMA is given in 09.Diagnostics. There is a section using `plotDensities` in conjunction with between-array normalization in the LIMMA User's Guide.

This function uses `density` and `matplot`.

### Examples

    ## Not run:
    #  Default is to plot red channels in red and green channels in green
    plotDensities(MA)

    #  Alternatively colors
    plotDensities(MA, col=c("red","blue"))

    #  Color by group, with three groups:
    plotDensities(MA,group=group,col=c("blue","orange","green"))

    ## End(Not run)

[Package limma version 3.42.2 Index]