plotDensities {limma} | R Documentation

## Individual-channel Densities Plot

### Description

Plots the densities of individual-channel intensities for two-color microarray data.

### Usage

    plotDensities(object, log=TRUE, arrays=NULL, singlechannels=NULL, groups=NULL, col=NULL)

### Arguments

`object` | an `RGList` or `MAList` object. `RGList` objects containing logged or unlogged intensities can be accommodated using the `log.transform` argument.
`log` | logical, should densities be formed and plotted for the log-intensities (`TRUE`) or raw intensities (`FALSE`)?
`arrays` | vector of integers giving the arrays from which the individual-channels will be selected to be plotted. Corresponds to columns of `M` and `A` (or `R` and `G`). Defaults to all arrays.
`singlechannels` | vector of integers indicating which individual-channels will be selected to be plotted. Values correspond to the columns of the matrix of `cbind(R,G)` and range between `1:ncol(R)` for red channels and `( (ncol(R)+1):(ncol(R)+ncol(G)) )` for the green channels in `object`. Defaults to all channels.
`groups` | vector of consecutive integers beginning at 1 indicating the groups of arrays or individual-channels (depending on which of `arrays` or `singlechannels` are non `NULL`). This is used to color any groups of the individual-channel densities. If `NULL` (default), `groups` correspond to the red and green channels. If both `arrays` and `singlechannels` are `NULL` all arrays are selected and groups (if specified) must correspond to the arrays.
`col` | vector of colors of the same length as the number of different groups. If `NULL` (default) the `col` equals `c("red","green")`. See details for more specifications.

### Details

This function is used as a data display technique associated with between-array normalization, especially individual-channel normalization methods such as quantile-normalization. See the section on between-array normalization in the LIMMA User's Guide.

If no `col` is specified, the default is to color individual channels according to red and green. If both `arrays` and `groups` are non-`NULL`, then the length of `groups` must equal the length of `arrays` and the maximum of `groups` (i.e. the number of groups) must equal the length of `col` otherwise the default color of black will be used for all individual-channels. If `arrays` is `NULL` and both `singlechannels` and `groups` are non-`NULL`, then the length of `groups` must equal the length of `singlechannels` and the maximum of `groups` (i.e. the number of groups) must equal the length of `col` otherwise the default color of black will be used for all individual-channels.

### Value

A plot is created on the current graphics device.

### Author(s)

Natalie Thorne

### See Also

An overview of diagnostic plots in LIMMA is given in 7.Diagnostics. There is a section using `plotDensities` in conjunction with between-array normalization in the LIMMA User's Guide.

### Examples

    library(sma)
    data(MouseArray)

    #  no normalization but background correction is done
    MA.n <- MA.RG(mouse.data)

    #  Default settings for plotDensities.
    plotDensities(MA.n)

    #  One can reproduce the default settings.
    plotDensities(MA.n,arrays=c(1:6),groups=c(rep(1,6),rep(2,6)),
    col=c("red","green"))

    #  Color R and G individual-channels by blue and purple.
    plotDensities(MA.n,arrays=NULL,groups=NULL,col=c("blue","purple"))

    #  Indexing individual-channels using singlechannels (arrays=NULL).
    plotDensities(MA.n,singlechannels=c(1,2,7))

    #  Change the default colors from c("red","green") to c("pink","purple")
    plotDensities(MA.n,singlechannels=c(1,2,7),col=c("pink","purple"))

    #  Specified too many colors since groups=NULL defaults to two groups.
    plotDensities(MA.n,singlechannels=c(1,2,7),col=c("pink","purple","blue"))

    #  Three individual-channels, three groups, three colors.
    plotDensities(MA.n,singlechannels=c(1,2,7),groups=c(1,2,3),
    col=c("pink","purple","blue"))

    #  Three individual-channels, one group, one color.
    plotDensities(MA.n,singlechannels=c(1,2,7),groups=c(1,1,1),
    col=c("purple"))

    #  All individual-channels, three groups (ctl,tmt,reference), three colors.
    plotDensities(MA.n,singlechannels=c(1:12),
    groups=c(rep(1,3),rep(2,3),rep(3,6)),col=c("darkred","red","green"))

[Package limma version 1.9.6 Index]