plotDensities {limma} | R Documentation

## Single-channel Densities Plot

### Description

Creates a plot of the densities of single-channels from two-color cDNA microarray data.

### Usage

    plotDensities(object, log.transform=FALSE, arrays=NULL, singlechannels=NULL,
                  groups=NULL, col=NULL)

### Arguments

`object` | must be either a list with components `M` containing log-ratios and `A` containing average intensities or a list with components `R` containing log2 red intensities and `G` containing log2 green intensities. If object is given as an `MAList` it is converted to an `RGList`.
`log.transform` | logical which needs to be `TRUE` if object supplied is an `RGList` of unlogged intensities.
`arrays` | vector of integers giving the arrays from which the single-channels will be selected to be plotted. Corresponds to columns of `M` and `A` (or `R` of `G`) If `NULL` (which is the default), arrays is given by `1:ncol(object$R)`.
`singlechannels` | vector of integers indicating which single-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 single-channels and `( (ncol(R)+1):(ncol(R)+ncol(G)) )` for the green single-channels in `object`.
`groups` | vector of consecutive integers beginning at 1 indicating the groups of arrays or single-channels (depending on which of `arrays` or `singlechannels` are non `NULL`). This is used to color any groups of the single-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 single-channel normalization. See the section on single-channel normalization in the LIMMA User's Guide.

If no `col` is specified, the default is to color singlechannels 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 single-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 single-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 6.Diagnostics. There is a section using `plotDensities` in conjunction with single-channel 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 single-channels by blue and purple.
    plotDensities(MA.n,arrays=NULL,groups=NULL,col=c("blue","purple"))

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

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

    #  All single-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"))

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