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 09.Diagnostics. There is a section using plotDensities in conjunction with between-array normalization in the LIMMA User's Guide.

Examples

## Not run: 
# This example is designed for work on a subset of the data
# from the ApoAI case study in Limma User's Guide
# This example was formerly loaded from sma package using
#   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"))

## End(Not run)
[Package limma version 3.10.2 Index]