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 7.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"))


[Package limma version 1.6.7 Index]