| plotDensities {limma} | R Documentation |
Plots the densities of individual-channel intensities for two-color microarray data.
plotDensities(object, log=TRUE, arrays=NULL, singlechannels=NULL, groups=NULL, col=NULL)
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. |
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.
A plot is created on the current graphics device.
Natalie Thorne
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.
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"))