| plotDensities {limma} | R Documentation |
Creates a plot of the densities of single-channels from two-color cDNA microarray data.
plotDensities(object, log.transform=FALSE, arrays=NULL, singlechannels=NULL,
groups=NULL, col=NULL)
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. |
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.
A plot is created on the current graphics device.
Natalie Thorne
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.
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"))