| plotDensities {limma} | R Documentation |
Plot the density of expression values for multiple arrays on the same plot.
## S3 method for class 'RGList'
plotDensities(object, log=TRUE, group=NULL, col=NULL, main="RG Densities",
bc.method="subtract", ...)
## S3 method for class 'MAList'
plotDensities(object, log=TRUE, group=NULL, col=NULL, main="RG Densities", ...)
## S3 method for class 'EListRaw'
plotDensities(object, log=TRUE, bc.method="subtract", ...)
## S3 method for class 'EList'
plotDensities(object, log=TRUE, ...)
## Default S3 method:
plotDensities(object, group=NULL, col=NULL, main=NULL, legend="topleft", ...)
object |
an |
log |
logical, should densities be plotted on the log2 scale? |
group |
optional vector or factor classifying the arrays into groups. Should be same length as |
col |
optional vector of colors of the same length as the number of groups. |
main |
the main title for the plot. |
bc.method |
background subtraction method passed to |
legend |
character string giving position to place legend.
See |
... |
other arguments are passed to |
This function is useful to display and contrast the distribution of expression values on different arrays. It can for example be used to display the effects of between-array normalization. See the section on between-array normalization in the LIMMA User's Guide.
A plot is created on the current graphics device.
Natalie Thorne and Gordon Smyth
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.
This function uses density and matplot.
## Not run:
# Default is to plot red channels in red and green channels in green
plotDensities(MA)
# Alternatively colors
plotDensities(MA, col=c("red","blue"))
# Color by group, with three groups:
plotDensities(MA,group=group,col=c("blue","orange","green"))
## End(Not run)