| plotModules {isa2} | R Documentation |
Make several image plots, one for each bicluster, and optionally one for the original data as well.
images(matrices, names=NULL, ...) ## S4 method for signature 'list': plotModules (modules, ...)
matrices |
A list of matrices to plot. Please note that this argument is always interpreted as a list, even if want to plot a single matrix, put it into a list. |
names |
Character vector, the labels to show above the image
plots. If you give the data argument to plotModules,
then the first label corresponds to that. |
... |
Additional arguments, for images these are passed
to levelplot, for plotModules see the
details below. |
modules |
The object with the ISA modules, as returned by the
isa function or other such functions. |
images creates image plots for a series of matrices, using
levelplot from the lattice package.
plotModules calls images from the
to create image plots for a set of modules. It can be called as
plotModules(modules, to.plot=seq_len(ncol(modules$rows)),
data, binary=TRUE, names=NULL, xlab="", ylab="",
...)
where the arguments are:
isa function or other such functions.modules$rows and
modules$columns. By default all modules will be plot.modules object. If given, then this matrix is plotted
first, before the modules.data argument to plotModules,
then the first label corresponds to that.levelplot.Note, that if you want to export these plots to a file, then a bitmap-based format might be more appropriate. For larger matrices vector formats tend to generate huge file because of the many dots.
Since these function use the lattice package, they return an
object of class trellis. You will need to print this
object to create the actual plots.
Gabor Csardi Gabor.Csardi@unil.ch
image and the other version: image
from the Matrix package, for alternatives to create image
plots.
## The following should plot the input matrix and the four modules
## found by ISA
set.seed(1) # to get same plot every time
data <- isa.in.silico(100, 100, num.fact=4)
modules <- isa(data[[1]], thr.row=2, thr.col=2)
plotModules(modules, data=data[[1]], binary=FALSE,
names=c("Input matrix",
paste("Module", seq_len(ncol(modules$rows)))))