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$rows)),
data, binary=TRUE, names=NULL, xlab="", ylab="",
\dots)
where the arguments are:
- modules
The object with the ISA modules, as returned by the
isa
function or other such functions.
- to.plot
Numeric vector, the modules to plot, the numbers
correspond to the columns in modules$rows
and
modules$columns
. By default all modules will be plot.
- data
An optional data matrix to plot. Most often this is the
original data. If given, its dimension must much the dimensions in
the modules
object. If given, then this matrix is plotted
first, before the modules.
- binary
Logical scalar, whether to binarize the biclusters
before plotting or use the actual ISA scores. By default the
biclusters are binarized.
- 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.
- xlab
Character scalar, the label to put on the horizontal
axis.
- ylab
Character scalar, the label to put on the vertical axis.
- ...
Further arguments are passed to
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.