R: Image plots of biclusters

plotModules {isa2} | R Documentation

## Image plots of biclusters

### Description

Make several image plots, one for each bicluster, and optionally one for the original data as well.

### Usage

    images(matrices, names=NULL, ...)
    ## S4 method for signature 'list'
     plotModules(modules, ...)

### Arguments

`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.

### Details

`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.

### Value

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.

### Author(s)

Gabor Csardi Gabor.Csardi@unil.ch

### See Also

`image` and the other version: `image` from the `Matrix` package, for alternatives to create image plots.

### Examples

    ## 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)))))

[Package isa2 version 0.3.5 Index]