ISA2heatmap {eisa} | R Documentation

## Heatmap of a transcription module

### Description

Create a heatmap plot for an ISA module.

### Usage

    ISA2heatmap (modules, module, eset, norm = c("raw", "feature", "sample"),
        scale = c("none", "row", "column"), ...)

### Arguments

`modules` | An `ISAModules` object.
`module` | Numeric scalar, the number of the module to plot.
`eset` | An `ExpressionSet` or `ISAExpressionSet` object. If an `ExpressionSet` object is supplied (and the `norm` argument is not set to ‘raw’), then it is normalised by calling `ISANormalize` on it. A subset of `eset` is selected that corresponds to the features included in `modules`.
`norm` | Character constant, specifies whether and how to normalize the expression values to plot. ‘raw’ plots the raw expression values, ‘feature’ the expression values scaled and centered for each feature (=gene) separately and if ‘sample’ is specified then the expression values are centered and scaled separately for each sample.
`scale` | Character scalar, passed to the `heatmap` function.
`...` | Additional arguments, they are passed to the `heatmap` function.

### Value

The same as `heatmap`.

### Author(s)

Gabor Csardi csardi.gabor@gmail.com

### References

Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.

### See Also

`heatmap`

### Examples

    library(ALL)
    data(ALL)
    data(ALLModulesSmall)

    if (interactive()) {
      ISA2heatmap(ALLModulesSmall, 1, ALL, norm="feature")
    }

[Package eisa version 1.40.0 Index]