ISA2heatmap: 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

heatmap.

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.

Examples

Run this code

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

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