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Last data update: 2014.03.03

R: Heatmap of a transcription module

ISA2heatmap

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.

Examples

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

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(eisa)
Loading required package: isa2
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/eisa/ISA2heatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ISA2heatmap
> ### Title: Heatmap of a transcription module
> ### Aliases: ISA2heatmap
> ### Keywords: cluster
> 
> ### ** Examples
> 
> library(ALL)
> data(ALL)
> data(ALLModulesSmall)
> 
> #if (interactive()) {
>   ISA2heatmap(ALLModulesSmall, 1, ALL, norm="feature")
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>