Compute a heatmap for the specified data, for either a GO category or a KEGG pathway.

Description

For a given GO category or KEGG pathway, all probes in the supplied data are mapped to the pathway and a heatmap is produced.

Usage

GO2heatmap(x, eset, data, ...)
KEGG2heatmap(x, eset, data, ...)

Arguments

Details

For the given pathway or GO category all matching probes are determined, these are used to subset the data and heatmap is invoked on that set of data. Extra parameters can be passed through to heatmap using the ... parameter. The annotation slot of the eset argument is used to determine the appropriate annotation data to use.

Value

The value returned by heatmap is passed back to the user.

Author(s)

R. Gentleman

See Also

heatmap

Examples

  library("hgu95av2.db")
  data(sample.ExpressionSet)
  KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")

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)

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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
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> library(annotate)
Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

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

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

Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/annotate/GO2heatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GO2heatmap
> ### Title: Compute a heatmap for the specified data, for either a GO
> ###   category or a KEGG pathway.
> ### Aliases: GO2heatmap KEGG2heatmap
> ###   KEGG2heatmap,character,eSet,character-method
> ###   KEGG2heatmap,character,matrix,character-method
> ### Keywords: manip
> 
> ### ** Examples
> 
>   library("hgu95av2.db")
Loading required package: org.Hs.eg.db


>   data(sample.ExpressionSet)
>   KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>