HeatmapEnrichedHelpfile

Description

Heatmap is a function that plots the top enriched regulatory element or GO terms for the first and second level of analysis in a heatmap. The number of terms to be displayed can be set.

Usage

Heatmap(object, outputformat="on screen", n.nodes.1stlevel="5",
    n.nodes.2ndlevel="5", mult.cor=TRUE, ...)

Arguments

Author(s)

Toma Tebaldi, Erik Dassi, Galena Kostoska

See Also

EnrichedSets RegulatoryEnrichment GOsets GOEnrichment GOsims

Examples

data(tRanslatomeSampleData)
Heatmap(CCEnrichment, ontology="MF")

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(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
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Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
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Attaching package: 'BiocGenerics'

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    clusterExport, clusterMap, parApply, parCapply, parLapply,
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    plotMA

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    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")'.


Attaching package: 'Biobase'

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    anyMissing, rowMedians

Loading required package: locfit
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    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
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groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/Heatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Heatmap
> ### Title: HeatmapEnrichedHelpfile
> ### Aliases: Heatmap
> ### Keywords: DEGs GO Regulatory enrichment analysis heatmap
> 
> ### ** Examples
> 
> data(tRanslatomeSampleData)
> Heatmap(CCEnrichment, ontology="MF")
[1] "GO:0005759"
[1] "mitochondrial matrix"
[1] "GO:0042627"
[1] "chylomicron"
[1] "GO:0034361"
[1] "very-low-density lipoprotein particle"
[1] "GO:0034366"
[1] "spherical high-density lipoprotein parti..."
         [,1]     [,2]
[1,] 1.452533 1.427709
[2,] 3.340559 1.427709
[3,] 4.512720 2.390726
[4,] 1.638965 1.489857
[1] 4 2
NULL
                                            transcriptome translatome
mitochondrial matrix                             1.452533    1.427709
chylomicron                                      3.340559    1.427709
very-low-density lipoprotein particle            4.512720    2.390726
spherical high-density lipoprotein parti...      1.638965    1.489857
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>