Graphical Representation of GO Based MLP Results

Description

Graphical Representation of GO Based MLP Results

Usage

  plotGOgraph(object, nRow = 5, main = NULL)

Arguments

Value

GO graph is plotted to the current device

Examples

if (require(GO.db) && require(Rgraphviz)){
  pathExampleMLPResult <- system.file("exampleFiles", "exampleMLPResult.rda", package = "MLP")
  load(pathExampleMLPResult)
  plotGOgraph(exampleMLPResult, main = "GO Graph")
}

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 'demo()' for some demos, 'help()' for on-line help, or
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> library(MLP)
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: affy
Loading required package: plotrix
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:plotrix':

    plotCI

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:IRanges':

    trim

The following object is masked from 'package:S4Vectors':

    first

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:BiocGenerics':

    combine

The following object is masked from 'package:stats4':

    nobs

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MLP/plotGOgraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGOgraph
> ### Title: Graphical Representation of GO Based MLP Results
> ### Aliases: plotGOgraph
> 
> ### ** Examples
> 
> if (require(GO.db) && require(Rgraphviz)){
+   pathExampleMLPResult <- system.file("exampleFiles", "exampleMLPResult.rda", package = "MLP")
+   load(pathExampleMLPResult)
+   plotGOgraph(exampleMLPResult, main = "GO Graph")
+ }
Loading required package: GO.db

Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid

Attaching package: 'Rgraphviz'

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

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: annotate
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode


Attaching package: 'annotate'

The following object is masked from 'package:Rgraphviz':

    toFile

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>