plot.MLP: Plot the Results of an MLP Run

In MLP: MLP

Description

Plot the Results of an MLP Run

Usage

## S3 method for class 'MLP'
plot(x, y = NULL, type = c("barplot", "GOgraph",
  "quantileCurves"), ...)

Arguments

x	object of class 'MLP'
y	argument added to comply with generic; not used, defaults to NULL
type	character of length one; one of 'barplot', 'GOgraph' or 'quantileCurves'
...	further arguments for the plot functions for each type

Value

for type = "barplot", the midpoints of the barplot

Examples

pathExampleMLPResult <- system.file("exampleFiles", "exampleMLPResult.rda", package = "MLP")
load(pathExampleMLPResult)
dev.new(width = 10, height = 10)
op <- par(mar = c(30, 10, 6, 2))
plot(exampleMLPResult, type = "barplot")
par(op)
plot(exampleMLPResult, type = "quantileCurves")
if (require(GO.db) && require(Rgraphviz)){
  plot(exampleMLPResult, type = "GOgraph")
}

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

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 object is masked from ‘package:base’:

    expand.grid

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
Registered S3 method overwritten by 'gdata':
  method         from  
  reorder.factor gplots
Loading required package: gdata
sh: 1: /usr/bin/perl: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: ‘gdata’

The following object is masked from ‘package:gplots’:

    reorder.factor

The following object is masked from ‘package:IRanges’:

    trim

The following objects are masked from ‘package:S4Vectors’:

    first, 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
Warning message:
In system(cmd, intern = TRUE) :
  running command ''/usr/bin/perl' '/usr/lib/R/site-library/gdata/perl/supportedFormats.pl'' had status 126
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

MLP documentation built on Nov. 8, 2020, 8:23 p.m.