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Last data update: 2014.03.03

R: show a ProbeSet as barplots

barplot.ProbeSet

R Documentation

show a ProbeSet as barplots

Description

Displays the probe intensities in a ProbeSet as a barplots

Usage

## S3 method for class 'ProbeSet'
barplot(height, xlab = "Probe pair", ylab = "Intensity",
    main = NA, col.pm = "red", col.mm = "blue", beside = TRUE, names.arg = "pp",
    ask = TRUE, scale, ...)

Arguments

`height`	an object of class `ProbeSet`.
`xlab`	label for x axis.
`ylab`	label for y axis.
`main`	main label for the figure.
`col.pm`	color for the ‘pm’ intensities.
`col.mm`	color for the ‘mm’ intensities.
`beside`	bars beside each others or not.
`names.arg`	names to be plotted below each bar or group of bars.
`ask`	ask before ploting the next barplot.
`scale`	put all the barplot to the same scale.
`...`	extra parameters to be passed to `barplot`.

Examples

if (require(affydata)) {
  data(Dilution)
  gn <- geneNames(Dilution)
  pps <- probeset(Dilution, gn[1])[[1]]

  barplot.ProbeSet(pps)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(affy)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/barplot.ProbeSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: barplot.ProbeSet
> ### Title: show a ProbeSet as barplots
> ### Aliases: barplot.ProbeSet
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+   gn <- geneNames(Dilution)
+   pps <- probeset(Dilution, gn[1])[[1]]
+ 
+   barplot.ProbeSet(pps)
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>