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Last data update: 2014.03.03

R: Density plots of log2 intensity values

densityplot

R Documentation

Density plots of log2 intensity values

Description

Plots the estimated density of log2 intensity values for two-color microarrays

Usage


## S4 method for signature 'RGList,missing'
densityplot(
    x,
    channel=c("G", "R"),
    group=NULL,
    subset=NULL, 
    ...)

## S4 method for signature 'list,missing'
densityplot(
    x,
    channel=c("G", "R"),
    group=NULL,
    subset=NULL, 
    ...)

Arguments

`x`	Either an `RGList` object, or a list containing `MAList` and/or `NChannelSet` objects
`channel`	The channel to use for calculating distances, one of either "G" (green or control channel) or "R" (red or experimental channel)
`group`	An optional character string specifying the name of a factor to create separate panel displays, which must be in `x$genes` (for `RGList` objects)
`subset`	An optional character vector specifying the which levels of `group` to use in creating separate panel displays
`...`	arguments to pass to `densityplot`

Methods

signature(x = "RGList", data = "missing"): For RGList objects, separate panel displays can be produced for different types of probes, as determined by the group argument.
signature(x = "list", data = "missing"): The method for list objects is intended to work with lists of normalized data sets, as either MAList or NChannelSet objects. This method will produce separate panel displays for each normalized data set, additionally subsetted by the group argument if supplied. The useOuterStrips function in the latticeExtra package can be used for ‘outer’ strip labels in the latter case.

References

D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, and M. Tewari. Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res, 37(2):e17, 2009.

Examples

data(PalateData)
res <- densityplot(PalateData, channel="G", group="probe.type", 
                   subset = c("Other miRNAs",   "MMU miRNAs", "Control"), 
                   col=rep(1:3, each=3), lty=rep(1:3, 3), 
                   key = list(lines=list(col=rep(1:3, each=3), lty=rep(1:3, 3)), 
                     columns=3))
print(res)

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(MmPalateMiRNA)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: xtable
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: statmod
Loading required package: lattice
Loading required package: vsn
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MmPalateMiRNA/densityplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: densityplot
> ### Title: Density plots of log2 intensity values
> ### Aliases: densityplot densityplot-methods
> ###   densityplot,RGList,missing-method densityplot,list,missing-method
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> data(PalateData)
> res <- densityplot(PalateData, channel="G", group="probe.type", 
+                    subset = c("Other miRNAs",   "MMU miRNAs", "Control"), 
+                    col=rep(1:3, each=3), lty=rep(1:3, 3), 
+                    key = list(lines=list(col=rep(1:3, each=3), lty=rep(1:3, 3)), 
+                      columns=3))
> print(res)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>