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Last data update: 2014.03.03

R: Density plot of a ExpressionSet object

density-methods

R Documentation

Density plot of a ExpressionSet object

Description

Creating density plot of sample intensities in a ExpressionSet object. It is equivalent to hist-methods.

Usage

## S4 method for signature 'ExpressionSet'
density(x, logMode=TRUE, xlab = NULL, ylab = "density", type = "l", 
	col=1:dim(x)[2], lty=1:dim(x)[2], lwd=1, xlim = NULL, index.highlight = NULL, color.highlight = 2, 
	symmetry = NULL, addLegend = TRUE, legendPos="topright", subset = NULL, main="", ...)

Arguments

`x`	a `ExpressionSet` object
`logMode`	determine whether the density plot is based on a log2 scale
`xlab`	xlab of the density plot
`ylab`	ylab of the density plot
`type`	parameter of plot function
`col`	line colors of the density plot
`lty`	line types of the density plot
`lwd`	line width of plot function
`xlim`	parameter of the plot function
`index.highlight`	the column index of the highlighted density curve
`color.highlight`	color of highlighted density curve
`symmetry`	the boundary position suppose to be symmetric distributed
`addLegend`	whether add legend to the plot or not
`legendPos`	the legend position. It can be a string specifying the position, or a length two vector specifying the x and y position. Please check `legend` for more details.
`subset`	subset of rows used to plot. It can be an index vector, or the length of a random subset
`main`	title for the plot
`...`	additional parameters for `density` function

See Also

LumiBatch-class, hist-methods, density

Examples

## load example data
data(example.lumi)

density(example.lumi)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(lumi)
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/density-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: density-methods
> ### Title: Density plot of a ExpressionSet object
> ### Aliases: density-methods density.ExpressionSet
> ###   density,ExpressionSet-method
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> 
> density(example.lumi)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>