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Last data update: 2014.03.03

R: Plot Densities

plotDensity

R Documentation

Plot Densities

Description

Plots the non-parametric density estimates using values contained in the columns of a matrix.

Usage



plotDensity(mat, ylab = "density", xlab="x", type="l", col=1:6,
            na.rm = TRUE, ...)

plotDensity.AffyBatch(x, col = 1:6, log = TRUE,
                      which=c("pm","mm","both"),
                      ylab = "density",
                      xlab = NULL, ...)

Arguments

`mat`	a matrix containing the values to make densities in the columns.
`x`	an object of class `AffyBatch`.
`log`	logical value. If `TRUE` the log of the intensities in the `AffyBatch` are plotted.
`which`	should a histogram of the PMs, MMs, or both be made?
`col`	the colors to use for the different arrays.
`ylab`	a title for the y axis.
`xlab`	a title for the x axis.
`type`	type for the plot.
`na.rm`	handling of `NA` values.
`...`	graphical parameters can be given as arguments to `plot`.

Details

The list returned can be convenient for plotting large input matrices with different colors/line types schemes (the computation of the densities can take some time).

To match other functions in base R, this function should probably be called matdensity, as it is sharing similarities with matplot and matlines.

Value

It returns invisibly a list of two matrices ‘x’ and ‘y’.

Author(s)

Ben Bolstad and Laurent Gautier

Examples

if (require(affydata)) {
  data(Dilution)
  plotDensity(exprs(Dilution), log="x")
}

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/plot.density.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDensity
> ### Title: Plot Densities
> ### Aliases: plotDensity plotDensity.AffyBatch
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+   plotDensity(exprs(Dilution), log="x")
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>