plot.density: Plot Densities

In affy: Methods for Affymetrix Oligonucleotide Arrays

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")
}

Example output

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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")'.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: affydata
     Package    LibPath                         Item      
[1,] "affydata" "/usr/local/lib/R/site-library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

affy documentation built on Nov. 8, 2020, 8:18 p.m.