# 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

 ```1 2 3 4 5 6 7``` ```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’.

## Examples

 ```1 2 3 4``` ```if (require(affydata)) { data(Dilution) plotDensity(exprs(Dilution), log="x") } ```

### Example output

```Loading required package: BiocGenerics

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':

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

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