plotDensity {affy} | 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")
    }

[Package affy version 1.68.0 Index]