imageplot {beadarray} | R Documentation

## imageplot for BeadArrays object

### Description

Plots an image plot of a bead level data object.

### Usage

    imageplot(BLData, array = 1, nrow = 100, ncol = 100, low= NULL,
               high = NULL, ncolors = 123, whatToPlot ="G", log=TRUE,
               zlim=NULL, main=whatToPlot, method="illumina", n = 3,
               trim=0.05, legend=TRUE, ...)

### Arguments

`BLData` | Object of class BLData
`array` | array to plot
`nrow` | How many rows should the array be divided into
`ncol` | How many columns should the array be divided into
`low` | Color for area of lowest intensity
`high` | color for area of highest intensity
`ncolors` | The number of color graduations between high and low
`whatToPlot` | character string specifying which intensities/values to plot. See `getArrayData` for a list of the possibilities
`log` | if TRUE, log2 intensities are plotted
`zlim` | numerical vector of length 2 giving the extreme values of 'z' to associate with colors 'low' and 'high'.
`main` | character string for plot title
`method` | chracter string specifying the summarisation method to use. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`. Refer to help `createBeadSummaryData` help page for further information.
`n` | use n median absolute deviations from the median as a cut-off for outliers. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`. Refer to help `createBeadSummaryData` help page for further information.
`trim` | fraction of intensities to remove from the bead summary calculations. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`. Refer to `createBeadSummaryData` help page for further information.
`legend` | logical, if `TRUE`, `zlim` and range of data is added to plot.
`...` | other graphical parameters to plot that can be specified

### Details

Because of the high volume of bead level data, this function works by mapping a grid (who's size is specified by the nrow and ncol) arguments and averages the intensities of the beads within each section of this grid.

The number of rows and columns may change the appearance of the plots. If the array is divided into too many squares it will be difficult to detect changes. We recommend using `nrow=20` and `ncol=200` for whole genome arrays, and `nrow=100` `ncol=100` for arrays on a SAM.

An imageplot of the log base 2 foreround intensities is produced by default. Other values can be plotted by changing the `whatToPlot` argument.

### Value

Plot is produced on current graphical device.

### Author(s)

Mike Smith, Mark Dunning

### Examples

    data(BLData)
    imageplot(BLData)

[Package beadarray version 1.6.0 Index]