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 = 18, ncol = 2, low= NULL,
               high = NULL, ncolors = 123, whatToPlot ="G", log=TRUE,
               zlim=NULL, main=whatToPlot, ...)

### 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 to plot. Possibilities are `"G"`, `"Gb"` for single channel data and `"G"`, `"Gb"`, `"R"` and `"Rb"` for two-colour data
`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
`...` | 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 (log base 2) 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 difficult to detect changes. We recommend using nrow=200 and ncol=20 for whole genome arrays.

An imageplot of the forgeround intensities is produced be default. Other intensities can be plotted by using the `which` argument.

### Value

Plot is produced on current graphical device.

### Author(s)

Mike Smith, Mark Dunning

### Examples

    data(BLData)

    imageplot(BLData, nrow=100, ncol=100)

[Package beadarray version 1.4.0 Index]