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]