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",zlim=NULL,...)

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 string identifying which matrix in BLData to use in the imageplot
zlim numerical vector of length 2 giving the extreme values of 'z' to associate with colors 'low' and 'high'.
... 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 sqaures 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 matrices in BLData can be plotted by using the whatToPlot argument. eg change to Gb to plot the background intensities.

Value

Plot is produced on current graphical device.

Author(s)

Mike Smith, Mark Dunning


[Package beadarray version 1.2.2 Index]