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]