imageplot {beadarray}R Documentation

imageplot for BeadLevelList object

Description

Generates an image plot for data from a BeadLevelList 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, SAM=FALSE, ...)

Arguments

BLData BeadLevelList
array integer specifying which strip/array to plot
nrow integer specifying the number of rows to divide the strip/array into
ncol integer specifying the number of columns to divide the strip/array into
low colour to use for lowest intensity
high colour to use for highest intensity
ncolors The number of colour graduations between high and low
whatToPlot character string specifying which intensities/values to plot. See getArrayData for a list of possibilities
log if TRUE, log2 intensities are plotted
zlim numerical vector of length 2 giving the extreme values of 'z' to associate with colours 'low' and 'high'.
main character string for plot title
method character string specifying the summarisation method to use. Only applicable when whatToPlot="residG", "residR" or "residM". Refer to the createBeadSummaryData help page for further information.
n numeric value specifying the number of median absolute deviations (MADs) from the median to use as a cut-off for outliers. The default value is 3. Only applicable when whatToPlot="residG", "residR" or "residM" and method="illumina". Refer to 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.
SAM logical, if TRUE, x and y coordinates are transposed.
... other graphical parameters to plot that can be specified

Details

Because of the large number of beads on each strip/array, this function works by mapping a grid of size specified by the nrow and ncol arguments and averaging the intensities of the beads within each section of the 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 the strips on a BeadChip, and nrow=100 ncol=100 for arrays on a SAM.

An imageplot of the log base 2 foreground intensities is produced by default. Other values can be plotted by changing the whatToPlot argument. The default colour scheme ranges from white for low values to blue for high values.

Value

A plot is produced on the current graphical device.

Author(s)

Mike Smith, Mark Dunning

Examples

data(BLData)
imageplot(BLData)

[Package beadarray version 1.10.0 Index]