imageplot {limma}R Documentation

Image Plot of Microarray Statistics

Description

Creates an image of shades of gray or colours, that represents the values of a statistic for each spot on the array. The statistic can be a log intensity ratio, quality information such as spot size or shape, or a t-statistic. This function can be used to explore whether there are any spatial effects in the data.

Usage

imageplot(z, layout, low = NULL, high = NULL, ncolors = 123, zerocenter = NULL, 
zlim = NULL, mar=rep(1,4), ...)

Arguments

z numeric vector or array. This vector can contain any spot statistics, such as log intensity ratios, spot sizes or shapes, or t-statistics. Missing values are allowed and will result in blank spots on the image.
layout a list specifying the dimensions of the spot matrix and the grid matrix.
low color associated with low values of z. May be specified as a character string such as "green", "white" etc, or as a rgb vector in which c(1,0,0) is red, c(0,1,0) is green and c(0,0,1) is blue. The default value is "green" if zerocenter=T or "white" if zerocenter=F.
high color associated with high values of z. The default value is "red" if zerocenter=T or "blue" if zerocenter=F.
ncolors number of color shades used in the image including low and high.
zerocenter should zero values of z correspond to a shade exactly halfway between the colors low and high? The default is TRUE if z takes positive and negative values, otherwise FALSE.
zlim numerical vector of length 2 giving the extreme values of z to associate with colors low and high. By default zlim is the range of z. Any values of z outside the interval zlim will be truncated to the relevant limit.
mar numeric vector of length 4 specifying the width of the margin around the plot. This argument is passed to par.
... any other arguments will be passed to the function image

Details

The image follows the layout of an actual microarray slide with the bottom left corner representing the spot (1,1,1,1). This function is very similar to the sma function plot.spatial but is intended to display spatial patterns and artefacts rather than to highlight extreme values. The function differs from plot.spatial most noticeably in that all the spots are plotted and the image is plotted from bottom left rather than from top left.

Value

An image is created on the current graphics device.

Author(s)

Gordon Smyth

See Also

maImage, image.

An overview of diagnostic functions available in LIMMA is given in 7.Diagnostics.

Examples

M <- rnorm(8*4*16*16)
imageplot(M,layout=list(ngrid.r=8,ngrid.c=4,nspot.r=16,nspot.c=16))

[Package limma version 1.6.7 Index]