limma: imageplot – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

imageplot

Image Plot of Microarray Statistics

Description

Creates an image of colors or shades of gray that represent the values of a statistic for each spot on a spotted microarray. This function can be used to explore any spatial effects across the microarray.

Usage

imageplot(z, layout, low = NULL, high = NULL, ncolors = 123, zerocenter = NULL, 
zlim = NULL, mar=c(2,1,1,1), legend=TRUE, ...)

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. Infinite values are not allowed.
`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`.
`legend`	logical, if `TRUE` the range of `z` and `zlim` is shown in the bottom margin
`...`	any other arguments will be passed to the function image

Details

This function may be used to plot the values of any spot-specific statistic, such as the log intensity ratio, background intensity or a quality measure such as spot size or shape. The image follows the layout of an actual microarray slide with the bottom left corner representing the spot (1,1,1,1). The color range is used to represent the range of values for the statistic. When this function is used to plot the red/green log-ratios, it is intended to be an in silico version of the classic false-colored red-yellow-green image of a scanned two-color microarray.

This function is related to the earlier plot.spatial function in the sma package and to the later maImage function in the marray package. It 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. It is intended to display spatial patterns and artefacts rather than to highlight only the extreme values as does plot.spatial. It differs from maImage in that any statistic may be plotted and in its use of a red-yellow-green color scheme for log-ratios, similar to the classic false-colored jpeg image, rather than the red-black-green color scheme associated with heat maps.

Value

An plot is created on the current graphics device.

Author(s)

Gordon Smyth

Examples

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

limma

Linear Models for Microarray Data

v3.46.0

GPL (>=2)

Authors

Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]

Initial release

2020-10-19