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))

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