arrayPlot {GLAD} | R Documentation

## Spatial image of microarray spots statistic

### Description

The function `arrayPlot` creates spatial images of shades of gray or colors that correspond to the values of a statistic for each spot on the array. The statistic can be the intensity log-ratio, a spot quality measure (e.g. spot size or shape), or a test statistic. This function can be used to explore whether there are any spatial effects in the data, for example, print-tip or cover-slip effects.

### Usage

    ## Default S3 method:
    arrayPlot(Statistic, Col, Row,
                      ArrCol, ArrRow, SpotCol, SpotRow,
                      mediancenter=FALSE,
                      col=myPalette("green", "red", "yellow"),
                      contour=FALSE, nlevels=5,
                      zlim=NULL, bar=c("none", "horizontal", "vertical"),
                      layout=TRUE, ...)

    ## S3 method for class 'arrayCGH'
    arrayPlot(arrayCGH, variable,
                       mediancenter=FALSE,
                       col=myPalette("green", "red", "yellow"),
                       contour=FALSE, nlevels=5,
                       zlim=NULL, bar=c("none", "horizontal", "vertical"),
                       layout=TRUE, ...)

### Arguments

`arrayCGH` | Object of class `arrayCGH`.
`variable` | Variable to be plotted
`Statistic` | Statistic to be plotted.
`Col` | Vector of columns coordinates.
`Row` | Vector of rows coordinates.
`ArrCol` | Number of columns for the blocs.
`ArrRow` | Number of rows for the blocs.
`SpotCol` | Number of column for each bloc.
`SpotRow` | Number of rows for each bloc.
`mediancenter` | If `mediancenter=TRUE`, values of `Statistic` are median-centered.
`col` | List of colors such as that generated by `Palettes`. In addition to these color palettes functions, a new function `myPalette` was defined to generate color palettes from user supplied low, middle, and high color values.
`contour` | If `contour=TRUE`, contour are plotted, otherwise they are not shown.
`nlevels` | Numbers of levels added by `contour` if `contour=TRUE`.
`zlim` | Numerical vector of length 2 giving the extreme values of `z` to associate with colors `low` and `high` of `myPalette`. By default `zlim` is the range of `z`. Any values of `z` outside the interval `zlim` will be truncated to the relevant limit.
`bar` | If `bar=='horizontal'` (resp. `'vertical'`), an horizontal (resp. vertical) calibration color bar is shown to the right of the image.
`layout` | If `layout==TRUE` plot layout is automatically set when a color bar is asked for
`...` | Graphical parameters can be given as arguments to function `image`.

N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes the values in 1:arrayCol*SpotCol

### Details

This function is very similar to the `maImage` written by Sandrine Dudoit (available in marrayPlots package) with added options `zlim`, `mediancenter` and `layout`.

### Value

An image is created on the current graphics device.

### Note

People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.

### Author(s)

Philippe HupÃ©, glad@curie.fr.

### See Also

`image`, `contour`, `arrayPersp`, `myPalette`.

### Examples

    data(arrayCGH)

    pdf(file="arrayCGH.pdf",height=21/cm(1),width=29.7/cm(1))
    arrayPlot(array2$Log2Rat, array2$Col, array2$Row, 4,4,21,22, main="Spatial Image of array CGH")
    dev.off()

    # object of class arrayCGH

    array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22))
    class(array) <- "arrayCGH"

    arrayPlot(array,"Log2Rat", main="Spatial Image of array CGH")

[Package GLAD version 2.50.0 Index]