arrayPlot: Spatial image of microarray spots statistic
In GLAD: Gain and Loss Analysis of DNA

Description Usage Arguments Details Value Note Author(s) See Also Examples

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.

## 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, ...)

`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

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

An image is created on the current graphics device.

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

Philippe HupÃ©, glad@curie.fr.

image, contour, arrayPersp, myPalette.

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")