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


arrayPlot.default(Statistic, Col, Row,
                  ArrCol, ArrRow, SpotCol, SpotRow,
                  mediancenter=FALSE,
                  col=myPalette("green","red","yellow"),
                  contour=FALSE, nlevels=5,
                  zlim=zlim, bar=TRUE, ...)

arrayPlot.arrayCGH(arrayCGH, variable,
                   mediancenter=FALSE,
                   col=myPalette("green","red","yellow"),
                   contour=FALSE, nlevels=5,
                   zlim=zlim, bar=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=TRUE, a calibration color bar is shown to the right of the image.
... 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 with added options zlim and mediancenter.

Value

An image is created on the current graphics device.

Author(s)

Philippe Hupé, http://www.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 1.0.1 Index]