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 Hupé, 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 2.44.0 Index]