arrayPersp: Perspective image of microarray spots statistic

In GLAD: Gain and Loss Analysis of DNA

Description

The function arrayPersp creates perspective 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:
arrayPersp(Statistic, Col, Row,
                   ArrCol, ArrRow, SpotCol, SpotRow,
                   mediancenter=FALSE,
                   col=myPalette("green","red","yellow"),
                   zlim=zlim, bar=TRUE, ...)


## S3 method for class 'arrayCGH'
arrayPersp(arrayCGH, variable,
   	            mediancenter=FALSE,
		    col=myPalette("green","red","yellow"),
	            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.
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 persp.

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

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, [e-mail].

See Also

persp, arrayPlot, myPalette.

Examples

## Not run: 
data(arrayCGH)


# object of class arrayCGH

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

arrayPersp(array,"Log2Rat", main="Perspective image of array CGH",
           box=FALSE, theta=110, phi=40)


## End(Not run)

GLAD documentation built on Nov. 8, 2020, 11:10 p.m.