marray (version 1.50.0)

maImage.func: Color image for cDNA microarray spot statistics

Description

This function 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 M, 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. This function is called by maImage.

Usage

maImage.func(x, L, subset=TRUE, col=heat.colors(12), contours=FALSE, overlay=NULL, ol.col=1,  ...)

Arguments

x

A "numeric" vector of spot statistics.

L

An object of class "marrayLayout", if L is missing we will assume the dimension of x.

subset

A "logical" or "numeric" vector indicating the subset of spots to display on the image.

col

A list of colors such as that generated by rainbow, heat.colors, topo.colors, terrain.colors, or similar functions. In addition to these color palette functions, a new function maPalette was defined to generate color palettes from user supplied low, middle, and high color values.

contours

If contours=TRUE, contours are plotted, otherwise they are not shown.

overlay

A logical vector of spots to be highlighted on the image plots.

ol.col

Color of the overlay spots.

...

Optional graphical parameters, see par.

References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software, Springer, New York.

See Also

image, maImage, maColorBar, maPalette.

Examples

# See examples for image.