maImage.func {marray} | R Documentation

## 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`.

### Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.

### 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.

[Package marray version 1.8.0 Index]