getColors.RawData: Generates colors for each of the specified spots
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Value Author(s) See Also Examples

Generates colors for each of the specified spots, which can be passed to the col argument in most plot functions. However, note that most of the plot functions in this package automatically recognize palettes if they are passed to the col argument.

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## S3 method for class 'RawData'
getColors(this, what=c("R", "G"), slide=1, include=NULL, exclude=NULL, palette=NULL, bgSubtract=FALSE, bg.subtract=bgSubtract, range=matrix(c(0, 16, 0, 16), nrow = 2), ...)

`what`	The fields to be used.
`slide`	Specifies for which slide the colors should be generated for.
`include`	The indices of the spots that should be included. If it is instead a name of one or more flags, the spots which have been flagged with these flags are considered. If `NULL` all spots are considered.
`exclude`	The indices of the spots that should be excluded. If it is instead a name of one or more flags, the spots which have been flagged with these flags are excluded.
`bgSubstract`	If `TRUE`, the background is subtracted from the foreground, before the colors are generated.
`palette`	The palette to be used. If `NULL` or `"auto"` the palette that is most applicable to the value of `what` will be used.
`range`	Cut-off range for data values. The format is a matrix with two rows and `length(what)` number of columns.

Returns a vector of colors.

Henrik Bengtsson (http://www.braju.com/R/)

For more information see RawData.

   SMA$loadData("mouse.data")
   layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
   raw <- RawData(mouse.data, layout=layout)
   col <- getColors(raw, what="G", slide=4);