getColors.MAData: 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 as a col argument in most plot functions.

1 2	## S3 method for class 'MAData' getColors(this, what=c("A", "M"), slide=1, include=NULL, exclude=NULL, palette=NULL, range="auto", ...)

`slide`	Specifies for which slide the colors should be generated for.
`include`	The spot indices to be plotted. If `NULL` all spots are considered.
`exclude`	The spot indices not to be plotted. If `NULL` no spots are excluded (from all or from the one specified by `include`).
`palette`	The palette to be used. Currently, only the `"redgreen"` palette is available.
`M.range`	The range of "normal" M values. All M values outside this range will be cutoff.
`A.range`	The range of "normal" A values. All A values outside this range will be cutoff.

Returns a vector of colors.

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

Colors. For more information see MAData.

   # The option 'dataset' is used to annotate plots.
   options(dataset="sma:MouseArray")

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