getColors.RawData: Generates colors for each of the specified spots

Description Usage Arguments Value Author(s) See Also Examples

Description

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.

Usage

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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), ...)

Arguments

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.

Value

Returns a vector of colors.

Author(s)

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

See Also

For more information see RawData.

Examples

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   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);
 

HenrikBengtsson/aroma documentation built on May 8, 2017, 3:58 p.m.