plotSpatial.QuantArrayData: Creates a spatial plot of a slide

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Creates a spatial plot of a slide.

Usage

## S3 method for class 'QuantArrayData'
plotSpatial(this, what=NULL, slide=1, pch=20, yaxt=NULL, col="auto", palette="redgreen", A.range=c(0, 16), M.range=c(-1, 1), style=c("real", "classic"), ...)

Arguments

slide	The slide to be plotted.
pch	The spot symbol. Default is 20 (solid disk).
col	The color of the spots. If NULL, default color is used.
palette	If col is not specified, colors are generated automaticially from the signals in the two foreground channels. If redgreen, a red to green colors scale will be used. If blueyellow, a blue to yellow colors scale will be used.
A.range	The range of the log (base 2) spot intensities. Used only for generating colors.
M.range	The range of the log (base 2) spot ratios. Used only for generating colors.
yaxt, ...	Parameters as accepted by plot.

Value

Returns nothing.

Author(s)

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

See Also

For more information see QuantArrayData.

Examples

 ## Not run: 
  # At the moment there is no QuantArray sample files in the package...
  # qa <- QuantArrayData$read("quantarray123.txt", path=system.file("data-ex", package="aroma"))
  # ...will use a GenePix sample file instead.
  qa <- GenePixData$read("gpr123.gpr", path=system.file("data-ex", package="aroma"))

  subplots(2)

  opar <- par(bg="black")
  plotSpatial(qa)
  par(opar)

  opar <- par(bg="black")
  plotSpatial(qa, palette="blueyellow")
  par(opar)
 
## End(Not run)

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.