plotSpatial.ScanAlyzeData: 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 'ScanAlyzeData'
plotSpatial(this, slide=1, pch=20, yaxt=NULL, col=NULL, palette="redgreen", A.range=c(0, 16), M.range=c(-1, 1), ...)

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 accepted by plot.

Details

The ScanAlyze software does not return the center position of a spot, but the TOP LEFT BOT and RIGHT coordinates. This method assumes that the center of the spot is in the center of this box.

Value

Returns nothing.

Author(s)

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

See Also

For more information see ScanAlyzeData.

Examples

  sa <- ScanAlyzeData$read("group4.dat", path=system.file("data-ex", package="aroma"))

  subplots(2)

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

  opar <- par(bg="black")
  plotSpatial(sa, palette="blueyellow")
  par(opar)

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