plotSpatial.MicroarrayData: Plots a spatial representation of one field

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

Description

Plots a spatial representation of one field. It is recommended to use the plot function instead of calling this method explicitly (see *plot()).

Usage

## S3 method for class 'MicroarrayData'
plotSpatial(this, what, slide=1, include=NULL, exclude=NULL, col="auto", xlab=NULL, ylab="", axes=FALSE, xaxs="i", yaxs="i", pch="auto", grid=TRUE, log=NULL, ..., cex=NULL, style=NULL)

Arguments

what	What to plot. Any field that can be retrieved by extract, is accepted.
slide	The slide to be plotted.
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. If NULL no spots are excluded.
col	The color(s) to be used for the plotted spots, i.e. for the spots after inclusion and exclusion. If the value is "redgreen" a red to green palette is used.
...	Common arguments accepted by most plot functions. For more information see par and plot.
cex	For internal use only! See above.
pch	For internal use only! See above.

Author(s)

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

See Also

*plot(). *plotXY(). *highlight(). *text(). For more information see MicroarrayData.

Examples

  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)

  subplots(4)
  plotSpatial(ma)                   # Spatial plot of log ratios before.
  normalizeWithinSlide(ma, "p")     # Printtipwise lowess normalization.
  plotSpatial(ma)                   # Spatial plot of log ratios after.

  plotSpatial(ma, include=(abs(ma$M) > 2))
  points(ma, include=(abs(ma$M) > 2), col="red")

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