plotXY.MicroarrayData: Plots a scatter plot of two fields
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Author(s) See Also Examples

Plots a scatter plot of two fields. It is recommended to use the plot function instead of calling this method explicitly (see *plot()).

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## S3 method for class 'MicroarrayData'
plotXY(this, what, style=NULL, slide=NULL, include=NULL, exclude=NULL, xlog=NULL, ylog=NULL, xlab=NULL, ylab=NULL, cex=NULL, col="auto", pch="auto", gridwise=FALSE, f=0.3, lim=NULL, xlim=NULL, ylim=NULL, ...)

`what`	What to plot. Any two field that can be retrieved by `extract` are 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.
`gridwise`	If `TRUE` a lowess line for each grid will be drawn, otherwise only the global lowess line will be drawn.
`xlog, ylog`	The logarithmic base to be used to take the logarithm of the x and the y values, respectively. If `NULL`, the non-logarithmic values are plotted. Note the difference from the definition in `par`.
`xlab, ylab`	The labels on the x and the y axis, respectively. If `NULL`, the fields default label will be used.
`cex`	The scale factor to be used. If `NULL` the system default scale factor will be used.
`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.
`pch`	The dot style. Default value is `176`, which is a small circle.
`f`	The bandwidth for the lowess lines.
`...`	Common arguments accepted by most plot functions. For more information see `par` and `plot`.

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

*plot(). *plotSpatial(). *highlight(). *text(). plotSymbols.Device. For more information see MicroarrayData.

  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)

  plotXY(ma)                    # Plot M vs A (default)
  plotXY(ma, what=c("M","A"))   # Plot A vs M.