plotPrintorder.MicroarrayData: Plots the data as a time series in the order it was printed
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Details Author(s) References See Also Examples

Plots the data as a time series in the order it was printed.

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## S3 method for class 'MicroarrayData'
plotPrintorder(this, what, slides=NULL, include=NULL, exclude=NULL, cex="auto", col="auto", pch="auto", xlab="in print order", ylab=NULL, ylog=NULL, groupfcn=NULL, breakpoints=NULL, ..., f=200/nbrOfSpots(this), style=NULL)

`field`	The field to be plotted. Any field that can be retrieved by `extract`, is accepted.
`slides`	The slide(s) to be plotted. If `NULL`, all slides are 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`.

If a vector of colors (col), symbol sizes (cex) or symbol types (pch) are specified, such vectors will be reordered according to the print order before being applied.

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

[1] Henrik Bengtsson, Plate Effects in cDNA microarray data, Matemathical Statistics, Centre for Matematical Sciences, Lund University, Sweden. Manuscript, 2002.

*plot(). *plotXY(). *highlight(). *text(). 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)

  plotPrintorder(ma, "M")       # Printorder plot of log ratios before.
  normalizeWithinSlide(ma, "p") # Printtipwise lowess normalization.
  plotPrintorder(ma, "M")       # Printorder plot of log ratios after.