boxplot.MicroarrayData: Plots a boxplot
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Author(s) See Also Examples

Creates a box plot for any data over all grids or over all slides. If the argument slide is given, an boxplot over the print-tips will be generated, others an across-slides boxplot will be generated.

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## S3 method for class 'MicroarrayData'
boxplot(x, what, style=NULL, slides=NULL, include=NULL, exclude=NULL, groupBy="slide", gridwise=FALSE, names=NULL, xlab=NULL, ylab=NULL, log=NULL, las=3, col=NULL, ...)

`what`	What data variable to do a boxplot for.
`slides`	The slide(s) that should be used to generate this plot. If `NULL` data from all slides are considered.
`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.
`groupBy`	The data can be grouped by either `"slide"` or `"printtip"`.
`gridwise`	(Deprecated) If `TRUE` a within-slide (across-grid) boxplot is generated, otherwise an across-slide boxplot is generated.
`names`	A string vector of names for each grid/slide. If `NULL` the grids will be named 1,2,3, etc.
`xlab, ylab`	Label on the x-axis (y-axis). If `NULL` the label will be automatically set.
`las`	Rotation style of the axis labels. Default value is 3 (always vertical). For more information see `par`.
`...`	Common arguments accepted by most plot functions. For more information see `par` and `plot`.

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

boxplot. 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)

  boxplot(ma, groupBy="printtip") # Log-ratios for printtips on all slides
  boxplot(ma)                     # Log-ratios for all slides.
  boxplot(ma, slides=c(1,3,5))    # Log-ratios for slides 1, 3 and 5.