highlight.MicroarrayData: Highlight spots in last plot

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

Description

Highlight spots in last plot.

Usage

## S3 method for class 'MicroarrayData'
highlight(this, include=NULL, exclude=NULL, col="black", ...)

Arguments

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.
pch	The point style to be used. Default value is 176 (a small open circle). For more information see par.
cex	The scale factor to be used. If NULL the system default scale factor will be used. For more information see par.
col	The color(s) to be used for the plotted spots, i.e. for the spots after inclusion and exclusion.
...	Common arguments accepted by most plot functions. For more information see par and plot.

Author(s)

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

See Also

*text(). points. 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)

  # Get all spots in the grid at row 1 and at column 2.
  layout <- getLayout(ma)
  idx <- getIndices(layout, 1,2, NULL,NULL)

  # Plot the data both highlighted and non-highlighted.
  layout(matrix(1:4, ncol=2, byrow=TRUE))
  plot(ma)
  plotSpatial(ma)
  plot(ma)
  highlight(ma, idx, col="purple")  # Highlight all spots in grid (1,2).
  plotSpatial(ma)
  highlight(ma, idx, col="purple")  # Highlight all spots in grid (1,2).

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