text.MicroarrayData: Puts labels to the spots in last plot

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

Description

Puts labels to the spots in last plot.

Usage

## S3 method for class 'MicroarrayData'
text(x, include=NULL, exclude=NULL, labels=NULL, col="black", offset=0.2, pos=4, xpd=TRUE, ...)

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.
labels	Labels of all the data points. If NULL first the labels of the belonging Layout object is retrieved. If there is no Layout object, the data points are labeled with indices of the plotted spots.
col	The color(s) to be used for the plotted spots, i.e. for the spots after inclusion and exclusion.
pos	A position specifier for the text. Values of 1, 2, 3 and 4, respectively indicate positions below, to the left of, above and to the right of the specified coordinates.
offset	When ‘pos’ is specified, this value gives the offset of the label from the specified coordinate in fractions of a character width.
xpd	A logical value or NA. If FALSE, all plotting is clipped to the plot region, if TRUE, all plotting is clipped to the figure region, and if NA, all plotting is clipped to the device region.
...	Common arguments accepted by most text labeling functions. For more information see text and par.

Author(s)

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

See Also

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

Examples

  # Loads the file 'gpr123.gpr' located in the data directory:
  gpr <- GenePixData$read("gpr123.gpr", path=system.file("data-ex", package="aroma"))
  raw <- getRawData(gpr);
  ma <- getSignal(raw)

  # Highlight and label the first 50 genes
  idx <- 1:50
  plot(ma)

  # Highlight all spots in grid (1,2)
  highlight(ma, idx, col="purple")

  # Add bold faced labels using the labels specified by the layout
  text(ma, idx, font=2)

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