plot.MicroarrayData: Plots spatial representation of a microarray spot statistics

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

Description

Plots spatial representation of a microarray spot statistics. Currently the statistics can be either the log-ratios (default) or the intensities.

Usage

## S3 method for class 'MicroarrayData'
plot(x, what, ..., style=NULL)

Arguments

what	What to plot. Common formats are "YvsX" and "spatialX" where X and Y are variables in the object.
...	Common arguments accepted by most plot functions. For more information see *plotXY(), *plotSpatial(), par, and plot.

See Also

*plotXY() and *plotSpatial(), which are called by plot. For highlightning and put labels on spots after plotting see *highlight() and *text(). 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)
  rg <- as.RGData(ma)

  layout(matrix(1:6, nrow=2, byrow=TRUE))
  plot(raw)            # Plots R vs Rb. Default is "RvsRb" and slide 1.
  plot(raw, "GvsGb")   # Plots G vs Gb.
  plot(rg)             # Plots R vs G. Default is "RvsG" and slide 1.
  plot(rg, "GvsR")     # Plots G vs R.
  plot(ma, slide=4)    # Plots M vs A for slide 4. Default is "MvsA".
  plot(ma, "spatialM") # Plots spatial plot of M's.

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