plotLocation: Plot a location on a cel image
In affy: Methods for Affymetrix Oligonucleotide Arrays

Description Usage Arguments Author(s) See Also Examples

Plots a location on a previously plotted cel image. This can be used to locate the physical location of probes on the array.

1	plotLocation(x, col="green", pch=22, ...)

`x`	a ‘location’. It can be obtained by the method of `AffyBatch` `indexProbes`, or made elsewhere (basically a location is nrows and two columns array. The first column corresponds to the x positions and the second columns corresponds to the y positions of n elements to locate).
`col`	colors for the plot.
`pch`	plotting type (see function `plot`).
`...`	other parameters passed to the function `points`.

Laurent

AffyBatch

if (require(affydata)) {
  data(Dilution)

  ## image of the celfile
  image(Dilution[, 1])

  ## genenames, arbitrarily pick the 101th
  n <- geneNames(Dilution)[101]

  ## get the location for the gene n
  l <- indexProbes(Dilution, "both", n)[[1]]
  ## convert the index to X/Y coordinates
  xy <- indices2xy(l, abatch=Dilution) 

  ## plot
  plotLocation(xy)
}