plotLocation: Plot a location on a cel image

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

Plot a location on a cel image

Description

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

Usage

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

Arguments

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.

Author(s)

Laurent

See Also

AffyBatch

Examples

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)
}

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.