plotLocation {affy} | R Documentation

## 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

      ## loading data
      data(affybatch.example)

      ## image of the celfile
      image(affybatch.example[1])

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

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

      ## plot
      plotLocation(xy)

[Package affy version 1.5.8-1 Index]