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

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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/plotLocation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotLocation
> ### Title: Plot a location on a cel image
> ### Aliases: plotLocation
> ### Keywords: aplot
> 
> ### ** 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)
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>