arrayImage: Function to visualize spatial distribution of raw intensities

Description Usage Arguments Value Author(s) See Also Examples

Description

Function to visualize spatial distribution of raw intensities on NimbleGen Oligoarrays. Requires RGList with component genes complete with genes$X and genes$X coordinates of probes on array. arrayImage is a synonym of image.RGList.

Usage

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## S3 method for class 'RGList'
image(x,arrayno,channel=c("red","green","logratio"),
         mycols=NULL, mybreaks=NULL, dim1="X", dim2="Y",
         ppch=20, pcex=0.3, verbose=TRUE, ...)

Arguments

x

object of class RGList containing red and green channel raw intensities; possibly result of readNimblegen.

arrayno

integer; which array to plot; one of 1:ncol(x$R)

channel

character; which channel to plot, either red, green or the logratio log2(red)-log2(green)

mycols

vector of colors to use for image; if NULL defaults to colorRampPalette(c("White", "Yellow", "Red"))(10)

mybreaks

optional numeric vector of breaks to use as argument breaks in image.default; default NULL means take length(mycols)+1 quantiles of the data as breaks.

dim1

string; which column of the 'genes' element of the supplied RGList indicates the first dimension of the reporter position on the microarray surface; for example this column is called 'X' with some NimbleGen arrays and 'Row' with some Agilent arrays.

dim2

string; which column of the 'genes' element of the supplied RGList indicates the second dimension of the reporter position on the microarray surface; for example this column is called 'Y' with some NimbleGen arrays and 'Col' with some Agilent arrays.

ppch

which symbol to use for intensities; passed on as pch to points..default

pcex

enlargement factor for intensity symbols; passed on as cex to points.default

verbose

logical; extended output to STDOUT?

...

further arguments passed on to plot.default and points.default

Value

invisibly returns NULL; function is called for its side effect, this is producing the plot

Author(s)

Joern Toedling

See Also

readNimblegen,plot.default, points

Examples

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   exDir <- system.file("exData",package="Ringo")
   exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
   image(exRG, 1, channel="red", mycols=c("black","darkred","red"))
   ## this example looks strange because the example data files only
   ## includes the probe intensities of probes mapped to the forward
   ## strand of chromosome 9.
   ## you can see these probes are distributed all over the array


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