arrayImage: Function to visualize spatial distribution of raw intensities

In Ringo: R Investigation of ChIP-chip Oligoarrays

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

## 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

   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

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.