| image.RGList {Ringo} | R Documentation |
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.
## S3 method for class 'RGList':
image(x,arrayno,channel=c("red","green","logratio"),
mycols=NULL, mybreaks=NULL,...)
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. |
... |
further arguments passed on to image.default |
invisibly returns matrix of raw intensities, in which rows and columns
correspond to X and Y coordinates on arrays. Can be directly plotted
with function image.default.
Joern Toedling toedling@ebi.ac.uk
exDir <- system.file("exData",package="Ringo")
exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
image(exRG,arrayno=1,channel="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