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, dim1="X", dim2="Y", ppch=20, pcex=0.3, verbose=TRUE, ...)
x |
object of class |
arrayno |
integer; which array to plot; one of |
channel |
character; which channel to plot, either |
mycols |
vector of colors to use for image; if |
mybreaks |
optional numeric vector of breaks to use as argument
|
dim1 |
string; which column of the 'genes' element of the
supplied |
dim2 |
string; which column of the 'genes' element of the
supplied |
ppch |
which symbol to use for intensities; passed on as
|
pcex |
enlargement factor for intensity symbols; passed on as
|
verbose |
logical; extended output to STDOUT? |
... |
further arguments passed on to |
invisibly returns NULL; function is called for its side effect, this is producing the plot
Joern Toedling
readNimblegen
,plot.default
,
points
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