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 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 |
invisibly returns NULL; function is called for its side effect, this is producing the plot
Joern Toedling toedling@ebi.ac.uk
readNimblegen
,plot.default
,
points.default
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