image.RGList {Ringo} | R Documentation

## Function to visualize spatial distribution of raw intensities

### 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

[Package Ringo version 1.58.0 Index]