image.dev {xps} | R Documentation

## Image for Device

### Description

Creates an image for each sample for the selected device.

### Usage

    image.dev(x, bg = FALSE, transfo = log2, col = gray((0:64)/64), names = "namepart", xlab = "", ylab = "", mar = c(1, 1, 2, 1), dev = "screen", outfile = "Image", w = 540, h = 540, ...)

### Arguments

`x` | object of class `DataTreeSet`.
`bg` | logical. If `FALSE`, intensities from slot `data` will be used; if `TRUE`, background intensities from slot `bgrd` will be used.
`transfo` | a valid function to transform the data, usually “log2”, or “0”.
`col` | color range for intensities.
`names` | optional vector of sample names.
`xlab` | a title for the x axis.
`ylab` | a title for the y axis.
`mar` | plot margins.
`dev` | graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.
`outfile` | the name of the output file.
`w` | the width of the device in pixels.
`h` | the height of the device in pixels.
`...` | optional arguments to be passed to `image`.

### Details

Creates an image for each array for the selected graphics device.

For `bgrd=TRUE` the distribution of the computed background intensities will be shown; this can be useful to see potential density gradients caused by hybridization conditions. For the computation of background intensities see function `bgcorrect`; it is suggested to use `bgcorrect.mas4` to identify density gradients.

For `names=NULL` full column names of slot `data` will be displayed while for `names="namepart"` column names will be displayed without name extension. If `names` is a vector of column names, only these columns will displayed as image.

### Note

Data must first be attached to class `DataTreeSet` using method `attachInten`.

### Author(s)

Christian Stratowa

### See Also

`image-methods`, `image`

### Examples

    ## first, load ROOT scheme file and ROOT data file
    scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
    data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

    ## need to attach scheme mask and data
    data.test3 <- attachMask(data.test3)
    data.test3 <- attachInten(data.test3)

    if (interactive()) {
    image.dev(data.test3)
    }

    ## to avoid memory comsumption of R remove data:
    data.test3 <- removeInten(data.test3)
    data.test3 <- removeMask(data.test3)

[Package xps version 1.4.10 Index]