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 1.2.10 Index]