plotImage: Plot Image(s) for Device

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Creates an image for each sample for the selected device.

Usage

plotImage(x,
          type     = character(),
          qualopt  = c("raw", "adjusted", "normalized"),
          transfo  = log2,
          col      = NULL,
          names    = character(),
          dev      = "screen",
          outfile  = "Image",
          w        = 800,
          h        = 800,
          verbose  = TRUE,
          ...) 

Arguments

x	object of class DataTreeSet or QualTreeSet.
type	character string specifying the type of image.
qualopt	character string specifying whether to draw residual image for “raw”, “adjusted”, or “normalized” intensities.
transfo	a valid function to transform the data, usually “log2”, or “0”.
col	color range for intensities.
names	vector of sample names.
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.
verbose	logical, if TRUE print status information.
...	optional arguments to be passed to image.

Details

Creates intensity image(s) or residual image(s), respectively, for each array for the selected graphics device, see image for more details.

For intensity image(s) type must be one of “intensity”.

For residual image(s) type must be one of “resids”,“pos.resids”, “neg.resids”, “sign.resids”, or “weights”. Furthermore, qualopt determines if images should be drawn for “raw”, “adjusted”, or “normalized” data.

For names="*" names of all samples will be displayed as images. If names is a vector of column names, only these samples will displayed as image(s).

Author(s)

Christian Stratowa

See Also

image-methods, image

Examples

## Not run: 
## 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="/"))

## qualification - rlm
rlm.all <- rmaPLM(data.test3, "tmp_Test3RLMall", filedir=getwd(), tmpdir="", qualopt="all", option="transcript", add.data=FALSE)

if (interactive()) {
## image(s) of raw data
plotImage(data.test3, type="intensity", names="*")
plotImage(data.test3, type="intensity", names="TestA2.cel")

## image(s) of residuals/weights
plotImage(rlm.all, type="weights", names="*")
plotImage(rlm.all, type="weights", qualopt="adjusted", names="*")
plotImage(rlm.all, type="resids", names="TestA2_raw.res")
}

## function image.dev() will be deprecated since it needs attachInten!!
## 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)

## End(Not run)

xps documentation built on Nov. 8, 2020, 6 p.m.