xps (version 1.32.0)

plotImage: Plot Image(s) for Device

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).

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)