image.dev {xps} | R Documentation |
Creates an image for each sample for the selected device.
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, ...)
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 . |
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.
Data must first be attached to class DataTreeSet
using method attachInten
.
Christian Stratowa
## 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)