cellHTS object.writeReport( raw, normalized=NULL, scored=NULL, cellHTSlist=NULL, outdir, force=FALSE, map=FALSE, plotPlateArgs=NULL, imageScreenArgs=NULL, posControls, negControls, mainScriptFile=NA, gseaModule=NULL, settings=list())cellHTS object. See
details.cellHTS
object. See details.cellHTS object. See
details.cellHTS objects. See
details. Note: this argument is deprecated. Please use the separate
arguments raw, normalized and scored instead. force. If
outdir is missing, it is set to file.path(getwd(),
name(cellHTSlist[['xraw']])), i.e. a directory with the name of the
cellHTS object(s) in the current working path.outdir exists and is not empty. If force is
TRUE, the function overwrites (removes and recreates)
outdir, otherwise it casts an error.settings to learn how to control the output of
writeReport. FALSE or TRUE. If FALSE or NULL,
the plate plots are omitted, this option is here because the
production of the plate plots takes a long time. See details. NOTE:
This argument is deprecated and will go away in the next
release. Please see settings to learn how to control
the output of writeReport.imageScreen. See details. NOTE: This argument is
deprecated and will go away in the next release. Please see
settings to learn how to control the output of
writeReport.writeReport. Please see settings for details.The function has to be called with the mandatory argument raw
corresponding to an unnormalized cellHTS object
(i.e. state(cellHTSlist[["raw"]])["normalized"]=FALSE). Additional
optional arguments are:
"normalized": a cellHTS object containing
normalized data
(i.e. state(cellHTSlist[["normalized"]])["normalized"]=TRUE and
state(cellHTSlist[["normalized"]])["scored"]=FALSE).
"scored": a cellHTS object containing data scored
data (i.e. state(cellHTSlist[["scored"]])["scored"]=TRUE). If
this component is available, then cellHTSlist[["normalized"]]
should also be given.
All of the above arguments have to be cellHTS objects containing
data from the same experiment, but in different preprocessing stages.
The cellHTS argument is deprecated and should no be used anymore.
The following elements are recognized for plotPlateArgs and
passed on to plotPlate: sdcol, the color
scheme for the standard deviation plate plot, sdrange, the sd
range to which the colors are mapped, xcol, the color scheme for
the intensity plate plot, xrange, the intensity range to which
the colors are mapped. If an element is not specified, default values
are used. Both sdrange and xrange can also be provided as
functions, which take the values to be plotted by platePlot as a
single argument and has to return a numeric vector of length 2. See its
documentation for details.
The following elements are recognized for imageScreenArgs and
passed on to imageScreen: ar, aspect
ratio, zrange, range, anno, gene annotation for the image
map (if map=TRUE).
From now on, all settings controlling the output of writeReport
should either be provided through the settings argument, or as
session-wide parameters set using setSettings. Please see
settings for details.
posControls and negControls should be given as a vector of
regular expression patterns specifying the name of the positive(s) and
negative(s) controls, respectivey, as provided in the plate
configuration file (and acccessed via wellAnno(objects)).
If the cellHTS object containing normalized data was provided as argument
norm, the length of posControls and
negControls should be equal to the number of channels in this
cellHTS object
(dim(Data(cellHTSlist[["normalized"]]))[3]). Otherwise, the
length of these vectors should be equal to the number of channels in the
unpreprocessed cellHTS object (i.e.,
dim(Data(cellHTSlist[["raw"]]))[3]).
By default, if posControls is not given, "pos" will be taken as
the name for the wells containing positive controls. Similarly, if
negControls is missing, by default "neg" will be considered as
the name used to annotate the negative controls. The content of
posControls and negControls will be passed to
regexpr for pattern matching within the well
annotation given in column controlStatus of the
featureData slot of the cellHTS object. If no controls are
available for a given channel, use "" or NA for that
channel. For example, posControls = c("", "(?i)^diap$") means
that channel 1 has no positive controls, while "diap" is the positive
control for channel 2.
The arguments posControls and negControls are particularly
useful in multi-channel data since the controls might be
reporter-specific, or after normalizing multi-channel data.
In the case of a two-way assay, where two types of "positive" controls
are used in the screen ("activators" and "inhibitors"),
posControls should be defined as a list with two components
(called act and inh), each of which should be vectors of
regular expressions of the same length as the current number of
reporters (as explained above).
By default, tooltips doing the mapping between the probe annotation and
the plate wells are not added to the plate plots and to the overall
screen plot. If any of the cellHTS objects in cellHTSlist
is annotated, the probe annotation uses the information contained
either in column GeneSymbol or column GeneID (if the
former is missing) of the featureData slot of the annotated
cellHTS object. Otherwise, the mapping simply uses the well
identifiers.
plotPlate,
imageScreen data(KcViabSmall)
pCtrls <- c("pos")
nCtrls <- c("neg")
## Not run:
# ## or for safety reasons (not a problem for the current well annotation, however)
# pCtrls <- c("^pos$")
# nCtrls <- c("^neg$")
# writeReport(raw=KcViabSmall, posControls=pCtrls, negControls=nCtrls)
# ## same as
# ## writeReport(raw=KcViabSmall)
# xn <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median")
# xsc <- scoreReplicates(xn, sign="-", method="zscore")
# xsc <- summarizeReplicates(xsc, summary="min")
# ## to turn on the tooltips in the plate plots and in the image screen plot:
# writeReport(raw=KcViabSmall, normalized=xn, scored=xsc, force=TRUE, map=TRUE, plotPlateArgs = TRUE, imageScreenArgs=list(zrange=c(-4,4)))
# ## End(Not run)
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