writeReport {cellHTS2} | R Documentation |
Creates a directory with HTML pages of linked tables and plots
documenting the contents of the preprocessing of a cellHTS
object.
writeReport( raw, normalized=NULL, scored=NULL, cellHTSlist=NULL, outdir, force=FALSE, map=FALSE, plotPlateArgs=FALSE, imageScreenArgs=NULL, posControls, negControls, mainScriptFile=NA)
raw |
the intitial raw cellHTS object. See
details. |
normalized |
a normalized cellHTS
object. See details. |
scored |
a scored cellHTS object. See
details. |
cellHTSlist |
a list of cellHTS objects. See
details. Note: this argument is deprecated. Please use the separate
arguments raw , normalized and scored instead. |
outdir |
a character of length 1 with the name of a directory
where to write the report HTML file and images. If the directory
does not exist, it is created. If it exists and is not empty, then
the behaviour depends on the value of 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. |
force |
a logical value, determines the behaviour of the function
if outdir exists and is not empty. If force is
TRUE , the function overwrites (removes and recreates)
outdir , otherwise it casts an error. |
map |
a logical value indicating whether tooltips with the annotation should be added to the plate plots and image screen. Default value is FALSE. |
plotPlateArgs |
either a list with parameters for the plate plots
of the per plate quality report pages, or a logical scalar with
values FALSE or TRUE . If FALSE , the plate
plots are omitted, this option is here because the production of the
plate plots takes a long time. See details. |
imageScreenArgs |
a list with parameters for the function
imageScreen . See details. |
posControls |
a list or vector of regular expressions specifying the name of the positive controls. See details. |
negControls |
a vector of regular expressions specifying the name of the negative controls. See details. |
mainScriptFile |
The path to the R script generating the current report. We strongly advice to store this script in the compendium for future reference. |
The function has to be called with the mandatory rgument 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.
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
).
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 in
cellHTSlist
, 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$")
means
that channel 1 has no positive controls, while "diap" is the positive
control for channel 2.
The arguments posControls
and negControls
are particularly
useful in multi-channel data since the controls might be
reporter-specific, or after normalizing multi-channel data.
In the case of a two-way assay, where two types of "positive" controls
are used in the screen ("activators" and "inhibitors"),
posControls
should be defined as a list with two components
(called act
and inh
), each of which should be vectors of
regular expressions of the same length as the current number of
reporters (as explained above).
By default, tooltips doing the mapping between the probe annotation and
the plate wells are not added to the plate plots and to the overall
screen plot. If any of the cellHTS
objects in cellHTSlist
is annotated, the probe annotation uses the information contained
whether in column GeneSymbol
or column GeneID
(if the
former is missing) of the featureData
slot of the annotated
cellHTS
object. Otherwise, the mapping simply uses the well
identifiers.
The function is called for its side-effect. It returns a character with the full path and name of the report index file, this is an HTML file which can be read by a web browser.
Florian Hahne fhahne@fhcrc.org, Ligia P. Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
data(KcViabSmall) pCtrls <- c("pos") nCtrls <- c("neg") ## Not run: ## or for safety reasons (not a problem for the current well annotation, however) pCtrls <- c("^pos$") 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)