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(cellHTSlist, outdir, force=FALSE, map=FALSE, plotPlateArgs=FALSE, imageScreenArgs=NULL, progressReport = interactive(), posControls, negControls)
cellHTSlist |
a list of cellHTS objects. See details. |
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. |
progressReport |
a logical, should a progress report window be displayed? |
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. |
Argument cellHTSlist
should be a list containing at least one component named "raw" which corresponds
to a unnormalized cellHTS
object (i.e. state(cellHTSlist[["raw"]])["normalized"]=FALSE
). Other possible components of cellHTSlist
can be:
"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 components of cellHTSlist
should be cellHTS
objects containing data from the same experiment, but in different preprocessing stages.
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$")
means that channel 1 has no
positive controls, while "diap" is the positive control for channel 2.
The arguments posControls
and negControls
are particularly useful in multi-channel data since the controls might be reporter-specific, or after normalizing multi-channel data.
In the case of a two-way assay, where two types of "positive" controls are used in the screen ("activators" and "inhibitors"), posControls
should be defined as a list with two components (called act
and inh
), each of which should be vectors of regular expressions of the same length as the current number of reporters (as explained above).
By default, tooltips doing the mapping between the probe annotation and the plate wells are not added to the plate plots and to the overall screen plot. If any of the cellHTS
objects in cellHTSlist
is annotated, the probe annotation uses the information contained whether in column GeneSymbol
or column GeneID
(if the former is missing) of the featureData
slot of the annotated cellHTS
object. Otherwise, the mapping simply uses the well identifiers.
The function is called for its side-effect. It returns a character with the full path and name of the report index file, this is an HTML file which can be read by a web browser.
Ligia P. Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
data(KcViabSmall) pCtrls <- c("pos") nCtrls <- c("neg") ## Not run: ## or for safety reasons (not a problem for the current well annotation, however) pCtrls <- c("^pos$") nCtrls <- c("^neg$") writeReport(list("raw"=KcViabSmall), posControls=pCtrls, negControls=nCtrls) ## same as ## writeReport(list("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(cellHTSlist=list("raw"=KcViabSmall, "normalized"=xn, "scored"=xsc), force=TRUE, map=TRUE, plotPlateArgs = TRUE, imageScreenArgs=list(zrange=c(-4,4))) ## End(Not run)