Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS experiment

Description

Creates a directory with HTML pages of linked tables and plots documenting the contents of the preprocessing of a cellHTS object.

Usage

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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())

Arguments

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. 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.

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 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.

imageScreenArgs

a list with parameters for the function 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.

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.

gseaModule

Add the output of a gene set enrichment analysis to the report. This is totally experimental at this time.

settings

A named list of settings controlling the output of writeReport. Please see settings for details.

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.

Value

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.

Author(s)

Florian Hahne florian.hahne@novartis.com, Ligia P. Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk, Gabor Bakos

References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

See Also

plotPlate, imageScreen

Examples

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    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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