writeReport: Create a directory with HTML pages of linked tables and plots...
In cellHTS: Analysis of cell-based screens

Description Usage Arguments Details Value Author(s) See Also Examples

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

writeReport(x,
  outdir=file.path(getwd(), x$name),
  force=FALSE,
  plotPlateArgs=FALSE,
  imageScreenArgs=NULL,
  progressReport = interactive(),
  posControls,
  negControls)

`x`	a `cellHTS` object.
`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`.
`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.
`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.

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, map, logical value indicating whether tooltips with the annotation should be added to the plot (default value is FALSE), anno, gene annotation for the image map.

posControls and negControls should be given as a vector of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectively, as provided in the plate configuration file (and stored in x$wellAnno). The length of these vectors should be equal to the number of reporters used in the screen (dim(x$xraw)[4] or to dim(x$xnorm)[4], in case x contains multi-channel data that have been normalized by combining the values from two or more channels). By default, if posControls is not given, "pos" will be taken as the name for the wells containing positive controls. Similarly, if negControls is missing, by default "neg" will be considered as the name used to annotate the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in x$wellAnno (see examples). 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 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 the cellHTS object x is annotated, the probe annotation is based on the information contained whether in x$geneAnno$GeneSymbol, or x$geneAnno$GeneID, if the former is missing. 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 Braz ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

plotPlate, imageScreen

    data(KcViabSmall)
    ## pCtrls <- c("pos") 
    ## nCtrls <- c("neg") 
    ## or for safety reasons (not a problem for the current well
    ## annotation, however)  
    ## pCtrls <- c("^pos$") 
    ## nCtrls <- c("^neg$")
    ## writeReport(KcViabSmall, posControls=pCtrls, negControls=nCtrls)
    ## same as 
    ## writeReport(KcViabSmall)
    ## Not run: 
    x <- normalizePlates(KcViabSmall, normalizationMethod="median",zscore="-")
    x <- summarizeReplicates(x, summary="min")
    writeReport(x, force=TRUE, plotPlateArgs = list(), imageScreenArgs=list(zrange=c(-4,4)))
    
## End(Not run)
    ## to turn on the tooltips in the overall screen image plot:
    ## writeReport(x, force=TRUE, plotPlateArgs = list(), imageScreenArgs = list(zrange=c(-4,4), map=TRUE))