writeQAReport: Create HTML report for (lists of) qaProcess objects

Description

This function combines all graphical output of multiple QA processes for one or several flowSets in a single hyperlinked HTML document.

Usage

writeQAReport(set, processes=NULL, globalProcess=NULL,  outdir = "./qaReport", grouping = NULL,pagebreaks=TRUE, pdf=TRUE)

Arguments

set

A flowSet or a list of several flowSets.

processes

A list of qaProcess objects or, in the case of multiple flowSets, a list of lists of qaProcess objects. See below for further details.

globalProcess

A list of qaProcess objects generated by multipanel comparison qaProcess functions, when set is a list of flowSets .

outdir

The directory to which the HTML report is to be saved. Each qaProcess object should have been created in the same directory.

grouping

A character scalar indicating a variable in the flowSet's phenoData that is used as a grouping factor in the output.

pagebreaks

A logical indicating whether the output should be on one long page, or split over several pages.

pdf

A logical indicating whether vectorized versions of the images should be included. Setting this to TRUE implies that the individual QA processes have also been created with setting pdf=TRUE.

Value

The function is mostly called for it's side effects, that is, the generation of a HTML quality report in outdir. A URL to an entry point for browsing of the report is returned.

Details

Both the information about graphical output generated as part of a QA process as well as the qunatitative or qualitative results are stored in objects of class qaProcess. The creation of such objects is abstracted in dedicated constructor function and the user should call these functions directly rather than creating qaProcess manually. writeQAReport takes lists of such objects and combines their information in a unified HTML document. A grouping factor can be specified to indicate subgroups of the data. In the case of multiple panels, a list of flowSets can be given to writeQAReport, and the function expects a list of lists of processes, where each process list is specific to one panel.

An entry point to the output of this function can be found at outdir/index.html.

Examples

Run this code

## Not run: 
# data(GvHD)
# GvHD <- transform(GvHD, "FL1-H"=asinh(`FL1-H`), "FL2-H"=asinh(`FL2-H`))
# dest <- tempdir()
# qp1 <- qaProcess.timeline(GvHD, channel="FL1-H", outdir=dest, cutoff=1)
# qp2 <- qaProcess.marginevents(GvHD, channels=c("FL1-H", "FL2-H"),
#   outdir=dest, cFactor=4)
# url <- writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
#   grouping="Patient")
# browseURL(url)
# ## End(Not run)

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