writeQAReport {flowQ}R Documentation

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, outdir = "./qaReport", grouping = NULL,
pagebreaks = TRUE)

Arguments

set A flowSet or a list of several flowSets
processes A list of A qaProcess objects or, in the case of multiple flowSets, a list of lists of qaProcess objects.
outdir The directory to which the HTML report is to be saved. Make sure that each qaProcess object was 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 on several pages.

Details

Both the information about graphical output and the results for a QA process are stored in objects of class qaProcess. The creation of such objects is abstracted in dedicated functions 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.

Value

The function is called for it's side effects

Author(s)

Florian Hahne

See Also

qaProcess.marginevents, qaReport, qaProcess, qaProcess.timeline

Examples

## 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)
writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
  grouping="Patient")
browseURL(file.path(dest, "index.html"))
## End(Not run)

[Package flowQ version 1.2.0 Index]