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 `flowSet`s in a single hyperlinked HTML document.

### Usage

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

### Arguments

`set` | A `flowSet` or a list of several `flowSet`s.
`processes` | A list of A `qaProcess` objects or, in the case of multiple `flowSet`s, a list of lists of `qaProcess` objects. See below for further details.
`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`.

### 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 `flowSet`s 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 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.

### 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)
    url <- writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
      grouping="Patient")
    browseURL(url)
    ## End(Not run)

[Package flowQ version 1.4.0 Index]