qaProcess.DensityPlot: Creates a QA process for comparisons of density plots across...
In flowQ: Quality control for flow cytometry

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

This function takes a list of flowSet as input and creates all necessary outputs for a 'DensityPlot' type QA process. Objects created by this function can be laid out as HTML using writeQAReport.

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  qaProcess.DensityPlot(flowList,dyes=NULL,outdir="QAReport",
		       alpha=0.05,absolute.value=NULL,sum.dimensions=NULL,
			   det.dimensions=NULL, pdf=TRUE,name="Density",...)

`flowList`	A list of `flowSet`
`dyes`	Flow parameters to be compared across multiple samples. If set to NULL, all parameters that are duplicated across the list of `flowSet` are identified and compared.
`outdir`	The directory to which the graphical output is to be saved. If multiple QA processes are to be combined, make sure to use the same directory every time.
`alpha`	Outlier mislabeling rate
`absolute.value`	If provided, the absolute.value is used for the outlier detection and the alpha argument is ignored. defualt is NULL
`sum.dimensions`	The dimensions of summary plot generated in inches, default is NULL where the dimensions are automatically selected
`det.dimensions`	the dimensions of each sub image generated by the QA process in inches, default is NULL where the dimensions are automatically selected.
`pdf`	boolen value determinining if pdf files or jpeg images will be produced by the QA process
`name`	The name of the process used for the headings in the HTML output.
`...`	Further arguments.

QA processes of type 'DensityPlot' detects differences in the density plots across multiple samples. A summary measure based on the sum of the pairwise KL Distances of density plots is used as a parameter to flag patient panels that are potential outliers.

For more details on how to layout qaProcess objects to HTML, see writeQAReport and qaReport.

An object of class qaProcess.

Nishant Gopalakrishnan

writeQAReport, qaReport, qaProcess, qaProcess.marginevents, qaProcess.ECDFPlot, qaProcess.2DStatsPlot

data(qData)
dest <- tempdir()
resDensityFSC <- qaProcess.DensityPlot(qData, dyes=c("FSC-A","SSC-A"),
                    outdir=dest, alpha=0.2, pdf=TRUE)