qaProcess.BoundaryPlot: Creates a QA process for comparison of the percentage of...

In flowQ: Quality control for flow cytometry

Description

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

Usage

 
 qaProcess.BoundaryPlot(flowList,dyes=NULL,
			  outdir="QAReport",cutoff=3,sum.dimensions=NULL,
			  det.dimensions=NULL,pdf=TRUE,name="Boundary",
			  side="both",...)

Arguments

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.
cutoff	A numeric value for the percentage of boundary events that is used by the process to identify samples that failed the QA process
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.
side	Object of class "character". The margin on which to evaluate the filter. Either upper for the upper margin or lower for the lower margin or both for both margins.
...	Further arguments.

Details

QA processes of type 'BoundaryPlot' helps identify samples that have a large number of boundary events that must be removed by further gating before detailed analysis of the data.

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

Value

An object of class qaProcess.

Author(s)

Nishant Gopalakrishnan

See Also

writeQAReport, qaReport, qaProcess, qaProcess.DensityPlot, qaProcess.ECDFPlot

Examples

data(qData)
dest <- tempdir()
resBoundary <- qaProcess.BoundaryPlot(qData, dyes=c("FSC-A","CD3"), 
                                      outdir=dest, cutoff=3, pdf=TRUE)
resBoundary

flowQ documentation built on Nov. 1, 2018, 3:38 a.m.