getFlowJoSummary: Summarize FlowJo Workspaces

In flowFlowJo: Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.

Description

Makes a table of the number and count of various gates, possibly broken out by FCS file in one or more FlowJo workspaces.

Usage

getFlowJoSummary(x, gatesByFile=TRUE, fileNamePatterns=".", ...)

Arguments

x	a flowJoList or flowJoObj
gatesByFile	a boolean. If TRUE (default) then the count of each gate type will be broken out for each referenced FCS file. Otherwise this method will just return a table with the total counts of each named gate listed in the FlowJo workspace(s).
fileNamePatterns	A list of patterns for picking out specific FCS files. Default = "." (ie. examines all of the FCS files)
...	Additional arguments: to simplifyGateNames such as stripFileName and removeParentalNames

Value

The method getFlowJoSummary returns a table summarizing the number of gates listed in the referenced FlowJo workspaces. This function is useful for ensuring that the cytometrist has used a consistent set of names in their process.

Author(s)

John Gosink

References

See also FlowJo from Treestar Inc, at: http://www.flowjo.com/

Examples

demoLocation <- system.file("extdata", "DemoWorkspace.wsp", package="flowFlowJo"); 
actualFCSLoc <- system.file("extdata/fcsFiles", package="flowFlowJo"); 
testList     <- readFlowJoList(demoLocation, altFileLocation=actualFCSLoc);

getFlowJoSummary(testList, gatesByFile=FALSE, removeParentalNames=TRUE);

flowFlowJo documentation built on Sept. 12, 2016, 6:14 a.m.