getFlowJoSummary {flowFlowJo} | R Documentation |
Makes a table of the number and count of various gates, possibly broken out by FCS file in one or more FlowJo workspaces.
getFlowJoSummary(x, gatesByFile=TRUE, fileNamePatterns=".", ...)
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 |
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.
John Gosink
See also FlowJo from Treestar Inc, at: http://www.flowjo.com/
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);