\HeaderA{getFlowJoSummary}{Summarize FlowJo Workspaces}{getFlowJoSummary}
\begin{Description}\relax
Makes a table of the number and count of various gates, possibly broken out by FCS file in one or more FlowJo workspaces.
\end{Description}
\begin{Usage}
\begin{verbatim}
getFlowJoSummary(x, gatesByFile=TRUE, fileNamePatterns=".", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a flowJoList or flowJoObj 
\item[\code{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). 
\item[\code{fileNamePatterns}] A list of patterns for picking out specific FCS files.  Default = "."  (ie. examines all of the FCS files) 
\item[\code{...}] Additional arguments: to simplifyGateNames such as stripFileName and removeParentalNames 
\end{ldescription}
\end{Arguments}
\begin{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.
\end{Value}
\begin{Author}\relax
John Gosink
\end{Author}
\begin{References}\relax
See also FlowJo from Treestar Inc, at:  \url{http://www.flowjo.com/}
\end{References}
\begin{Examples}
\begin{ExampleCode}

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);

\end{ExampleCode}
\end{Examples}

