Gather up and organize all of the gates, transformations, and compensation matrices in a FlowJo workspace or list of FlowJo workspaces.
a list (or vector or single character string) of the path to FlowJo workspace(s) one wants to parse
an alternate location to the FCS files may be supplied. See details below
FlowJo is a commercial flow cytometry application from the company TreeStar, Inc. The 'save' format for FlowJo is the FlowJo workspace. A FlowJo workspace is an XML document that specifies all of the information necessary to recapitulate the exact user experience in the program at the time of the save. This files includes information on the location of all the relevant FCS files, their grouping, transformation, compensation, gating, and graphical displays last used by the researcher.
In some cases a FlowJo workspace and the associated FCS files need to be moved on the file system. If this is done the paths to the FCS files as embedded in the workspace will be stale (wrong). The altFileLocation argument allows the user to supply an alternate path to the FCS files.
The readFlowJoList method parses one or more FlowJo workspaces collecting all of the gate structures designed by the user. These gating structures are converted to flowCore style filter objects. Furthermore, because FlowJo users are often interested in not only the results of the final (i.e. terminal tip) gate, but also the results of many of the intermediate gates, readFlowJoList collects together all possible ordered subgates and chains them together as intersect-filter objects. Thus, if the user specifies the following gating scheme in FlowJo:
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Gate_A | ----> Gate_B | -----> Gate_C
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Gate_A Gate_A & Gate_B Gate_A & Gate_B & Gate_C Gate_C
readFlowJoList returns a flowJoList. A flowJoList is essentially a list of lists containing the gating structures, compensation matrices, and other information related to a set of FlowJo workspaces.
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