createFlowReport         package:flowFlowJo         R Documentation

_P_r_o_d_u_c_e _a _d_e_n_o_r_m_a_l_i_z_e_d _d_a_t_a _f_r_a_m_e _o_f _s_u_m_m_a_r_y _s_t_a_t_i_s_t_i_c_s _a_n_d _o_t_h_e_r _i_n_f_o_r_m_a_t_i_o_n _o_n _a _s_e_t _o_f _F_l_o_w_J_o _g_a_t_e_d _F_C_S _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This method produces a data frame that has one row per cell
     population per FCS file per channel for one or more FCS files as
     gated using the commercial software, FlowJo.

_U_s_a_g_e:

     createFlowReport(summaryList, ...)

_A_r_g_u_m_e_n_t_s:

summaryList: a flowFlowJo object that is a list of data structures
          providing many bits of summary information about each gated
          population in a gated FCS file.  See also
          _collectSummaryFlowInfo_ 

     ...: Additional factors detailed below.

_D_e_t_a_i_l_s:

     Additional arguments also include the following:  


         factorsFrame    - an additional data frame with various types
     of meta data related to the experiment in question 
         populations     - a list of cell population names to be
     reported on.  By default, the summary statistics on all the cell
     populations will be reported. 
         channels        - a list of scatter and non-scatter
     (fluorescent) channels to be reported on.  By default, the summary
     statistics for all channels will be reported. 
         includeKeywords - a boolean with the default = TRUE.  If
     FALSE, then none of the keywords from the headers of the FCS files
     that were harvested in an earlier step will be reported. 
         joinFactors     - if the user supplies an optional data frame
     with additional meta data about the experiment, these columns in
     the data frame will be used to match up items in the data frame
     with the correct FCS files. The default is
     joinFactors=c("FCSFilename", "FlowJoWorkspace")
         dropJoinFactors - a boolean with default = TRUE.  If set to
     FALSE, then the name (and path) of the FCS file and the FlowJo
     workspace will be included in every  line of the report.  That
     would make the report very ugly to read.   


_V_a_l_u_e:

     The _collectSummaryFlowInfo_ method produces a large and
     complicated data structure that tracks every FCS file location,
     gate structure, compensation matrix, as well as the summary
     statistics for every file referenced in a FlowJo workspace.  This
     method, _createFlowReport_ distills out a simple data frame of the
     summary statistics that is convenient and easy to read, plot, and
     otherwise analyze.

_A_u_t_h_o_r(_s):

     John Gosink

_E_x_a_m_p_l_e_s:

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

     # This next statement may take a few moments to run as it is parsing through a FlowJo workspace
     # and two dozen FCS files...
     summaryStatsObj <- collectSummaryFlowInfo(testList);

     # And here are some of the summary statistics for this workspace
     flowReport      <- createFlowReport(summaryStatsObj);
     head(flowReport);

