GetFlowJoLabels {FlowSOM} | R Documentation

## Process a flowjo workspace file

### Description

Reads a flowjo workspace file using the `flowWorkspace` library and returns a list with a matrix containing gating results and a vector with a label for each cell from a set of specified gates

### Usage

    GetFlowJoLabels(
      files,
      wspFile,
      group = "All Samples",
      cellTypes = NULL,
      getData = FALSE,
      ...
    )

### Arguments

`files` | The fcs files of interest
`wspFile` | The FlowJo wsp file to read
`group` | The FlowJo group to parse. Default "All Samples".
`cellTypes` | Cell types to use for final labeling the cells. Should correspond with a subset of the gate names in FlowJo.
`getData` | If true, flowframes are returned as well.
`...` | Extra arguments to pass to CytoML::flowjo_to_gatingset

### Value

This function returns a list, which for every file contains a list in which the first element ("matrix") is a matrix containing filtering results for each specified gate and the second element ("manual") is a vector which assigns one label to each cell. If only one file is given, only one list is returned instead of a list of lists.

### See Also

`PlotPies`

### Examples

    # Identify the files
    fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM")
    wspFile <- system.file("extdata", "gating.wsp", package = "FlowSOM")

    # Specify the cell types of interest for assigning one label per cell
    cellTypes <- c("B cells",
                    "gd T cells", "CD4 T cells", "CD8 T cells",
                    "NK cells", "NK T cells")

    # Parse the FlowJo workspace
    gatingResult <- GetFlowJoLabels(fcs_file, wspFile,
                                    cellTypes = cellTypes,
                                    getData = TRUE)

    # Check the number of cells assigned to each gate
    colSums(gatingResult$matrix)

    # Build a FlowSOM tree
    flowSOM.res <- FlowSOM(gatingResult$flowFrame,
                           colsToUse = c(9, 12, 14:18),
                           nClus = 10,
                           seed = 1)

     # Plot pies indicating the percentage of cell types present in the nodes
     PlotPies(flowSOM.res,
              gatingResult$manual,
              backgroundValues = flowSOM.res$metaclustering)

[Package FlowSOM version 2.2.0 Index]