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# Read FlowJo Workspace

Source: `R/data_load_and_transform.R`
`prep_fjw.Rd`

Loading and transforming the data to create a flow cytometry dataset from a Gate Set object for the analysis with the cyCONDOR workflow.

`prep_fjw` takes a gate set object as input and returns a `fcd` with the FlowJo gating information saved in `fcd$anno$cell_anno`.

## Usage

    prep_fjw(
      data_gs,
      inverse.transform = FALSE,
      transformation = NULL,
      remove_param = NULL,
      merge_anno = FALSE,
      anno_table = NULL,
      separator_anno = ",",
      filename_col = NULL
    )

## Arguments

data_gs

  Gate Set object, e.g. created by using `open_flowjo_xml` and `flowjo_to_gatingset` from the CytoML package.

inverse.transform

  Logical: if the data should be reverse transformed or kept with FlowJo transformation (default = FALSE).

transformation

  If `inverse.transform = TRUE`, type of new transformation to perform. Select one of the following: `"auto_log"` (autologicle, recommended for flow cytometry data), `"arcsinh"` (arcsinh transformation), `"clr"` (centered-log-ratio) or `"none"` (no transformation).

remove_param

  Parameters to be removed from the `fcd`.

merge_anno

  Logical: If sample anno should be merged to the `fcd`.

anno_table

  If `merge_anno = TRUE`, path to the annotation table text file. The annotation table should contain one column with the file names of all .fcs or .csv files to read in and optionally additional columns with further sample information (e.g. "sample_id", "condition").

separator_anno

  Separator used in the annotation file, by default `separator_anno = ","`.

filename_col

  Name of the column of the `anno_table` containing the file name matching with the .fcs files.

## Value

An object of class 'flow cytometry dataframe' (`fcd`) is returned.

read_flowjo_workspace

## Details

Read FlowJo workspace