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_xmlandflowjo_to_gatingsetfrom 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_tablecontaining the file name matching with the .fcs files.