Function to parse a FACSDiva Workspace, generate a GatingHierarchy or GatingSet object, and associated flowCore gates.

diva_to_gatingset(
  obj,
  name = NULL,
  subset = NULL,
  path = obj@path,
  worksheet = c("normal", "global"),
  swap_cols = list(`FSC-H` = "FSC-W", `SSC-H` = "SSC-W"),
  verbose = FALSE,
  ...
)

Arguments

obj

diva_workspace

name

sample group to be parsed, either numeric index or the group name

subset

samples to be imported. either numeric index or the sample name. Default is NULL, which imports all samples.

path

the FCS data path

worksheet

select worksheet to import. either "normal" or "global"

swap_cols

diva seems to swap some data cols during importing fcs to experiments this argument provide a list to tell the parser which cols to be swapped default is list(`FSC-H` = 'FSC-W',`SSC-H` = 'SSC-W')

verbose

whether print more messages during the parsing

...

other arguments