wsp_get_ff: Get (subsetted) flowFrames from one or many flowjo workspaces

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

Get (subsetted) flowFrames from one or many flowjo workspaces

Description

From a flowjo workspace with gated populations and the respective fcs files flowframes are generated. Under the hood CytoML::flowjo_to_gatingset applies the geometric gate definitions and filters relevant rows (indices) of fcs files. The compensation matrix as defined in flowjo will be used to compensate fluorescence intensities.

Usage

wsp_get_ff(
  wsp,
  FCS.file.folder = NULL,
  groups = NULL,
  population,
  invert_groups = F,
  samples = NULL,
  invert_samples = F,
  return_untransformed = T,
  return_transformed = T,
  downsample = 1,
  remove_redundant_channels = F,
  lapply_fun = lapply,
  seed = 42,
  channels = NULL,
  leverage_score_for_sampling = F,
  ...
)

Arguments

wsp	vector of paths to flowjo workspaces
FCS.file.folder	path to folder(s) of FCS files; may be one path for all wsp or a vector of paths, one for each wsp; if not provided fcs file paths are derived individually from the wsp (xml). If the workspace was generated and saved on another computer you will have to provide the path to FCS files on the current computer.
groups	vector or list of groups in flowjo to consider; if a list, each index corresponds to the same index in wsp; if NULL samples from all groups are read
population	which population (=node, =gate) to subset flowFrames on; use fcexpr::wsx_get_poppaths to get paths
invert_groups	logical whether to invert group selection
samples	vector or list of samples to select (names of FCS files), each index corresponds to the index in wsp; if NULL all samples (from selected groups) are read
invert_samples	logical whether to invert sample selection
return_untransformed	logical; do return untransformed (inverse) data
return_transformed	logical; do return transformed data (transformation as in flowjo?!)
downsample	numeric, if < 0 then a fraction of events is sampled, if > 0 an absolute number of events is sampled; or set to "min" which will lead to downsampling each flowframe to the number of events in the flowframe with lowest number of events; can be a single value to treat all FCS files equally or can be a vector of same length as FCS files
remove_redundant_channels	remove channels that are not part of the gating tree, mainly to reduce memory load
lapply_fun	lapply function name, unquoted; lapply, pbapply::pblapply or parallel::mclapply are suggested
seed	set a seed to reproduce downsampling
channels	channels to use for leverage score calculation; use wsx_get_keywords to retrieve channel names/descriptions
leverage_score_for_sampling	logical whether to use leverage scores for downsampling
...	additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen

Details

If it is intended to pass flowframes to fcexpr::dr_to_fcs, it is recommended to have transformed and untransformed expression values returned.

Value

a list of (subsetted) flowframes with events that are within the gated population only

Examples

## Not run: 
ff_list <- fcexpr::wsp_get_ff(wsp = "mypath/my.wsp", population = "CD8+")
# ff.list[[1]] may be passed to fcexpr::dr_to_fcs for instance

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.