wsp_get_indices.RdEvery row in a fcs file represents an event. Every column is a parameter (channel). Gates select a subset (rows) of events by applying limits to usually one or two channels. A sub-population of gated events hence may be defined by a vector of (row-) indices (TRUE - events is included in gate; FALSE - event is not included). A whole gating tree may be represented by a matrix with n columns for n gates and m rows for m events. The output of this function may be saved to disk and applied to fcs files with fcexpr::inds_get_ff in order to obtain subsetted flowfframes representing gated populations in flowjo.
wsp_get_indices(
wsp,
FCS.file.folder = NULL,
groups = NULL,
invert_groups = F,
samples = NULL,
invert_samples = F,
lapply_fun = lapply,
...
)vector of paths to flowjo workspaces
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 (NULL) fcs file paths are derived individually from wsps (xml)
vector or list of groups in flowjo to consider; if a list, each index corresponds to the index in wsp; if NULL samples from all groups are read
logical whether to invert group selection
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
logical whether to invert sample selection
lapply function name, unquoted; lapply, pbapply::pblapply or parallel::mclapply are suggested
additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen
list of matrices, one for each selected sample; each column of the matrices holds the indices for the respective population
Geometric gate definitions from flowjo are applied with CytoML::flowjo_to_gatingset and indices matrices are obtained with flowWorkspace::gh_pop_get_indices_mat. This process may take a while depend upon size of fcs files as a .h5 file is written to disk for every fcs file before indices can be derived. Hence, it is recommended to save the indices-matrices to disk in case of large FCS files.
if (FALSE) {
ind_mat <- fcexpr::wsp_get_indices("mypath/my.wsp")
}