Write UMAP-annotated FCS files for FlowJo
Usage
export_flowjo_fcs(
cells,
outdir,
concat = TRUE,
groups = TRUE,
group_col = "cohort",
log = message
)Arguments
- cells
data.frame/data.table of per-cell rows, or a path to cells_umap.csv. Requires sample_id, umap_1, umap_2, population_label.
- outdir
directory to create and write into.
- concat
also write the concatenated _ALL_SAMPLES.fcs.
- groups
also write one concatenated GROUP
.fcs per study group. - group_col
column holding the study group. Defaults to
cohort, the name the pipeline gives the grouping variable in cells_umap.csv; absent that column the group files are skipped with a note rather than failing, since an ungrouped run is legitimate.- log
message sink; the main pipeline passes its own log_msg so the export's progress lands in the same run log as everything else.