Counts of analysis units and cells, overall and per arm. The reported counts of an assay are themselves an analysis output: once they are generated from the object that was analyzed, a count in the write-up cannot drift away from the data it describes.
Arguments
- experiment
A
cr_experiment.- by
Character vector of grouping columns from
designorcells. Defaults to"treatment"when that column exists, and to no grouping otherwise.- unit
Optional name of the column that identifies the analysis unit. May be a column of
cellsor ofdesign. IfNULL(default) the experiment'sunit_varslot is used when present, and the spatial unit otherwise.- total
Whether to append a row holding the overall counts. The grouping columns of that row carry the label
"(total)".
Value
A tibble with the grouping columns (as character), n_units,
n_cells and median_cells_per_unit.
See also
Other quantification:
cr_compute_metrics(),
cr_fold_change(),
cr_summarize_wells()
Examples
exp <- cr_example_experiment(seed = 1, n_cells_per_well = 20)
cr_table_disposition(exp)
#> # A tibble: 7 × 4
#> treatment n_units n_cells median_cells_per_unit
#> <chr> <int> <int> <dbl>
#> 1 CompoundA_high 16 324 20.5
#> 2 CompoundA_low 16 341 21
#> 3 CompoundB 16 350 23
#> 4 CompoundC 16 335 20
#> 5 PosControl 16 303 19
#> 6 Untreated 16 308 19
#> 7 (total) 96 1961 20
cr_table_disposition(exp, by = "group")
#> # A tibble: 5 × 4
#> group n_units n_cells median_cells_per_unit
#> <chr> <int> <int> <dbl>
#> 1 combination 32 685 21.5
#> 2 control 16 308 19
#> 3 positive 16 303 19
#> 4 treated 32 665 20.5
#> 5 (total) 96 1961 20