Summarize cell-level data to the analysis unit

Aggregates the per-cell values of one channel to a single number per analysis unit. By default the analysis unit is the spatial unit of the experiment (well or slide), which is the unit of replication for most plate-based assays. Pass unit to aggregate to a merged analysis unit instead — for example when one physical unit was acquired as several files and the acquisitions were assigned a common identifier.

Usage

cr_summarize_wells(experiment, channel, fun = stats::median, unit = NULL)

Arguments

experiment

A cr_experiment.

channel

Channel name (a column of experiment$cells).

fun

Aggregation function. Default stats::median. The function is called with na.rm = TRUE when it accepts that argument (directly or through ...), and with the values only otherwise. It must return a single number.

unit

Optional name of the column that identifies the analysis unit. May be a column of cells or of design. If NULL (default) the experiment's unit_var slot is used when present, and the spatial unit otherwise.

Value

A tibble with one row per analysis unit containing the unit identifier, n_cells, the aggregated value, and the design columns. Design columns that are not constant within a unit are returned as NA.

See also

cr_compute_metrics() for a richer per-unit summary and cr_table_disposition() for unit and cell counts per arm.

Other quantification: cr_compute_metrics(), cr_fold_change(), cr_table_disposition()

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 30)
cr_summarize_wells(exp, channel = "marker_1")
#> # A tibble: 96 × 11
#>    well  n_cells value treatment   dose dose_unit group replicate plate interval
#>    <chr>   <int> <dbl> <chr>      <dbl> <chr>     <chr>     <int> <chr> <chr>   
#>  1 A01        26 2525. Untreated      0 uM        cont…         1 Plat… 15min   
#>  2 A02        16  458. Untreated      0 uM        cont…         3 Plat… 60min   
#>  3 A03        26 5385. PosControl   100 uM        posi…         1 Plat… 15min   
#>  4 A04        26 5378. PosControl   100 uM        posi…         3 Plat… 60min   
#>  5 A05        29 1038. CompoundA…    50 uM        trea…         1 Plat… 15min   
#>  6 A06        33 1023. CompoundA…    50 uM        trea…         3 Plat… 60min   
#>  7 A07        29 4885. CompoundA…   500 uM        trea…         1 Plat… 15min   
#>  8 A08        27 3488. CompoundA…   500 uM        trea…         3 Plat… 60min   
#>  9 A09        22  739. CompoundB     50 uM        comb…         1 Plat… 15min   
#> 10 A10        26  761. CompoundB     50 uM        comb…         3 Plat… 60min   
#> # ℹ 86 more rows
#> # ℹ 1 more variable: timepoint <dbl>

# aggregate with a different estimator
cr_summarize_wells(exp, channel = "marker_1", fun = mean)
#> # A tibble: 96 × 11
#>    well  n_cells value treatment   dose dose_unit group replicate plate interval
#>    <chr>   <int> <dbl> <chr>      <dbl> <chr>     <chr>     <int> <chr> <chr>   
#>  1 A01        26 2833. Untreated      0 uM        cont…         1 Plat… 15min   
#>  2 A02        16  524. Untreated      0 uM        cont…         3 Plat… 60min   
#>  3 A03        26 5509. PosControl   100 uM        posi…         1 Plat… 15min   
#>  4 A04        26 5783. PosControl   100 uM        posi…         3 Plat… 60min   
#>  5 A05        29 1223. CompoundA…    50 uM        trea…         1 Plat… 15min   
#>  6 A06        33 1139. CompoundA…    50 uM        trea…         3 Plat… 60min   
#>  7 A07        29 6379. CompoundA…   500 uM        trea…         1 Plat… 15min   
#>  8 A08        27 3972. CompoundA…   500 uM        trea…         3 Plat… 60min   
#>  9 A09        22  869. CompoundB     50 uM        comb…         1 Plat… 15min   
#> 10 A10        26  823. CompoundB     50 uM        comb…         3 Plat… 60min   
#> # ℹ 86 more rows
#> # ℹ 1 more variable: timepoint <dbl>