Skip to contents

Assign cells to analysis units

Source: R/import-units.R
cr_assign_units.Rd

Derives the identifier of the analysis unit — the spatial unit that is the unit of replication — for every row of a cell table, merging the files that belong to the same unit according to a cr_merge_rules() set.

Usage

cr_assign_units(
  x,
  key_vars,
  replicate_var = "replicate",
  rules = cr_merge_rules(),
  id_col = "well_id",
  sep = "|",
  call = rlang::caller_env()
)

Arguments

x

A data frame of cells (or of files) carrying the design columns and a replicate index.

key_vars

Character vector of column names that, together with the replicate index, identify one unit.

replicate_var

Name of the replicate index column. Default "replicate".

rules

A cr_merge_rules() object.

id_col

Name of the unit identifier column to add. Default "well_id".

sep

Separator used to build the identifier. Default "|".

call

The execution environment of the calling function. Used for error reporting; experts only.

Value

x with two columns added: replicate_merged (the replicate index after merging) and the unit identifier named by id_col. The number of units is attached as the "n_units" attribute.

Details

The unit identifier is the combination of key_vars and the merged replicate index. Files that share it are one unit; files that do not are separate replicates. Because a unit may be assembled from more than one file, cr_unit_map() should be used afterwards to see which units were merged and from how many files.

See also

cr_unit_map(), cr_merge_rules(), cr_centroid_overlap().

Other import: cr_centroid_overlap(), cr_column_map(), cr_extract_markers(), cr_filename_grammar(), cr_marker_rules(), cr_merge_rules(), cr_parse_paths(), cr_path_spec(), cr_read_cellprofiler(), cr_read_cells(), cr_read_design(), cr_read_export(), cr_read_exports(), cr_read_qupath(), cr_read_segmantr(), cr_unit_map()

Examples

files <- tibble::tibble(
  compound = "CompoundA",
  plate = "Plate_1",
  mode = "treated",
  replicate = c("1", "1.1", "2", "2.2"),
  merge_unit = c(FALSE, TRUE, FALSE, FALSE),
  reacquisition = FALSE
)
units <- cr_assign_units(files, key_vars = c("compound", "plate", "mode"))
units[, c("replicate", "replicate_merged", "well_id")]
#> # A tibble: 4 × 3
#>   replicate replicate_merged well_id                      
#>   <chr>     <chr>            <chr>                        
#> 1 1         1                CompoundA|Plate_1|treated|1  
#> 2 1.1       1                CompoundA|Plate_1|treated|1  
#> 3 2         2                CompoundA|Plate_1|treated|2  
#> 4 2.2       2.2              CompoundA|Plate_1|treated|2.2