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Extract file-name markers into typed flags

Source: R/import-markers.R
cr_extract_markers.Rd

Applies a cr_marker_rules() set to a table that carries a file-name column, adding one logical column per rule plus a character variant column holding any unmatched trailing parenthetical.

Usage

cr_extract_markers(
  x,
  name_col = "source_file",
  container_col = NULL,
  rules = cr_marker_rules(),
  stem_col = NULL,
  strip_ext = TRUE,
  call = rlang::caller_env()
)

Arguments

x

A data frame with one row per file (or per cell).

name_col

Name of the column holding the file name. Default "source_file".

container_col

Optional name of the column holding the container (plate or directory) name that partial_plate is matched against.

rules

A cr_marker_rules() object.

stem_col

Optional name of a column to write the marker-stripped name into.

strip_ext

Logical. Remove a trailing file extension before matching. Default TRUE.

call

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

Value

x with the columns merge_unit, partial_plate, omitted_reagent, reacquisition, lot (all logical) and variant (character) added. Columns for rules that were not supplied are FALSE throughout.

See also

cr_marker_rules(), cr_parse_paths().

Other import: cr_assign_units(), cr_centroid_overlap(), cr_column_map(), 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(
  source_file = c("CompoundA_10uM_treated_1.csv",
                  "CompoundA_10uM_treated_1.1 (split).csv",
                  "CompoundA_vehicle_1 (no reagent).csv",
                  "CompoundA_vehicle_2 (weekend).csv"),
  plate = c("Plate_1", "Plate_1", "Plate_1", "Plate_2 (partial)")
)
cr_extract_markers(
  files,
  container_col = "plate",
  rules = cr_marker_rules(merge_unit = "\\(split\\)",
                          partial_plate = "\\(partial\\)",
                          omitted_reagent = "\\(no reagent\\)")
)
#> # A tibble: 4 × 8
#>   source_file plate merge_unit partial_plate omitted_reagent reacquisition lot  
#>   <chr>       <chr> <lgl>      <lgl>         <lgl>           <lgl>         <lgl>
#> 1 CompoundA_… Plat… FALSE      FALSE         FALSE           FALSE         FALSE
#> 2 CompoundA_… Plat… TRUE       FALSE         FALSE           FALSE         FALSE
#> 3 CompoundA_… Plat… FALSE      FALSE         TRUE            FALSE         FALSE
#> 4 CompoundA_… Plat… FALSE      TRUE          FALSE           FALSE         FALSE
#> # ℹ 1 more variable: variant <chr>