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Parse design facts out of export paths

Source: R/import-paths.R
cr_parse_paths.Rd

Turns a vector of export paths into one row of design information per file: the directory levels below root, the file-name markers, the replicate index and the grammar tokens.

Usage

cr_parse_paths(
  paths,
  root = NULL,
  levels = NULL,
  grammar = NULL,
  markers = NULL,
  strict = TRUE,
  spec = NULL,
  call = rlang::caller_env()
)

Arguments

paths

Character vector of file paths.

root

Directory the paths sit under. Required when levels is given.

levels

Directory level specification; see cr_path_spec().

grammar

A cr_filename_grammar(), or NULL.

markers

A cr_marker_rules() object, or NULL.

strict

Logical. Abort on an unparseable file name. When spec is supplied and strict is not, the spec's setting is used.

spec

Optional cr_path_spec() supplying any of levels, grammar, markers and strict that are not given directly.

call

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

Value

A tibble with one row per path: source_file, source_path, one column per directory level, the marker flag columns, variant, core, replicate, one column per grammar token, and the parse_ok / parse_error outcome.

Details

With strict = TRUE (the default) a file name that matches no core_patterns entry of the grammar aborts the parse. That is the intended behaviour: a name that parses to defaults instead of failing loudly can move a treated unit into a control arm without anything in the analysis noticing.

See also

cr_path_spec(), cr_filename_grammar(), cr_marker_rules(), cr_read_exports().

Other import: cr_assign_units(), cr_centroid_overlap(), cr_column_map(), cr_extract_markers(), cr_filename_grammar(), cr_marker_rules(), cr_merge_rules(), 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

root <- file.path(tempdir(), "cr_paths_demo")
paths <- file.path(
  root, "Run1", "CompoundA", "Plate_1",
  c("CompoundA_vehicle_1.csv", "CompoundA_5min_10uM_treated_1.csv")
)
cr_parse_paths(
  paths,
  root = root,
  levels = c("run", "compound", "plate"),
  grammar = cr_filename_grammar(
    tokens = list(interval = "[0-9]+min", dose = "[0-9]+uM"),
    defaults = list(interval = "none", dose = "vehicle"),
    prefix_strip = "CompoundA"
  )
)
#> # A tibble: 2 × 17
#>   source_file          source_path run   compound plate merge_unit partial_plate
#>   <chr>                <chr>       <chr> <chr>    <chr> <lgl>      <lgl>        
#> 1 CompoundA_vehicle_1… /tmp/Rtmpb… Run1  Compoun… Plat… FALSE      FALSE        
#> 2 CompoundA_5min_10uM… /tmp/Rtmpb… Run1  Compoun… Plat… FALSE      FALSE        
#> # ℹ 10 more variables: omitted_reagent <lgl>, reacquisition <lgl>, lot <lgl>,
#> #   variant <chr>, core <chr>, replicate <chr>, interval <chr>, dose <chr>,
#> #   parse_ok <lgl>, parse_error <chr>