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Write a synthetic export tree

Source: R/example-exports.R
cr_example_exports.Rd

Writes a nested directory of single-acquisition export files whose design information lives in the directory layout and the file names rather than inside the files. This is the input the multi-file ingest functions were written for, so that cr_read_exports(), cr_parse_paths() and cr_extract_markers() can be demonstrated on real files.

Usage

cr_example_exports(
  dir = tempdir(),
  seed = 42,
  n_cells = 20,
  format = c("csv", "xlsx")
)

Arguments

dir

Directory to write the tree into. Created when it does not exist.

seed

Random seed. NULL uses the current RNG state.

n_cells

Number of cells written per file.

format

File format, "csv" (default) or "xlsx". Writing "xlsx" needs the writexl package.

Value

A character vector of the written file paths, invisibly.

Details

The layout below dir is Run1/<compound>/<experiment>/<plate>/<file>, and the file names follow the grammar <compound>_<interval>_<dose>_<mode>_<replicate> in which an absent token is meaningful: a name carrying no exposure token is a vehicle control. Parenthetical markers are attached to three files – a two-pass acquisition, a repeated read and a reagent-omitted acquisition – and one directory is marked as a partly filled plate.

Column headers are raw instrument names rather than analysis names, and one of them carries a unit glyph, so that a cr_column_map() is genuinely required to read them.

See also

cr_read_exports(), cr_path_spec(), cr_example_screen(), cr_example_path().

Other example data: cr_example_design(), cr_example_experiment(), cr_example_files(), cr_example_path(), cr_example_screen()

Examples

d <- file.path(tempdir(), "cr_example_exports")
files <- cr_example_exports(d, seed = 1, n_cells = 5)
basename(files)
#>  [1] "CompoundA_15min_vehicle_1.csv"                   
#>  [2] "CompoundA_15min_250uM_treated_1.csv"             
#>  [3] "CompoundA_15min_250uM_treated_1.1 (split).csv"   
#>  [4] "CompoundA_60min_vehicle_2.csv"                   
#>  [5] "CompoundA_60min_250uM_treated_2.csv"             
#>  [6] "CompoundA_60min_250uM_treated_2 (repeat).csv"    
#>  [7] "CompoundA_60min_250uM_treated_2.2.csv"           
#>  [8] "CompoundB_15min_vehicle_1.csv"                   
#>  [9] "CompoundB_15min_250uM_treated_1.csv"             
#> [10] "CompoundB_15min_250uM_treated_1 (no reagent).csv"

map <- cr_column_map(
  exact = c("Event Label" = "cell_id",
            "Target - Signal Mean" = "target_signal"),
  prefix = c("^Nuclei - Area" = "area")
)
cells <- cr_read_exports(d, column_map = map, progress = FALSE)
head(cells[, c("source_file", "cell_id", "target_signal", "area")], 3)
#> # A tibble: 3 × 4
#>   source_file                                   cell_id target_signal  area
#>   <chr>                                         <chr>           <dbl> <dbl>
#> 1 CompoundA_15min_250uM_treated_1.1 (split).csv E0001           2316.  146.
#> 2 CompoundA_15min_250uM_treated_1.1 (split).csv E0002            805.  201.
#> 3 CompoundA_15min_250uM_treated_1.1 (split).csv E0003            594.  227.