collapse_pipeline: Collapse benchmark_tbl into a two column summary

In Shians/CellBench: Construct Benchmarks for Single Cell Analysis Methods

Collapse benchmark_tbl into a two column summary

Description

Collapse benchmark_tbl into two columns: "pipeline" and "result". The "pipeline" column will be the concatenated values from the data and methods columns while the "result" column remains unchanged from the benchmark_tbl. This is useful for having a string summary of the pipeline for annotating.

Usage

collapse_pipeline(
  x,
  sep = arrow_sep("right"),
  drop.steps = TRUE,
  data.name = TRUE
)

pipeline_collapse(
  x,
  sep = arrow_sep("right"),
  drop.steps = TRUE,
  data.name = TRUE
)

Arguments

x	the benchmark_tbl to collapse
sep	the separator to use for concatenating the pipeline steps
drop.steps	if the data name and methods steps should be dropped from the output. TRUE by default.
data.name	if the dataset name should be included in the pipeline string. Useful if only a single dataset is used.

Value

benchmark_tbl with pipeline and result columns (and all other columns if drop.steps is FALSE)

See Also

as_pipeline_list

Examples

# list of data
datasets <- list(
    set1 = rnorm(500, mean = 2, sd = 1),
    set2 = rnorm(500, mean = 1, sd = 2)
)

# list of functions
add_noise <- list(
    none = identity,
    add_bias = function(x) { x + 1 }
)

res <- apply_methods(datasets, add_noise)
collapse_pipeline(res)

Shians/CellBench documentation built on Oct. 16, 2023, 7:54 a.m.