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Status of everything held in a single cell object's caches

get_sc_cache_status.Rd

One row per cached artefact, saying whether it still agrees with the current cell set and with the artefacts it was derived from. Artefacts computed before provenance stamping existed report stamped = FALSE and are never flagged stale, because nothing is known about them either way.

Usage

get_sc_cache_status(object)

Arguments

object

SingleCells, SingleCellsSubset, MetaCells or SingleCellsMultiModal class.

Value

A data.table with the columns

  • modality - The modality the artefact lives in.

  • artefact - One of pca, embedding, knn, snn, magic.

  • name - The embedding name, NA for the others.

  • stamped - Whether the artefact carries a provenance stamp.

  • stale - Whether it disagrees with the current state.

  • reason - Why it is stale, NA otherwise.

  • id - The artefact's stamp id.

  • from - List column of the parent stamp ids.

Examples

# what the object holds and whether it still agrees with the cells
sc <- demo_single_cells()
get_sc_cache_status(sc)
#>    modality artefact   name stamped  stale reason               id
#>      <char>   <char> <char>  <lgcl> <lgcl> <char>           <char>
#> 1:      rna      pca   <NA>    TRUE  FALSE   <NA> a16d75257d474473
#> 2:      rna      knn   <NA>    TRUE  FALSE   <NA> 7da01e49de1a4131
#> 3:      rna      snn   <NA>    TRUE  FALSE   <NA> d0b50fdbe9ffe377
#>                from
#>              <list>
#> 1:                 
#> 2: a16d75257d474473
#> 3: 7da01e49de1a4131

unlink(sc@dir_data, recursive = TRUE, force = TRUE)