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Reset the cells to keep

reset_cells_to_keep.Rd

Restores every cell found in the binary count file and wipes the cache, taking the object back to a pristine state. Filtering only ever flips a to_keep flag in the DuckDB, so nothing was deleted and nothing is lost by resetting.

Wiping the cache is not optional: a PCA or a kNN computed on a filtered subset does not describe the full cell set, and keeping it would recreate exactly the mismatch this guards against. With force = FALSE you are asked to confirm before that happens.

Usage

reset_cells_to_keep(object, force = FALSE)

## S7 method for class <bixverse::MetaCells>
reset_cells_to_keep(object, force = FALSE)

## S7 method for class <bixverse::SingleCells>
reset_cells_to_keep(object, force = FALSE)

## S7 method for class <bixverse::SingleCellsMultiModal>
reset_cells_to_keep(object, force = FALSE)

## S7 method for class <bixverse::SingleCellsSubset>
reset_cells_to_keep(object, force = FALSE)

Arguments

object

SingleCells or SingleCellsMultiModal class.

force

Boolean. Skip the confirmation prompt. Defaults to FALSE, in which case an interactive session asks before wiping the cache and a non-interactive one errors, because there is no one there to ask.

Value

The object with every cell restored and an empty cache. Unchanged if the confirmation was declined.

Examples

# a filter taken back off, cache wiped with it
sc <- demo_single_cells(prepped = FALSE)
sc <- set_cells_to_keep(sc, get_cell_names(sc)[1:100])
sc <- reset_cells_to_keep(sc, force = TRUE)
length(get_cells_to_keep(sc))
#> [1] 500

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