bixverse single cell subset class

Subset view onto a SingleCells() object, restricted to cells belonging to a single level of a grouping variable. The Rust count connection is shared with the parent (no data copy). obs_table and var_table are held in memory; sc_map is rebuilt to point only at the subset cells but stays in the original index space so Rust calls remain valid without further translation.

Usage

SingleCellsSubset(sc_object, grouping_column, group)

Arguments

sc_object

A SingleCells() object to subset.

grouping_column

String. Column in the obs table that defines the grouping.

group

String. Level of grouping_column to retain.

Value

A SingleCellsSubset object.

Properties

count_connection

Shared Rust pointer to the on-disk counts.

dir_data

Directory holding the binary count files.

obs_table

Subset obs (rows for the chosen group only). cell_idx keeps the original 1-indexed position in the parent.

var_table

Variable/feature table (unchanged from parent).

grouping_column

Column in obs used to define the subset.

group

Value of grouping_column represented by this subset.

sc_cache

Fresh ScCache for subset-specific PCA, kNN, sNN, embeddings.

sc_map

ScMap restricted to the subset cells. cell_mapping stays 1-indexed and cells_to_keep_idx stays 0-indexed, both in the original parent index space.

subset_to_original

Integer vector. 1-indexed original cell positions, in subset row order. subset_to_original[i] is the parent position of subset row i.

dims

c(n_cells_subset, n_genes).

Examples

# a view onto one cell type, sharing the parent's counts on disk
sc <- demo_single_cells(prepped = FALSE)
subset_obj <- SingleCellsSubset(
  sc_object = sc,
  grouping_column = "cell_grp",
  group = "cell_type_1"
)
dim(subset_obj)
#> [1] 167  50

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