Stream in h5ad to SingleCells (alias) — stream

Convenience alias for load_h5ad(streaming = 2L). Kept for backwards compatibility - forwards directly to load_h5ad() with heavy streaming enabled. Prefer calling load_h5ad directly with an explicit streaming level.

Usage

stream_h5ad(
  object,
  h5_path,
  sc_qc_param = params_sc_min_quality(),
  raw_count_slot = c("auto", "X", "raw.X", "layers.counts"),
  max_genes_in_memory = 2000L,
  cell_batch_size = 100000L,
  .verbose = TRUE
)

Arguments

object: SingleCells class.
h5_path: File path to the h5ad object.
sc_qc_param: List. Output of params_sc_min_quality().
raw_count_slot: Where raw counts live. "auto" detects per file via detect_raw_count_slot(); otherwise one of "X", "raw.X", "layers.counts".
max_genes_in_memory: Integer. Genes held in memory at once. Defaults to 2000L.
cell_batch_size: Integer. Cell batch size. Defaults to 100000L.
.verbose: Boolean.

Value

The class with updated shape information.

Examples

# same as load_h5ad(streaming = 2L)
data <- generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(n_cells = 200L, n_genes = 40L)
)
f_path <- tempfile(fileext = ".h5ad")
write_h5ad_sc(f_path, data$counts, data$obs, data$var, .verbose = FALSE)
dir_data <- tempfile("sc_stream")
dir.create(dir_data, recursive = TRUE)
sc <- stream_h5ad(
  object = SingleCells(dir_data = dir_data),
  h5_path = f_path,
  sc_qc_param = params_sc_min_quality(
    min_unique_genes = 5L,
    min_lib_size = 25L,
    min_cells = 5L
  ),
  .verbose = FALSE
)
dim(sc)
#> [1] 200  40

unlink(c(f_path, dir_data), recursive = TRUE, force = TRUE)