Helper function to write data to a dense h5ad file

Helper to write synthetic data to h5ad with /X stored as a dense 2D dataset (cells x genes). Useful for exercising the dense ingestion path.

Usage

write_h5ad_sc_dense(
  f_path,
  counts,
  obs,
  var,
  overwrite = TRUE,
  .verbose = TRUE
)

Arguments

f_path

String. The filepath to which to save the data

counts

Matrix or sparse matrix; sparse input is densified.

obs

data.table. The observations. Needs nrow(obs) == nrow(counts).

var

data.table. The variable data. Needs nrow(var) == ncol(counts).

overwrite

Boolean. Shall any found h5ad file be overwritten.

.verbose

Boolean. Controls verbosity of the function.

Value

Returns invisible

Examples

# the same data with a dense /X, which reads back as DENSE_ROW
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_dense(
  f_path, data$counts, data$obs, data$var, .verbose = FALSE
)
get_h5ad_dimensions(f_path)$type
#> [1] "DENSE_ROW"

unlink(f_path)