Generate a mock synthetic dataset with different types of columns and layers. This is primarily designed for use in tests, examples, vignettes and other documentation but is also provided to users for creating reproducible examples.
Use get_generator_types() to get the available types for each slot.
Usage
generate_dataset(
n_obs = 10L,
n_vars = 20L,
x_type = "numeric_matrix",
layer_types = get_generator_types(slot = "layers"),
obs_types = get_generator_types(slot = "obs"),
var_types = get_generator_types(slot = "var"),
obsm_types = get_generator_types(slot = "obsm"),
varm_types = get_generator_types(slot = "varm"),
obsp_types = get_generator_types(slot = "obsp"),
varp_types = get_generator_types(slot = "varp"),
uns_types = get_generator_types(slot = "uns"),
example = FALSE,
format = c("list", "AnnData", "SingleCellExperiment", "Seurat")
)
get_generator_types(example = FALSE, slot = NULL)Arguments
- n_obs
Number of observations to generate
- n_vars
Number of variables to generate
- x_type
Type of matrix to generate for
X- layer_types
Types of matrices to generate for
layers- obs_types
Types of vectors to generate for
obs- var_types
Types of vectors to generate for
var- obsm_types
Types of matrices to generate for
obsm- varm_types
Types of matrices to generate for
varm- obsp_types
Types of matrices to generate for
obsp- varp_types
Types of matrices to generate for
varp- uns_types
Types of objects to generate for
uns- example
If
TRUE, the types will be overridden with a small subset of types. This is useful for documentation.- format
Object type to output, one of "list", "AnnData", "SingleCellExperiment", or "Seurat".
- slot
Which slot to return types for, if
NULLa named list of all slots is returned
Value
For generate_dataset(), an object as defined by output containing
the generated dataset
For get_generator_types(), a named list of character vectors or a
single character vector if slot is not NULL
Details
To generate no data for a given slot, set the matching type argument to
NULL or an empty vector, e.g. obs_types = c() will generate an empty
obs data frame.
When generating SingleCellExperiment or Seurat objects, only some of the
generated slots will be included in the output object. To generate a more
complete object, use format = "AnnData" followed by
adata$as_SingleCellExperiment() or adata$as_Seurat().
Use get_generator_types() to get a list of the available types for each
slot, or for a specific slot by setting slot. If example = TRUE, only the
example types are returned.
Examples
# Generate all types as a list
dummy <- generate_dataset()
# Generate the example types
dummy_example <- generate_dataset(example = TRUE)
# Generate an AnnData
dummy_anndata <- generate_dataset(format = "AnnData", example = TRUE)
# Generate a SingleCellExperiment
if (rlang::is_installed("SingleCellExperiment")) {
dummy_sce <- generate_dataset(format = "SingleCellExperiment", example = TRUE)
}
# Generate a Seurat object
if (rlang::is_installed("SeuratObject")) {
dummy_seurat <- generate_dataset(format = "Seurat", example = TRUE)
}
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
# Get all available generator types
get_generator_types()
#> $X
#> [1] "numeric_matrix" "numeric_dense"
#> [3] "numeric_csparse" "numeric_rsparse"
#> [5] "numeric_matrix_with_nas" "numeric_dense_with_nas"
#> [7] "numeric_csparse_with_nas" "numeric_rsparse_with_nas"
#> [9] "integer_matrix" "integer_csparse"
#> [11] "integer_rsparse" "integer_matrix_with_nas"
#> [13] "integer_csparse_with_nas" "integer_rsparse_with_nas"
#>
#> $layers
#> [1] "numeric_matrix" "numeric_dense"
#> [3] "numeric_csparse" "numeric_rsparse"
#> [5] "numeric_matrix_with_nas" "numeric_dense_with_nas"
#> [7] "numeric_csparse_with_nas" "numeric_rsparse_with_nas"
#> [9] "integer_matrix" "integer_csparse"
#> [11] "integer_rsparse" "integer_matrix_with_nas"
#> [13] "integer_csparse_with_nas" "integer_rsparse_with_nas"
#>
#> $obs
#> [1] "character" "integer"
#> [3] "factor" "factor_ordered"
#> [5] "logical" "numeric"
#> [7] "character_with_nas" "integer_with_nas"
#> [9] "factor_with_nas" "factor_ordered_with_nas"
#> [11] "logical_with_nas" "numeric_with_nas"
#>
#> $var
#> [1] "character" "integer"
#> [3] "factor" "factor_ordered"
#> [5] "logical" "numeric"
#> [7] "character_with_nas" "integer_with_nas"
#> [9] "factor_with_nas" "factor_ordered_with_nas"
#> [11] "logical_with_nas" "numeric_with_nas"
#>
#> $obsm
#> [1] "numeric_matrix" "numeric_dense"
#> [3] "numeric_csparse" "numeric_rsparse"
#> [5] "numeric_matrix_with_nas" "numeric_dense_with_nas"
#> [7] "numeric_csparse_with_nas" "numeric_rsparse_with_nas"
#> [9] "integer_matrix" "integer_csparse"
#> [11] "integer_rsparse" "integer_matrix_with_nas"
#> [13] "integer_csparse_with_nas" "integer_rsparse_with_nas"
#> [15] "character" "integer"
#> [17] "factor" "factor_ordered"
#> [19] "logical" "numeric"
#> [21] "character_with_nas" "integer_with_nas"
#> [23] "factor_with_nas" "factor_ordered_with_nas"
#> [25] "logical_with_nas" "numeric_with_nas"
#>
#> $varm
#> [1] "numeric_matrix" "numeric_dense"
#> [3] "numeric_csparse" "numeric_rsparse"
#> [5] "numeric_matrix_with_nas" "numeric_dense_with_nas"
#> [7] "numeric_csparse_with_nas" "numeric_rsparse_with_nas"
#> [9] "integer_matrix" "integer_csparse"
#> [11] "integer_rsparse" "integer_matrix_with_nas"
#> [13] "integer_csparse_with_nas" "integer_rsparse_with_nas"
#> [15] "character" "integer"
#> [17] "factor" "factor_ordered"
#> [19] "logical" "numeric"
#> [21] "character_with_nas" "integer_with_nas"
#> [23] "factor_with_nas" "factor_ordered_with_nas"
#> [25] "logical_with_nas" "numeric_with_nas"
#>
#> $obsp
#> [1] "numeric_matrix" "numeric_dense"
#> [3] "numeric_csparse" "numeric_rsparse"
#> [5] "numeric_matrix_with_nas" "numeric_dense_with_nas"
#> [7] "numeric_csparse_with_nas" "numeric_rsparse_with_nas"
#> [9] "integer_matrix" "integer_csparse"
#> [11] "integer_rsparse" "integer_matrix_with_nas"
#> [13] "integer_csparse_with_nas" "integer_rsparse_with_nas"
#>
#> $varp
#> [1] "numeric_matrix" "numeric_dense"
#> [3] "numeric_csparse" "numeric_rsparse"
#> [5] "numeric_matrix_with_nas" "numeric_dense_with_nas"
#> [7] "numeric_csparse_with_nas" "numeric_rsparse_with_nas"
#> [9] "integer_matrix" "integer_csparse"
#> [11] "integer_rsparse" "integer_matrix_with_nas"
#> [13] "integer_csparse_with_nas" "integer_rsparse_with_nas"
#>
#> $uns
#> [1] "scalar_character" "scalar_integer"
#> [3] "scalar_factor" "scalar_factor_ordered"
#> [5] "scalar_logical" "scalar_numeric"
#> [7] "scalar_character_with_nas" "scalar_integer_with_nas"
#> [9] "scalar_factor_with_nas" "scalar_factor_ordered_with_nas"
#> [11] "scalar_logical_with_nas" "scalar_numeric_with_nas"
#> [13] "vec_character" "vec_integer"
#> [15] "vec_factor" "vec_factor_ordered"
#> [17] "vec_logical" "vec_numeric"
#> [19] "vec_character_with_nas" "vec_integer_with_nas"
#> [21] "vec_factor_with_nas" "vec_factor_ordered_with_nas"
#> [23] "vec_logical_with_nas" "vec_numeric_with_nas"
#> [25] "df_character" "df_integer"
#> [27] "df_factor" "df_factor_ordered"
#> [29] "df_logical" "df_numeric"
#> [31] "df_character_with_nas" "df_integer_with_nas"
#> [33] "df_factor_with_nas" "df_factor_ordered_with_nas"
#> [35] "df_logical_with_nas" "df_numeric_with_nas"
#> [37] "mat_numeric_matrix" "mat_numeric_dense"
#> [39] "mat_numeric_csparse" "mat_numeric_rsparse"
#> [41] "mat_numeric_matrix_with_nas" "mat_numeric_dense_with_nas"
#> [43] "mat_numeric_csparse_with_nas" "mat_numeric_rsparse_with_nas"
#> [45] "mat_integer_matrix" "mat_integer_csparse"
#> [47] "mat_integer_rsparse" "mat_integer_matrix_with_nas"
#> [49] "mat_integer_csparse_with_nas" "mat_integer_rsparse_with_nas"
#> [51] "list"
#>
# Get generator types for a specific slot
get_generator_types(slot = "obs")
#> [1] "character" "integer"
#> [3] "factor" "factor_ordered"
#> [5] "logical" "numeric"
#> [7] "character_with_nas" "integer_with_nas"
#> [9] "factor_with_nas" "factor_ordered_with_nas"
#> [11] "logical_with_nas" "numeric_with_nas"
# Get generator types used when example = TRUE
get_generator_types(example = TRUE)
#> $X
#> [1] "numeric_matrix"
#>
#> $layers
#> [1] "numeric_matrix" "numeric_dense" "numeric_csparse"
#>
#> $obs
#> [1] "character" "integer" "factor"
#>
#> $var
#> [1] "character" "integer" "factor"
#>
#> $obsm
#> [1] "numeric_matrix" "numeric_dense" "numeric_csparse"
#>
#> $varm
#> [1] "numeric_matrix" "numeric_dense" "numeric_csparse"
#>
#> $obsp
#> [1] "numeric_matrix" "numeric_dense" "numeric_csparse"
#>
#> $varp
#> [1] "numeric_matrix" "numeric_dense" "numeric_csparse"
#>
#> $uns
#> [1] "scalar_character" "vec_integer" "df_logical"
#> [4] "mat_numeric_matrix"
#>