sparank.SimulationConfig

class sparank.SimulationConfig(total_samples=100000, n_threads=8, cells_mean=10, cells_min=1, cells_max=50, cells_std=5, cell_sample_method='gaussian', sim_buffer=10, batch_request_size=100000, batch_key=None)

Bases: object

Parameters for pseudo-spot simulation via SPACEL.

Parameters:

• total_samples (int)

• n_threads (int)

• cells_mean (int)

• cells_min (int)

• cells_max (int)

• cells_std (int)

• cell_sample_method (str)

• sim_buffer (int)

• batch_request_size (int)

• batch_key (str | None)

__init__(total_samples=100000, n_threads=8, cells_mean=10, cells_min=1, cells_max=50, cells_std=5, cell_sample_method='gaussian', sim_buffer=10, batch_request_size=100000, batch_key=None)

Parameters:

• total_samples (int)

• n_threads (int)

• cells_mean (int)

• cells_min (int)

• cells_max (int)

• cells_std (int)

• cell_sample_method (str)

• sim_buffer (int)

• batch_request_size (int)

• batch_key (str | None)

Return type:

None

Methods

__init__([total_samples, n_threads, ...])

Attributes

batch_key	Column in adata.obs to batch by during simulation.
batch_request_size	Size of batch requests.
cell_sample_method	"gaussian" or "lognormal".
cells_max	Maximum number of cells per pseudo-spot.
cells_mean	Mean number of cells per pseudo-spot.
cells_min	Minimum number of cells per pseudo-spot.
cells_std	Standard deviation of cells per pseudo-spot.
n_threads	Number of threads for parallel processing.
sim_buffer	Buffer size used during simulation.
total_samples	Total number of simulated samples to generate.

batch_key: str | None = None

Column in adata.obs to batch by during simulation.

batch_request_size: int = 100000

Size of batch requests.

cell_sample_method: str = 'gaussian'

“gaussian” or “lognormal”.

Type:

Method for sampling cells. Options

cells_max: int = 50

Maximum number of cells per pseudo-spot.

cells_mean: int = 10

Mean number of cells per pseudo-spot.

cells_min: int = 1

Minimum number of cells per pseudo-spot.

cells_std: int = 5

Standard deviation of cells per pseudo-spot.

n_threads: int = 8

Number of threads for parallel processing.

sim_buffer: int = 10

Buffer size used during simulation.

total_samples: int = 100000

Total number of simulated samples to generate.