popari.simulation_framework.SimulationParameters#
- class popari.simulation_framework.SimulationParameters(num_cells=None, num_genes=100, annotation_mode='domain', num_real_metagenes=10, num_noise_metagenes=3, real_metagene_parameter=4.0, noise_metagene_parameter=4.0, spatial_distributions=None, cell_type_definitions=None, metagene_variation_probabilities=None, domain_key='domain', width=1.0, height=1.0, minimum_distance=None, grid_size=None, sig_y_scale=3.0, sig_x_scale=3.0, lambda_s=1.0)[source]#
Container for simulation parameters.
- Parameters:
num_cells (int | None) – number of cells to simulate
num_genes (int) – number of total genes to simulate
annotation_mode (str) – whether the Canvas is annotating domain or cell_type
num_real_metagenes (int) – number of real metagenes
num_noise_metagenes (int) – number of noise metagenes
real_metagene_parameter (float) – shape parameter for Gamma distribution from which real metagene weights are sampled
noise_metagene_parameter (float) – shape parameter for Gamma distribution from which noise metagene weights are sampled
spatial_distributions (dict) – proportions of cell types in each domain of the simulation
cell_type_definitions (dict) – definitions of simulated cell types by metagene proportion
metagene_variation_probabilities (Sequence) – variation of metagene weight definitions between metagenes
domain_key (str) – key in .obs where the domain identity of each cell is stored
width (float) – width of the canvas
height (float) – height of the canvas
minimum_distance (float) – minimum distance between simulated datapoints
grid_size (int) – number of rows/columns for grid-based simulation. Alternative to num_cells parameter.
sig_y_scale (float) – standard deviation of additive Gaussian noise used during sampling of gene expression
sig_x_scale (float) – standard deviation of additive Gaussian noise used during sampling of latent states
lambda_s (float) – shape parameter used for sampling cell sizes
Attributes
Methods