Creation: cell_type

class cytomulate.creation.cell_type.CreationCellType(label, cell_id, n_markers)[source]

Bases: GeneralCellType

generate_marker_expression_patterns(cell_types, cell_graph)[source]

Generate marker patterns for the cell types

Parameters:

  • cell_types (dict) – A dictionary of CreationCellType objects

  • cell_graph (CreationCellGraph) – A cell graph object

Return type:

None

generate_marker_expressions(cell_types, cell_graph, high_expressions, low_expressions)[source]

Generate the actual expressions

Parameters:

  • cell_types (dict) – A dictionary of CreationCellType objects

  • cell_graph (CreationCellGraph) – A cell graph object

  • high_expressions (np.ndarray) – An array of high expression levels

  • low_expressions (np.ndarray) – An array of low expression levels

Return type:

None

generate_model(n_components, variance_mode=0.01)[source]

Randomly generate models for cell types

Parameters:

  • n_components (int) – Number of components in a GMM

  • variance_mode (float) – The mode of the variance of the inverse wishart distribution

Return type:

None