Module: cell_graph_general
- class cytomulate.cell_graph_general.GeneralCellGraph[source]
Bases:
object- generate_trajectories(cell_types, **kwargs)[source]
Generate the actual differential paths
- Parameters:
cell_types (dict) – A dictionary of CellType objects
kwargs – Extra parameters needed for non-default path generation algorithms, which are passed to
cytomulate.utilities.trajectories.
- Return type:
None
- sample_graph(n_samples, cell_label, beta_alpha=0.4, beta_beta=1.0)[source]
Draw random samples of a cell type from the cell differentiation graph
- Parameters:
n_samples (int) – Number of samples
cell_label (str or int) – The label of the cell needed
beta_alpha (float) – The alpha parameter of the beta distribution
beta_beta (float) – The beta parameter of the beta distribution
- Return type:
Tuple[ndarray,ndarray,list]- Returns:
G (np.ndarray) – The additive values of the path
pseudo_time (np.ndarray) – The pseudo times
labels (list) – The cell types to which the cell is differentiating