dynamo.tl.cell_growth_rate

dynamo.tl.cell_growth_rate(adata, group, source, target, L0=0.3, L=1.2, k=0.001, birth_genes=None, death_genes=None, clone_column=None, **kwargs)[source]

Estimate the growth rate via clone information or logistic equation of population dynamics.

Growth rate is calculated as 1) number_of_cell_at_source_time_in_the_clone / number_of_cell_at_end_time_in_the_clone when there is clone information ([clone_column, time_column, source_time, target_time] are all not None); 2) estimate via logistic equation of population growth and death.

Parameters:

  • adata (AnnData) – AnnData object that contains the reconstructed vector field function in the uns attribute.

  • group (str or None (default: None)) – The column key in .obs points to the collection time of each cell, required for calculating growth rate with clone information.

  • source (str or None (default: None)) – The column key in .obs points to the starting point from collection time of each cell, required for calculating growth rate with clone information.

  • target (str or None (default: None)) – The column key in .obs points to the end point from collection time of each cell, required for calculating growth rate with clone information.

  • L0 (float (default: 0.3)) – The base growth/death rate.

  • L (float (default: 1.2)) – The maximum growth/death rate.

  • k (float (default: `0.001)) – The steepness of the curve.

  • birth_genes (list or None (default: None)) – The gene list associated with the cell cycle process. If None, GSEA’s KEGG_CELL_CYCLE will be used.

  • death_genes (list or None (default: None)) – The gene list associated with the cell cycle process. If None, GSEA’s KEGG_APOPTOSIS will be used.

  • clone_column (str or None (default: None)) – The column key in .obs points to the clone id if there is any. If a cell doesn’t belong to any clone, the clone id of that cell should be assigned as np.nan

  • kwargs – Additional arguments that will be passed to score_cells function.

Returns:

An updated adata object that includes growth_rate column or growth_rate, birth_score, death_score in its .obs attribute when the clone based or purely expression based growth rate was calculated.