dynamo.tl.cell_growth_rate

dynamo.tl.cell_growth_rate(adata, group, source=None, target=None, 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.

Parameters:
  • adata (AnnData) – An AnnData object.

  • group (str) – The column key in .obs points to the collection time of each cell, required for calculating growth rate with clone information.

  • source (Optional[str]) – The value in the group column representing the starting point from collection time of each cell, required for calculating growth rate with clone information.

  • target (Optional[str]) – The value in the group column representing the end point from collection time of each cell, required for calculating growth rate with clone information.

  • L0 (float) – The base growth/death rate. Defaults to 0.3.

  • L (float) – The maximum growth/death rate. Defaults to 1.2.

  • k (float) – The steepness of the curve. Defaults to 1e-3.

  • birth_genes (Optional[List[str]]) – The gene list associated with the cell cycle process. If None, GSEA’s KEGG_CELL_CYCLE will be used. Defaults to None.

  • death_genes (Optional[List[str]]) – The gene list associated with the cell cycle process. If None, GSEA’s KEGG_APOPTOSIS will be used. Defaults to None.

  • clone_column (Optional[str]) – 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. Defaults to None.

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

Raises:
Return type:

AnnData

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.