- 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)
Estimate the growth rate via clone information or logistic equation of population dynamics.
AnnData) – An AnnData object.
str) – The column key in .obs points to the collection time of each cell, required for calculating growth rate with clone information.
float) – The base growth/death rate. Defaults to 0.3.
float) – The maximum growth/death rate. Defaults to 1.2.
float) – The steepness of the curve. Defaults to 1e-3.
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.
- Return type:
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.