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:
ValueError – clone_name or group not in .obs.
ValueError – source or target not in .obs.
- Return type:
- 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.