c2v.tl.smooth

c2v.tl.smooth(adata, field='X', names=None, key_added='smoothed', graph_key='connectivities', progress_bar=False, n_steps=3)

Performing kNN smoothing on adata.X, adata.layers[layer], adata.obs[name], or adata.obsm[name] for n_steps iterations using adata.obsp[graph_key].

Parameters:

adata AnnData

Annotated data matrix at the clone level.

field Literal["X", "layer", "obs", "obsm"], optional

Field to smooth, by default “X”.

names str | list[str] | None, optional

Key(s) in adata.layers, adata.obs, or adata.obsm containing field to smooth, by default None.

key_added str, optional

Key for adata.layers, adata.obs, or adata.obsm to store smoothed field.

graph_key str, optional

Key in adata.obsp containing kNN graph, by default “connectivities”.

progress_bar bool, optional

Whether to display a progress bar, by default False.

n_steps int, optional

Number of smoothing iterations, by default 3.

Return type:

None

Returns:

None Smoothed field is stored in adata.layers[“X_” + key_added], adata.layers[name + “_” + key_added], adata.obs[name + “_” + key_added], or adata.obsm[name + “_” + key_added].