scFates.pp.diffusion¶
- scFates.pp.diffusion(adata, n_components=10, knn=30, alpha=0, multiscale=True, n_eigs=None, device='cpu', n_pcs=50, save_uns=False, copy=False)¶
Wrapper to generate diffusion maps using Palantir.
- Parameters
- adata :
AnnData
Annotated data matrix.
- n_components :
int
(default:10
) Number of diffusion components.
- knn :
int
(default:30
) Number of nearest neighbors for graph construction.
- alpha :
float
(default:0
) Normalization parameter for the diffusion operator.
- multiscale :
bool
(default:True
) Whether to get mutliscale diffusion space (calls palantir.utils.determine_multiscale_space).
- n_eigs :
int
|None
Optional
[int
] (default:None
) if multiscale is True, how much components to retain.
- device : {‘cpu’, ‘gpu’}
Literal
[‘cpu’, ‘gpu’] (default:'cpu'
) Run method on either cpu or on gpu.
- do_PCA
Whether to perform PCA or not.
- n_pcs :
int
(default:50
) Number of PC components.
- seed
Get reproducible results for the GPU implementation.
- copy :
bool
(default:False
) Return a copy instead of writing to adata.
- adata :
- Returns
adata – if copy=True it returns AnnData, else it update field to adata:
- .obsm[‘X_diffusion’]
if multiscale = False, diffusion space.
- .obsm[‘X_multiscale_diffusion’]
if multiscale = True, multiscale diffusion space.
- .uns[‘diffusion’]
dict containing results from Palantir.
- Return type