scFates.tl.slide_cells¶
- scFates.tl.slide_cells(adata, root_milestone, milestones, win=50, mapping=True, copy=False, ext=False)¶
Assign cells in a probabilistic manner to non-intersecting windows along pseudotime.
- Parameters
- adata :
AnnData Annotated data matrix.
- root_milestone
tip defining progenitor branch.
- milestones
tips defining the progenies branches.
- win :
int(default:50) number of cell per local pseudotime window.
- mapping :
bool(default:True) project cells onto tree pseudotime in a probabilistic manner.
- copy :
bool(default:False) Return a copy instead of writing to adata.
- ext :
bool(default:False) Output the list externally instead of writting to anndata
- adata :
- Returns
adata – if copy=True it returns subsetted or else subset (keeping only significant features) and add fields to adata:
- .uns[‘root_milestone->milestoneA<>milestoneB’][‘cell_freq’]
List of np.array containing probability assignment of cells on non intersecting windows.
- Return type