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

Returns:

adata : anndata.AnnData 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.