scFates.tl.subset_tree

scFates.tl.subset_tree(adata, root_milestone=None, milestones=None, mode='extract', t_min=None, t_max=None, copy=False)

Subset the fitted tree.

if pseudotime parameter used, cutoff tree by removing cells/nodes after or before defined pseudotime.

Parameters:

adata AnnData

Annotated data matrix.

root_milestone Optional[str] (default: None)

tip defining progenitor branch.

milestones Optional[Iterable] (default: None)

tips defining the progenies branches.

mode Literal['extract', 'substract', 'pseudotime'] (default: 'extract')

whether to substract or extract the mentionned path.

copy bool (default: False)

Return a copy instead of writing to adata.

Returns:

adata : anndata.AnnData subsetted dataset if copy=True it returns or else subsets these fields to adata:

.uns[‘graph’][‘B’]

subsetted adjacency matrix of the principal points.

.uns[‘graph’][‘R’]

subsetted updated soft assignment of cells to principal point in representation space.

.uns[‘graph’][‘F’]

subsetted coordinates of principal points in representation space.

.obs[‘old_milestones’]

previous milestones from initial tree.