phlower.tl.trajs_matrix

phlower.tl.trajs_matrix(adata: AnnData, graph_name: str | None = None, evector_name: str | None = None, embedding='umap', eigen_n: int = -1, trajs: str | List[List[int]] = 'knn_trajs', edge_w: List | None = None, iscopy=False, verbose=True)

1. embed the trajectories to be the flows of SC

2. embed the flow to be the harmonics space of the graph

Parameters:

adata: AnnData

AnnData object

graph_name: str

the graph with holes to be used, adata.uns[“graph_basis”] + “_triangulation_circle” by default if None

evector_name: str

the L1 decomposed eigen vectors from the graph_name, adata.uns[“graph_basis”] + “_triangulation_circle_L1Norm_decomp_vector” by default if None

embedding: str

the embedding for visualize the clustering results, “umap” by default

eigen_n: int

the number of eigen vectors to be used, -1 by default, which means all eigen vectors with 0 eigen values

trajs: str or List[List[int]]

the trajectories to be used, “knn_trajs” by default in adata.uns

edge_w: List

the weights of the edges in the graph, None by default, which means all edges have the same weight 1

iscopy: bool

whether to return a copy of adata or not, False by default