pegasus.infer_path

pegasus.infer_path(data, cluster, clust_id, path_name, k=10)[source]

Inference on path of a cluster.

Parameters

  • data (anndata.AnnData) – Annotated data matrix with rows for cells and columns for genes.

  • cluster (str) – Cluster name. Must exist in data.obs.

  • clust_id – Cluster label. Must be a value of data.obs[cluster].

  • path_name (str) – Key name of the resulting path information.

  • k (int, optional, default: 10) – Number of nearest neighbors on Diffusion Map coordinates used in path reference.

Returns

  • None

  • Update data.obs –

    • data.obs[path_name]: The inferred path information on Diffusion Map about a specific cluster.

Examples

>>> pg.infer_path(adata, cluster = 'leiden_labels', clust_id = '1', path_name = 'leiden_1_path')