dynamo.tl.vlm_to_adata

dynamo.tl.vlm_to_adata(vlm, n_comps=30, basis='umap', trans_mats=None, cells_ixs=None)[source]

Conversion function from the velocyto world to the dynamo world. Code original from scSLAM-seq repository

Parameters:

vlm (VelocytoLoom Object) – The VelocytoLoom object that will be converted into adata.
n_comps (int (default: 30)) – The number of pc components that will be stored.
basis (str (default: umap)) – The embedding that will be used to store the vlm.ts attribute. Note that velocyto doesn’t usually use umap as embedding although umap as set as default for the convenience of dynamo itself.
trans_mats (None or dict) – A dict of all relevant transition matrices
cell_ixs (list of int) – These are the indices of the subsampled cells

Returns: