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) – The VelocytoLoom object that will be converted into adata.
n_comps (
int) – The number of pc components that will be stored. Defaults to 30.basis (
str) – 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. Defaults to “umap”.trans_mats (
Optional[dict]) – A dict of all relevant transition matrices. Defaults to None.cells_ixs (
Optional[List[int]]) – These are the indices of the subsampled cells. Defaults to None.
- Return type:
- Returns:
The updated AnnData object.