cellbender.py
Overview
This module contains helper functions for pipeline_cellbender.py
- cellhub.tasks.cellbender.anndata_from_h5(file: str, analyzed_barcodes_only: bool = True) AnnData
Load an output h5 file into an AnnData object for downstream work.
- Parameters:
file – The h5 file
analyzed_barcodes_only – False to load all barcodes, so that the size of the AnnData object will match the size of the input raw count matrix. True to load a limited set of barcodes: only those analyzed by the algorithm. This allows relevant latent variables to be loaded properly into adata.obs and adata.obsm, rather than adata.uns.
- Returns:
- The anndata object, populated with inferred latent variables
and metadata.
- Return type:
adata
- cellhub.tasks.cellbender.dict_from_h5(file: str) Dict[str, ndarray]
Read in everything from an h5 file and put into a dictionary.