larry._datasets._anndata_configuration

Module Contents

Classes

ExpressionMatrix	Container for parsing the expression matrix.
AnnDataConfiguration	Construct AnnData from constituent components.

Functions

_read_format_df(path, **kwargs)

larry._datasets._anndata_configuration._read_format_df(path, **kwargs)

class larry._datasets._anndata_configuration.ExpressionMatrix(mtx_path: str)

Bases: larry._utils.AutoParseBase

Container for parsing the expression matrix.

property npz_path: pathlib.Path

property npz_exists: bool

read_mtx() → None

save_mtx_as_npz() → None

__call__() → scipy.sparse.csr_matrix

Load the expression matrix.

None

X

type: scipy.sparse.csr_matrix

Given a path to a .mtx file, initializes the ExpressionMatrix class. Looks for the .npz file. If it’s not there, the .mtx file is parsed and saved as .npz.

class larry._datasets._anndata_configuration.AnnDataConfiguration(X_path, obs_path, var_path, X_clone_path, silent=False)

Bases: larry._utils.AutoParseBase

Construct AnnData from constituent components.

property X: scipy.sparse.csr_matrix

returns expression matrix

property var: pandas.DataFrame

returns var pd.DataFrame

property obs: pandas.DataFrame

returns obs pd.DataFrame

property X_clone: scipy.sparse.csr_matrix

returns cell x clonal barcode matrix

property adata

returns formatted AnnData object