cellink.DonorData

class cellink.DonorData(*, G, C, donor_id='donor_id', var_dims_to_sync=None, uns={})

Store and manage donor-related data with single-cell readouts.

This class allows donor-level, especially genetic, analysis with single-cell datasets. It holds AnnData objects for donor-level/genetic (G) and single-cell (C) data

G(AnnData)

Type:

Donor-level AnnData

C(AnnData)

Type:

Cell-level AnnData

donor_id(str)

Type:

Key for donor information in C.obs

Returns:

DonorData object

Attributes table

C
G
shape

Methods table

aggregate(*[, key_added, layer, obs, obsm, ...])	Aggregate single-cell data to donor-level.
copy()
prep_repr()	String representation of DonorData showing side-by-side dd.G and dd.C views.
sel(*[, G_obs, G_var, C_obs, C_var])
write_dd(path, dd[, fmt])	Write the DonorData object to the specified file paths for both gene expression data (G) and cell-type data (C).
write_h5_dd(path)	Write the DonorData object to the specified file path.
write_zarr_dd(path)	Write the DonorData object to the specified file paths for both gene expression data (G) and cell-type data (C).

Attributes

DonorData.C

DonorData.G

DonorData.shape

Methods

DonorData.aggregate(*, key_added=None, layer=None, obs=None, obsm=None, filter_key=None, filter_value=None, add_to_obs=False, func='mean', sync_var=False, verbose=False)

Aggregate single-cell data to donor-level.

Return type:

None

If neither layer, obsm, or obs is provided, adata.X is aggregated. Args:

key_added:

The key in gdata to store the aggregated data.

layer:

The layer in adata to aggregate. Defaults to None.

obs:

The key in adata.obs to aggregate. Defaults to None.

obsm:

The key in adata.obsm to aggregate. Defaults to None.

filter_key:

The key in adata.obs to filter by. Defaults to None.

filter_value:

The value in adata.obs[filter_key] to filter by. Defaults to None.

add_to_obs:

Whether to add the aggregated data to adata.obs. Defaults to False.

func:

The aggregation function to use. Defaults to “mean”.

sync_var:

Whether to set the variable dimensions of the aggregated data to sync with the variable dimensions of the single-cell data. Defaults to False.

verbose:

Whether to print verbose output. Defaults to False.

DonorData.copy()

Return type:

DonorData

DonorData.prep_repr()

String representation of DonorData showing side-by-side dd.G and dd.C views.

Return type:

str

DonorData.sel(*, G_obs=slice(None, None, None), G_var=slice(None, None, None), C_obs=slice(None, None, None), C_var=slice(None, None, None))

DonorData.write_dd(path, dd, fmt=None)

Write the DonorData object to the specified file paths for both gene expression data (G) and cell-type data (C).

Parameters:

path (str | Path) – Path where the donor-data object should be saved.

Return type:

None

Example

write_dd(‘path/to/donor_data.dd.h5’)

DonorData.write_h5_dd(path)

Write the DonorData object to the specified file path.

Parameters:

path (str | Path) – Path where the donor-data object should be saved.

Return type:

None

Example

write_dd(‘path/to/donor_data.dd.h5’)

DonorData.write_zarr_dd(path)

Write the DonorData object to the specified file paths for both gene expression data (G) and cell-type data (C).

Parameters:

path (str | Path) – Path where the donor-data object should be saved.

Return type:

None

Example

write_dd(‘path/to/donor_data.dd.zarr’)