dotools_py.get.pcts_cells

Contents

dotools_py.get.pcts_cells#

dotools_py.get.pcts_cells(adata, group_by, features=None, min_expr=0.0)[source]#

Calculate the percentage of cells that express a feature.

Parameters:
adata

Annotated data matrix.

group_by str | list

Column in obs to group by. Several columns can be provided.

features str | list (default: None)

Features to use for the calculation. If set to None, all features will be used.

min_expr float (default: 0.0)

Minimum value to use for the estimation of percentages.

Return type:

DataFrame

Returns:

Returns a DataFrame with the percentage of cells expressing a feature in each group.

Example

>>> import dotools_py as do
>>> adata = do.dt.example_10x_processed()
>>> df = do.get.pcts_cells(adata, group_by=["condition", "annotation"])
>>> df.head(5)
        genes  disease_B_cells  ...  healthy_T_cells  healthy_pDC
0  ATP2A1-AS1             0.00  ...             0.01         0.00
1      STK17A             0.57  ...             0.49         0.17
2    C19orf18             0.00  ...             0.00         0.00
3        TPP2             0.03  ...             0.18         0.17
4       MFSD1             0.03  ...             0.06         0.50
[5 rows x 11 columns]
Contents