sccoda.util.cell_composition_data.from_scanpy¶
-
sccoda.util.cell_composition_data.
from_scanpy
(adata, cell_type_identifier, sample_identifier, covariate_key=None, covariate_df=None)¶ Creates a compositional analysis dataset from a single anndata object, as it is produced by e.g. scanpy.
The anndata object needs to have a column in adata.obs that contains the cell type assignment, and one column that specifies the grouping into samples. Covariates can either be specified via a key in adata.uns, or as a separate DataFrame.
NOTE: The order of samples in the returned dataset is determined by the first occurence of cells from each sample in
adata
- Parameters
- adata :
AnnData
AnnData
list of scanpy data sets
- cell_type_identifier :
str
str
column name in adata.obs that specifies the cell types
- sample_identifier :
str
str
column name in adata.obs that specifies the sample
- covariate_key :
str
,None
Optional
[str
] (default:None
) key for adata.uns, where covariate values are stored
- covariate_df :
DataFrame
,None
Optional
[DataFrame
] (default:None
) DataFrame with covariates
- adata :
- Return type
- Returns
A compositional analysis data set
data – A compositional analysis data set