sccoda.util.cell_composition_data.from_pandas

sccoda.util.cell_composition_data.from_pandas(df, covariate_columns)

Converts a Pandas DataFrame into a compositional analysis data set. The DataFrame must contain one row per sample, columns can be cell types or covariates

Note that all columns that are not specified as covariates are assumed to be cell types.

Usage: data = from_pandas(df, covariate_columns=["cov1", "cov2"])

Parameters

df : DataFrameDataFrame

A pandas DataFrame with each row representing a sample; the columns can be cell counts or covariates

covariate_columns : List[str]List[str]

List of column names that are interpreted as covariates; all other columns will be seen as cell types

Return type

AnnDataAnnData

Returns

• A compositional analysis data set

• data – A compositional analysis data set