5a4260be766333d81bddbb0fa5fd591fc78bd763,scanpy/get.py,,obs_df,#,70

Before Change

            var_bool = adata.raw.var.index.isin(var_names)
            print(var_names, var_symbol)
        else:
            var_bool = adata.var.index.isin(var_names)
        matrix = X[:, var_bool]
        from scipy.sparse import issparse
        if issparse(matrix):
            matrix = matrix.toarray()

After Change

        if use_raw:
            var_idx = adata.raw.var_names.get_indexer(var_names)
        else:
            var_idx = adata.var_names.get_indexer(var_names)

        // for backed AnnData is important that the indices are ordered
        var_order = np.argsort(var_idx)
        matrix = X[:, var_idx[var_order]]
        from scipy.sparse import issparse

        if issparse(matrix):
            matrix = matrix.toarray()
        df = df.join(
            pd.DataFrame(
                matrix, columns=np.array(var_symbol)[var_order], index=adata.obs.index
            )
        )

Instances