U Åmœddã@s dZdZdZdZdZdZdZdS)z9Shared docstrings for preprocessing function parameters. z³layer If provided, use `adata.layers[layer]` for expression values instead of `adata.X`. use_raw If True, use `adata.raw.X` for expression values instead of `adata.X`.aXqc_vars Keys for boolean columns of `.var` which identify variables you could want to control for (e.g. "ERCC" or "mito"). percent_top Which proportions of top genes to cover. If empty or `None` don't calculate. Values are considered 1-indexed, `percent_top=[50]` finds cumulative proportion to the 50th most expressed gene.z\expr_type Name of kind of values in X. var_type The kind of thing the variables are.uÅObservation level metrics include: `total_{var_type}_by_{expr_type}` E.g. "total_genes_by_counts". Number of genes with positive counts in a cell. `total_{expr_type}` E.g. "total_counts". Total number of counts for a cell. `pct_{expr_type}_in_top_{n}_{var_type}` – for `n` in `percent_top` E.g. "pct_counts_in_top_50_genes". Cumulative percentage of counts for 50 most expressed genes in a cell. `total_{expr_type}_{qc_var}` – for `qc_var` in `qc_vars` E.g. "total_counts_mito". Total number of counts for variabes in `qc_vars`. `pct_{expr_type}_{qc_var}` – for `qc_var` in `qc_vars` E.g. "pct_counts_mito". Proportion of total counts for a cell which are mitochondrial.aVariable level metrics include: `total_{expr_type}` E.g. "total_counts". Sum of counts for a gene. `n_genes_by_{expr_type}` E.g. "n_genes_by_counts". The number of genes with at least 1 count in a cell. Calculated for all cells. `mean_{expr_type}` E.g. "mean_counts". Mean expression over all cells. `n_cells_by_{expr_type}` E.g. "n_cells_by_counts". Number of cells this expression is measured in. `pct_dropout_by_{expr_type}` E.g. "pct_dropout_by_counts". Percentage of cells this feature does not appear in.z adata Annotated data matrix.N)Ú__doc__Z doc_expr_repsZdoc_obs_qc_argsZdoc_qc_metric_namingZdoc_obs_qc_returnsZdoc_var_qc_returnsZdoc_adata_basic©rrúS/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/preprocessing/_docs.pyÚs