U md+ @sddlmZmZddlZddlZddlmZddl m Z ddl m Z ddlmZddlmZd d lmZd d lmZeed deeeeeeeefee eeedddZdS))OptionalUnionN)AnnData)pyplot)Axes)_utils)doc_show_save_ax)normalize_total) _doc_params)Z show_save_axF)adatan_topshowsaveax gene_symbolslogcKsbddl}ddlm} t|ddd} | | drt| djddj} t| ddd d|} | ddd| fj} n@| djdd} t| ddd d|} | ddd| f} |dkr|j | n |j || }t j | |j |d } |s |d d }tjd |fd\}}|jf| d|dd||d|r@|dtjd||d|dkr^|SdS)u9 Fraction of counts assigned to each gene over all cells. Computes, for each gene, the fraction of counts assigned to that gene within a cell. The `n_top` genes with the highest mean fraction over all cells are plotted as boxplots. This plot is similar to the `scater` package function `plotHighestExprs(type = "highest-expression")`, see `here `__. Quoting from there: *We expect to see the “usual suspects”, i.e., mitochondrial genes, actin, ribosomal protein, MALAT1. A few spike-in transcripts may also be present here, though if all of the spike-ins are in the top 50, it suggests that too much spike-in RNA was added. A large number of pseudo-genes or predicted genes may indicate problems with alignment.* -- Davis McCarthy and Aaron Lun Parameters ---------- adata Annotated data matrix. n_top Number of top {show_save_ax} gene_symbols Key for field in .var that stores gene symbols if you do not want to use .var_names. log Plot x-axis in log scale **kwds Are passed to :func:`~seaborn.boxplot`. Returns ------- If `show==False` a :class:`~matplotlib.axes.Axes`. rN)issparsedF)Z target_sumZinplaceX)Zaxis)indexcolumnsg?g?)Zfigsizehr)dataZorientrZ fliersizez% of total countsrhighest_expr_genes)rr)ZseabornZ scipy.sparserr ZmeanA1npZargsortAZ var_namesvarpdZ DataFrameZ obs_namespltZsubplotsZboxplotZ set_xlabelZ set_xscalerZsavefig_or_show)rrrrrrrkwdsZsnsrZ norm_dictZ mean_percentZtop_idxZcounts_top_genesrheightZfigr'L/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/plotting/_qc.pyrs:0        r)r NNNNF)typingrrnumpyr Zpandasr#ZanndatarZ matplotlibrr$Zmatplotlib.axesrrZ_docsr Zpreprocessing._normalizationr r intboolstrrr'r'r'r(s2