scanpy.pl.highest_expr_genes
- scanpy.pl.highest_expr_genes(adata, n_top=30, show=None, save=None, ax=None, gene_symbols=None, log=False, **kwds)
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_topgenes with the highest mean fraction over all cells are plotted as boxplots.This plot is similar to the
scaterpackage functionplotHighestExprs(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 :
AnnData Annotated data matrix.
- n_top :
int(default:30) Number of top
- show :
Optional[bool] (default:None) Show the plot, do not return axis.
- save :
Union[str,bool,None] (default:None) If
Trueor astr, save the figure. A string is appended to the default filename. Infer the filetype if ending on {'.pdf','.png','.svg'}.- ax :
Optional[Axes] (default:None) A matplotlib axes object. Only works if plotting a single component.
- gene_symbols :
Optional[str] (default:None) Key for field in .var that stores gene symbols if you do not want to use .var_names.
- log :
bool(default:False) Plot x-axis in log scale
- **kwds
Are passed to
boxplot().
- adata :
- Returns:
: If
show==FalseaAxes.