, 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_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

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 True or a str, 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


Are passed to boxplot().


If show==False a Axes.