scanpy.pl.highest_expr_genes

scanpy.pl.highest_expr_genes(adata, n_top=30, show=None, save=None, ax=None, gene_symbols=None, **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

Parameters
adata : AnnData

Annotated data matrix.

n_top : int, optional (default:30)

Number of top

show

Show the plot, do not return axis.

save

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

A matplotlib axes object. Only works if plotting a single component.

gene_symbols : str, optional (default:None)

Key for field in .var that stores gene symbols if you do not want to use .var_names.

**kwds : keyword arguments

Are passed to seaborn.boxplot.

Returns

If show==False a Axes.