scanpy.pl.highest_expr_genes

scanpy.pl.highest_expr_genes(adata, n_top=30, *, layer=None, gene_symbols=None, log=False, show=None, save=None, ax=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 (default: 30)

Number of top

layer str | None (default: None)

Layer from which to pull data.

gene_symbols str | None (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

show bool | None (default: None)

Show the plot, do not return axis.

save 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 Axes | None (default: None)

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

**kwds

Are passed to boxplot().

Returns:

If show==False a Axes.