scanpy.pl.rank_genes_groups_violin

scanpy.pl.rank_genes_groups_violin(adata, groups=None, n_genes=20, gene_names=None, gene_symbols=None, use_raw=None, key=None, split=True, scale='width', strip=True, jitter=True, size=1, ax=None, show=None, save=None)

Plot ranking of genes for all tested comparisons.

Parameters:

adata : AnnData

Annotated data matrix.

groups : Optional[Sequence[str]] (default: None)

List of group names.

n_genes : int (default: 20)

Number of genes to show. Is ignored if gene_names is passed.

gene_names : Optional[Iterable[str]] (default: None)

List of genes to plot. Is only useful if interested in a custom gene list, which is not the result of scanpy.tl.rank_genes_groups().

gene_symbols : Optional[str] (default: None)

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

use_raw : Optional[bool] (default: None)

Use raw attribute of adata if present. Defaults to the value that was used in rank_genes_groups().

split : bool (default: True)

Whether to split the violins or not.

scale : str (default: 'width')

See violinplot().

strip : bool (default: True)

Show a strip plot on top of the violin plot.

jitter : Union[int, float, bool] (default: True)

If set to 0, no points are drawn. See stripplot().

size : int (default: 1)

Size of the jitter points.

show : Optional[bool] (default: None)

Show the plot, do not return axis.

save : Optional[bool] (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.