scanpy.pl.rank_genes_groups

scanpy.pl.rank_genes_groups(adata, groups=None, n_genes=20, gene_symbols=None, key='rank_genes_groups', fontsize=8, ncols=4, sharey=True, show=None, save=None, ax=None, **kwds)

Plot ranking of genes.

Parameters:

adata : AnnData: Annotated data matrix.
groups : Union[str, Sequence[str], None] (default: None): The groups for which to show the gene ranking.
gene_symbols : Optional[str] (default: None): Key for field in .var that stores gene symbols if you do not want to use .var_names.
n_genes : int (default: 20): Number of genes to show.
fontsize : int (default: 8): Fontsize for gene names.
ncols : int (default: 4): Number of panels shown per row.
sharey : bool (default: True): Controls if the y-axis of each panels should be shared. But passing sharey=False, each panel has its own y-axis range.
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.

Examples

import scanpy as sc
adata = sc.datasets.pbmc68k_reduced()
sc.pl.rank_genes_groups(adata)

../_images/scanpy-pl-rank_genes_groups-1.png

Plot top 10 genes (default 20 genes)

sc.pl.rank_genes_groups(adata, n_genes=10)

../_images/scanpy-pl-rank_genes_groups-2.png