dynamo.pl.highest_frac_genes

dynamo.pl.highest_frac_genes(adata, n_top=30, gene_prefix_list=None, gene_prefix_only=True, show=True, save_path=None, ax=None, gene_annotations=None, gene_annotation_key='use_for_pca', log=False, store_key='highest_frac_genes', orient='v', figsize=None, layer=None, title=None, v_rotation=35, **kwargs)[source]

Plot the top genes.

Parameters:

  • adata (AnnData) – an AnnData object.

  • n_top (int (default: 30)) – the number of top genes to show. Defaults to 30.

  • gene_prefix_list (Optional[List[str]] (default: None)) – a list of gene name prefix. Defaults to None.

  • gene_prefix_only (bool (default: True)) – whether to show prefix of genes only. It only takes effect if gene prefix is provided. Defaults to True.

  • show (bool (default: True)) – whether to show the plots. Defaults to True.

  • save_path (Optional[str] (default: None)) – the path to save the figure. Defaults to None.

  • ax (Optional[Axes] (default: None)) – the axis on which the graph will be plotted. If None, a new axis would be created. Defaults to None.

  • gene_annotations (Optional[List[str]] (default: None)) – annotations for genes, or annotations for gene prefix subsets. Defaults to None.

  • gene_annotation_key (str (default: 'use_for_pca')) – gene annotations key in adata.var. Defaults to “use_for_pca”.

  • log (bool (default: False)) – whether to use log scale. Defaults to False.

  • store_key (str (default: 'highest_frac_genes')) – the key for storing expression percent results. Defaults to “highest_frac_genes”.

  • orient (Literal['v', 'h'] (default: 'v')) – the orientation of the graph. Can be one of ‘v’ or ‘h’. ‘v’ for genes in x-axis and ‘h’ for genes on y-axis. Defaults to “v”.

  • figsize (Optional[Tuple[float]] (default: None)) – the size of each panel of the figure. Defaults to None.

  • layer (Optional[str] (default: None)) – layer on which the gene percents will be computed. Defaults to None.

  • title (Optional[str] (default: None)) – the title of the figure. Defaults to None.

  • v_rotation (float (default: 35)) – rotation of text sticks when the direction is vertica. Defaults to 35.

Raises:
Return type:

Axes

Returns:

The matplotlib Axes of the figure.