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 top genes

Parameters

  • adata (AnnData) – adata input

  • n_top (int, optional) – #top genes to show, by default 30

  • gene_prefix_list (list, optional) – A list of gene name prefix, by default None

  • gene_prefix_only (bool, optional) – whether to show prefix of genes only. It only takes effect if gene prefix list is provided, by default True

  • show (Optional[bool]) – whether to show the results, by default True

  • save_path (str, optional) – path to save the figure, by default None

  • ax (Optional[Axes]) – use an existing ax, by default None

  • gene_annotations (Optional[list], optional) – Annotations for genes, or annotations for gene prefix subsets, by default None

  • gene_annotation_key (str, optional) – gene annotations key in adata.var, by default “use_for_pca”. This option is not available for gene_prefix_list and thus users should pass gene_annotations argument for the prefix list.

  • log (bool, optional) – whether to use log scale, by default False

  • store_key (str, optional) – key for storing expression percent results, by default “highest_frac_genes”

  • v_rotation (float) – rotation of text sticks when the direction is vertical