dynamo.pp.highest_frac_genes

dynamo.pp.highest_frac_genes(adata, store_key='highest_frac_genes', n_top=30, gene_prefix_list=None, gene_prefix_only=False, layer=None)[source]

Compute top genes df and store results in adata.uns

Parameters:

  • adata (AnnData) – an AnnData object

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

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

  • gene_prefix_list (Optional[List[str]] (default: None)) – a list of gene name prefixes used for gathering/calculating expression percents from genes with these prefixes. Defaults to None.

  • gene_prefix_only (bool (default: False)) – whether to calculate percentages for gene groups with the specified prefixes only. It only takes effect if gene prefix list is provided. Defaults to False.

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

Return type:

AnnData

Returns:

An updated adata with top genes df stored in adata.uns