rnalysis.enrichment.kegg_pathway_graph

rnalysis.enrichment.kegg_pathway_graph(pathway_id: str, marked_genes: Sequence[str] | None, gene_id_type: str | Literal['auto'] | Literal['UniProtKB AC/ID', 'UniParc', 'UniRef50', 'UniRef90', 'UniRef100', 'Gene Name', 'CRC64', 'Ensembl', 'Ensembl Genomes', 'Ensembl Genomes Protein', 'Ensembl Genomes Transcript', 'Ensembl Protein', 'Ensembl Transcript', 'GeneID', 'KEGG', 'PATRIC', 'UCSC', 'WBParaSite', 'WBParaSite Transcript/Protein', 'ArachnoServer', 'Araport', 'CGD', 'ConoServer', 'dictyBase', 'EchoBASE', 'euHCVdb', 'FlyBase', 'GeneCards', 'GeneReviews', 'HGNC', 'LegioList', 'Leproma', 'MaizeGDB', 'MGI', 'MIM', 'neXtProt', 'OpenTargets', 'Orphanet', 'PharmGKB', 'PomBase', 'PseudoCAP', 'RGD', 'SGD', 'TubercuList', 'VEuPathDB', 'VGNC', 'WormBase', 'WormBase Protein', 'WormBase Transcript', 'Xenbase', 'ZFIN', 'eggNOG', 'GeneTree', 'HOGENOM', 'OMA', 'OrthoDB', 'TreeFam', 'CCDS', 'EMBL/GenBank/DDBJ', 'EMBL/GenBank/DDBJ CDS', 'GI number', 'PIR', 'RefSeq Nucleotide', 'RefSeq Protein', 'ChiTaRS', 'GeneWiki', 'GenomeRNAi', 'PHI-base', 'CollecTF', 'BioCyc', 'PlantReactome', 'Reactome', 'UniPathway', 'CPTAC', 'ProteomicsDB'] = 'auto', title: str | Literal['auto'] = 'auto', ylabel: str = '', graph_format: Literal['pdf', 'png', 'svg', 'none'] = 'none', dpi: PositiveInt = 300) → Figure | None

Generate a KEGG Pathway graph.

Parameters:

  • pathway_id (str) – KEGG ID of the pathway to be plotted.

  • marked_genes (sequence of str or None) – a set of genes/genomic features to be highlighted on the pathway graph. The gene ID type of those genes should match the parameter gene_id_type.

  • gene_id_type – the identifier type you want to use when displaying genes in the graph (for example: ‘UniProtKB’, ‘WormBase’, ‘RNACentral’, ‘Entrez Gene ID’). :type gene_id_type: str or ‘auto’ (default=’auto’)

  • title (str or 'auto' (default='auto')) – plot title.

  • ylabel (str (default="$log_2$(Fold Enrichment)")) – plot y-axis label.

  • graph_format ('pdf', 'png', 'svg', or 'none' (default='none')) – if graph_format is not ‘none’, the ontology graph will additonally be generated in the specified file format.

  • dpi (int (default=300)) – resolution of the ontology graph in DPI (dots per inch).