KEGG/General Relation Construction (Post-KEGG Parsing)

pdb.construct_kegg_relations

Constructs Gene-Gene and Compound-Compound relationships from an initial Gene-Compound bipartite DataFrame. Relations are based on shared partners, and the shared partners (evidence) are aggregated and counted.

Parameter	Type	Default	Description
gene_compound_df	pd.DataFrame		DataFrame with gene and compound columns.
gene_col	str	"symbol"	Column name for genes in the input DataFrame.
compound_col	str	"compound"	Column name for compounds in the input DataFrame.
output_gene_col	str	"gene"	Base name for gene columns in the output DataFrames (gene1,gene2).
output_compound_col	str	"compound"	Base name for compound columns in the output DataFrames (compound1,compound2).

Returns

Tuple[pd.DataFrame,pd.DataFrame]: A tuple containing:

1. gene_relation_df: Gene-Gene relations (columns: ’gene1’, ’gene2’, ’shared_compounds’, ’shared_compound_count’).

2. compound_relation_df: Compound-Compound relations (columns: ’compound1’, ’compound2’, ’shared_genes’, ’shared_gene_count’).

Usage

# Assuming kegg_gc_df has 'kegg_gene_id' and 'kegg_compound_id'
kegg_gg_df, kegg_cc_df = pdb.construct_kegg_relations(
    gene_compound_df=kegg_gc_df,
    gene_col="kegg_gene_id",
    compound_col="kegg_compound_id",
    output_gene_col="kegg_gene",
    output_compound_col="kegg_compound",
)