Merge pathway name and pathway ID from KEGG database

 If an organism is listed in KEGG database, one can easily get a list of its pathways and map a list of genes to the pathways (see here for an example about how to do it in R/bioconductor).

However, the pathway mapping result only provides the pathway IDs and not pathway names. To merge pathway IDs with pathway names, we only need to add  one more column of pathway names for each pathway ID listed in the same row of the mapping result dataframe. The R code below provides an example.

my_organism.gene_pathway <- mapGeneToPathway(organism) # map each gene to pathway ID.
my_organism.pathway_id_name <- mapPathwayToName(organism) # get the pathway name for each pathway ID.

# adding pathway names to mapped pathway IDs.
for (gene in row.names(my_orgranism.gene_pathway)) { 
  pathway_id <- my_orgranism.gene_pathway[gene, 'pathway_id']
  pathway_id <- strsplit(pathway_id, ";")[[1]]
  
  if (length(pathway_id) == 1) {        # if a gene maps to a single pathway
    pathway_name <- my_orgranism.pathway_id_name[pathway_id, "pathway_name"]
    my_orgranism.gene_pathway[gene,"pathway_name"] = pathway_name
  } else {                              # if a gene mapes to multiple pathways
    for (a_id in pathway_id) {
      if (is.null(my_orgranism.gene_pathway[gene, "pathway_name"])) {
        my_orgranism.gene_pathway[gene, "pathway_name"] = my_orgranism.pathway_id_name[a_id, "pathway_name"]
      } else {
        name <- my_orgranism.gene_pathway[gene, "pathway_name"]
        if (is.na(name)) {
          name <- my_orgranism.pathway_id_name[a_id, "pathway_name"]
        } else {
          name <- paste(name, my_orgranism.pathway_id_name[a_id, "pathway_name"], sep=";")
        }
        my_orgranism.gene_pathway[gene, "pathway_name"] <- name
      }
    }
  }
}
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