GeneraPipe:

create_pathway_maps = function(results, chip_type, paths, annotation, pheno_kegg){

  topall_res = results@topall_res
  eset       = results@eset
  #volc_all   = results@volc_all
  index_case = results@index_case
  index_ctrl = results@index_ctrl
  hgnc_symbols = annotation@hgnc_symbols
  hgnc_names = annotation@hgnc_names
  keggdata = pheno_kegg$kegg
  
  package_path = paths@package_path
  pathway_maps_path = paths@pathway_maps_path

  if (! dir.exists(pathway_maps_path)){
    dir.create(pathway_maps_path)
  } 

  #if (chip_type %in% c("hgu133plus2")){
  #  hgnc_symbols = as.character(unlist(BiocGenerics::mget(rownames(volc_all), hgu133plus2.db::hgu133plus2SYMBOL)))
  
  #} else if ( chip_type %in% c("hgu133a")){
  #  hgnc_symbols = as.character(unlist(BiocGenerics::mget(rownames(volc_all), hgu133a.db::hgu133aSYMBOL)))
  
  #} else if ( chip_type %in% c("pd.hugene.2.0.st", "pd.huex.1.0.st.v2")){
  #  if ((! ("HGNC_symb" %in% colnames(topall_res))) | (length(topall_res$HGNC_symb) == 0)){
  #    print("Pathway map creation error: topall_res$HGNC_symb does no exist")
  #    quit()
  #  }
  #  hgnc_symbols = stringr::str_trim(unlist(lapply(volc_all$geneassignment, FUN = GeneraPipe:::split_fun, 2)))
  #  hgnc_names   = stringr::str_trim(unlist(lapply(volc_all$geneassignment, FUN = GeneraPipe:::split_fun, 3)))

  #} else{ 
    # note: check if this works for affy 
  #  hgnc_symbols = stringr::str_trim(unlist(lapply(fData(eset)$geneassignment, FUN = GeneraPipe:::split_fun, 2)))
  #  hgnc_names   = stringr::str_trim(unlist(lapply(fData(eset)$geneassignment, FUN = GeneraPipe:::split_fun, 3)))  
  #}

  ensembl     = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  entrez_ids  = biomaRt::getBM(attributes = c("entrezgene", "hgnc_symbol"), values = unique(hgnc_symbols), filters = "hgnc_symbol", mart = ensembl)
  hgnc_map    = match(hgnc_symbols, entrez_ids$hgnc_symbol, nomatch = 0)
  entrez      = rep("", length(hgnc_symbols))
  entrez[which(hgnc_map != 0)] = entrez_ids$entrezgene[hgnc_map]
  entrez[is.na(entrez)] = ""

  exprs_case = round(rowMeans(exprs(eset)[, index_case]), 2 )
  exprs_ctrl = round(rowMeans(exprs(eset)[, index_ctrl]), 2 )
  dif_exp    = round(exprs_case - exprs_ctrl, 2)

  res_all_path = data.frame(
    "logFC"  = dif_exp,
    "HGNC"   = hgnc_symbols,
    "entrez" = entrez
  )

  setwd(pathway_maps_path)
  Kegg_id = as.character(keggdata$Kegg_id)

  ent = res_all_path$entrez
  ent = ent[ent != ""]
  exp_dat = res_all_path$logFC[res_all_path$entrez != ""]
  names(exp_dat) = res_all_path$entrez[res_all_path$entrez != ""]

  kegg = BiocGenerics::mget(as.character(ent), KEGG.db::KEGGEXTID2PATHID, ifnotfound = list(NA))

  library("pathview")
  for (id in Kegg_id){
    pathview::pathview(gene.data = exp_dat, pathway.id = id, kegg.native = TRUE, limit = max(abs(exp_dat)))
  }

  system("rm *.xml")
  system("ls | grep -v 'pathview.png$' | xargs rm")

  setwd(package_path)
}