###R code for the enrichment analysis of differential gene

library(clusterProfiler)
library(enrichplot)
library(org.Mm.eg.db)
library(org.Hs.eg.db)

#GO and KEGG enrichment analysis
########main parameters: 
#pvalueCutoff: Adjusted pvalue cutoff on enrichment tests to report.
#qvalueCutoff: Qvalue cutoff on enrichment tests to report as significant.
#setReadable: Mapping ENTREZID to gene Symbol
#DEGs: differentially expressed genes
#resultdir: output path
#GO_TERM2GENE: Mapping relationship between go_term and gene saved in Rdata format.
########
orgDb = c('org.Hs.eg.db','org.Mm.eg.db')
enrich_GO_plot = function(DEGs,studyid,GO_TERM2GENE,orgDb){
  go_result <- clusterProfiler::enricher(DEGs,TERM2GENE = GO_TERM2GENE,pvalueCutoff = 1,qvalueCutoff = 1)
  go_result = clusterProfiler::setReadable(x,orgDb,keyType="ENTREZID")	
  GOenrich_result = go_result@result
  write_tsv(GOenrich_result,paste0(resultdir,studyid,'/',studyid,"_GO.tsv"))
}

########main parameters: 
#pvalueCutoff: Adjusted pvalue cutoff on enrichment tests to report.
#qvalueCutoff: Qvalue cutoff on enrichment tests to report as significant.
#KEGG_TERM2GENE: Mapping relationship between KEGG_term and gene saved in Rdata format.
#setReadable: Mapping ENTREZID to gene Symbol
########
enrich_KEGG_plot = function(DEGs,studyid,KEGG_TERM2GENE,orgDb){
  kegg_result <- clusterProfiler::enricher(DEGs,TERM2GENE = KEGG_TERM2GENE,pvalueCutoff =1,qvalueCutoff = 1)
  kegg_result = clusterProfiler::setReadable(x,orgDb,keyType="ENTREZID")
  KEGGenrich_result = kegg_result@result
  write_tsv(KEGGenrich_result,paste0(resultdir,studyid,'/',studyid,"_KEGG.tsv"))
}