KEGG PATHWAY分析及画图

用david转换成ENTREZID基因

gene<-read.csv(file="id.csv",header = T)
gene_diff<-gene$To#ENTREZID基因

kk.diff <- enrichKEGG(gene         = gene_diff,
                        organism     = 'mmu',
#可以更换物种，这是小鼠的，人类是hsa
                        pvalueCutoff = 0.05)
  head(kk.diff)[,1:6]
  dotplot(kk.diff );ggsave('kk.diff.dotplot.png')#点图

  kegg_diff_dt <- as.data.frame(kk.diff)
  diff_kegg<-kegg_diff_dt[kegg_diff_dt$pvalue<0.05,];diff_kegg$group=-1

对KEGG富集结果可视化

kegg_plot <- function(diff_kegg){
    dat<-diff_kegg
    colnames(dat)
    dat$pvalue = -log10(dat$pvalue)
    dat$pvalue=dat$pvalue*dat$group 
    dat=dat[order(dat$pvalue,decreasing =F),]
    g_kegg<- ggplot(dat, aes(x=reorder(Description,order(pvalue, decreasing =T)), y=pvalue, fill=group)) + 
      geom_bar(stat="identity") + 
      scale_fill_gradient(low="blue",high="red",guide = FALSE) + 
      scale_x_discrete(name ="Pathway names") +
      scale_y_continuous(name ="log10P-value") +
      coord_flip() + theme_bw()+
      theme(text = element_text(size=8),plot.title = element_text(hjust = 0.1))+
      ggtitle("Pathway Enrichment") 
  }
  g_kegg<-kegg_plot(diff_kegg)
  print(g_kegg)
  ggsave(g_kegg,filename = 'kegg_up_down.pdf')

画出来选定某一通路的图形

BiocManager::install("pathview")
  require(pathview)
  geneList<-gene#选定的基因
pathview(gene.data = "genelist", pathway.id = "hsa04110",
                    species="hsa",limit =list(gene=max(abs(geneList)),cpd=1))

画出来选定某一通路的图形，我们的基因集中在该通路出现的基因变成绿色显示在该通路中

hsa04110.pathview.png