occdn.limour.top/source/_posts/clusterprofiler：gson格式初探.md

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title: clusterProfiler：gson格式初探 tags: [] id: '2126' categories:

• - 通路富集 comments: false date: 2022-07-21 06:43:59 ---

更新包

• conda activate clusterprofile
• ~/dev/xray/xray -c ~/etc/xui2.json &
• wget -e "https_proxy=http://127.0.0.1:20809" https://github.com/YuLab-SMU/clusterProfiler/archive/refs/heads/master.zip -O clusterProfiler-master.zip
• wget -e "https_proxy=http://127.0.0.1:20809" https://github.com/YuLab-SMU/DOSE/archive/refs/heads/master.zip -O DOSE-master.zip
• devtools::install_local('DOSE-master.zip')
• devtools::install_local('clusterProfiler-master.zip')

保存gson到本地

• library(clusterProfiler)
• kk <- gson_KEGG('hsa')
• gson::write.gson(kk, file = './KEGG.hsa.gson')

使用本地gson进行KEGG分析

• library(clusterProfiler)
• kk <- gson::read.gson('KEGG.hsa.gson')
• rres <- readRDS('deg.rds')

• rres <- rres[order(rres$log2FoldChange),]

  require(org.Hs.eg.db)
  f_id2name_kk <- function(lc_cgene, keytype="SYMBOL", columns="ENTREZID"){
  res=AnnotationDbi::select(org.Hs.eg.db::org.Hs.eg.db,keys=lc_cgene,columns=columns, keytype=keytype)
  res <- subset(res, !is.na(ENTREZID))
  res$ENTREZID
  }
  require(tidyverse)
  require(enrichplot)
  require(DOSE)
  f_kegg_p <- function(keggr2, n = 15){
  keggr <- subset(keggr2@result, p.adjust < 0.05)
  keggr[['-log(Padj)']] <- -log10(keggr[['p.adjust']])
  keggr[['geneRatio']] <- parse_ratio(keggr[['GeneRatio']])
  keggr$Description <- factor(keggr$Description, 
                                     levels=keggr[order(keggr$geneRatio),]$Description)
  ggplot(head(keggr,n),aes(x=geneRatio,y=Description))+
      geom_point(aes(color=`-log(Padj)`,
               size=`Count`))+
      theme_bw()+
      scale_color_gradient(low="blue1",high="brown1")+
      labs(y=NULL) + 
      theme(axis.text.x=element_text(angle=90,hjust = 1,vjust=0.5, size = 12),
           axis.text.y=element_text(size = 15))
  }
  f_title <- function(gp,title){
  gp + labs(title = title) + theme(plot.title = element_text(hjust = 0.5))
  }
  kegg.d <- enrichKEGG(gene = f_id2name_kk(subset(rres, log2FoldChange < -0.1 & padj < 0.05)$symbol),
    organism = kk,
    universe = f_id2name_kk(rres$symbol),
    pAdjustMethod = "fdr",
    qvalueCutoff =0.05)
  f_kegg_p(kegg.d, n =15) %>% f_title("kegg.d")