结合clusterProfiler进行GO富集分析可视化

org.Hs.eg.db进行基因id转换

clusterProfiler进行GO可视化

#GO可视化

BiocManager::install("clusterProfiler")BiocManager::install("org.Hs.eg.db")
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("org.Hs.eg.db",force = TRUE)
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("clusterProfiler",force = TRUE)



library(org.Hs.eg.db)
library(clusterProfiler)
load("Desktop/go_genename.rda") ##加载数据

原始数据gene_list

#根据自己数据来
gene_list = c("MTLL3","MTLL14")

转换id的两种方法：

#org.Hs.eg.db：
ensembls <- mapIds(org.Hs.eg.db, keys = m6a_sym, keytype = "SYMBOL", column="ENSEMBL")
#一次性转换到ENSEMBL ID,ENTREZ ID和UNIPROT ID
AnnotationDbi::select(org.Hs.eg.db, keys=m6a_sym,keytype="SYMBOL", columns = c("ENSEMBL","ENTREZID","UNIPROT"))
#clusterProfiler：
s2ens = bitr(m6a_sym, fromType="SYMBOL", toType="ENSEMBL", OrgDb="org.Hs.eg.db")
#一次性转换多种id：
bitr(m6a_sym, fromType="SYMBOL", toType=c("ENSEMBL","ENTREZID"), OrgDb="org.Hs.eg.db")

怎么知道哪些数据格式可以进行转换：

keytypes(org.Hs.eg.db)    
columns(org.Hs.eg.db)

运行代码可得结果（即以下都可进行转换）

 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT" 
 [5] "ENSEMBLTRANS" "ENTREZID"     "ENZYME"       "EVIDENCE"    
 [9] "EVIDENCEALL"  "GENENAME"     "GENETYPE"     "GO"          
[13] "GOALL"        "IPI"          "MAP"          "OMIM"        
[17] "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
[21] "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"      
[25] "UCSCKG"       "UNIPROT"   

mapIds(org.Hs.eg.db, keys=数据, “数据格式”, “想转换的格式”)

gene1 <-  mapIds(org.Hs.eg.db, keys=gene_list, "SYMBOL", "ENSEMBL") #转化id形式   

all <- enrichGO(gene   = gene_list,    
                OrgDb  = org.Hs.eg.db,
                keyType = "SYMBOL",
                ont   = "ALL"  ,    ##同时展示mf，bp和cc
                pAdjustMethod = "BH",    
                pvalueCutoff  = 0.01,    
                qvalueCutoff  = 0.05)

barplot(all,showCategory=30)

分子功能（Molecular Function，MF ）
细胞组分（Cellular Component ，CC）
生物过程（Biological Process ，BP）

#仅展示bp
BP <- enrichGO(   gene   = gene,    
                  OrgDb  = org.Hs.eg.db,    
                  ont   = "BP"  ,    
                  pAdjustMethod = "BH",    
                  pvalueCutoff  = 0.01,    
                  qvalueCutoff  = 0.05) 

barplot(BP, showCategory=30)
#点图
dotplot(all,showCategory=30)