R语言做GO分析及画圈图

主要用到两个包，一个是GO分析的clusterProfiler包，一个是画图用的GOplot包。

R包下载及加载

install.packages("clusterProfiler")
install.packages("org.Hs.eg.db")
install.packages("GOplot")
install.packages("stringr")

library(clusterProfiler)
library(org.Hs.eg.db)
library(GOplot)
library(stringr)

导入前面的差异分析数据

load("GSE54236_deg.Rdata")
deg[1:4,1:4]    #查看一下数据
#           logFC   AveExpr         t      P.Value
#CLEC1B -3.495104  8.500043 -8.506637 1.114997e-14
#CXCL14 -3.441625 10.542112 -7.771404 8.318569e-13
#FCN2   -3.394742 10.373211 -8.619044 5.693455e-15
#EPCAM  -3.373903  8.789720 -7.337014 9.829431e-12
deg = deg[deg$g != "stable",]
gene = rownames(deg)    #拿到差异表达基因名

GO分析

#基因转ID
sig_DP_entrezId = mapIds(x = org.Hs.eg.db,
                         keys = gene,
                         keytype = "SYMBOL",
                         column = "ENTREZID")
#去除NA值
table(is.na(sig_DP_entrezId))
sig_DP_entrezId <- na.omit(sig_DP_entrezId)
#GO分析
go_ALL <- enrichGO(gene = sig_DP_entrezId,
                   OrgDb = org.Hs.eg.db,
                   keyType = "ENTREZID",
                   ont = "ALL",
                   pvalueCutoff = 0.5,
                   qvalueCutoff = 0.5,
                   readable = TRUE)
#将结果转为数据框
go_all <- as.data.frame(go_ALL@result)

GO结果画圈图前数据处理

colnames(go_all)
#[1] "ONTOLOGY"    "ID"          "Description" "GeneRatio"  
#[5] "BgRatio"     "pvalue"      "p.adjust"    "qvalue"     
#[9] "geneID"      "Count"
go_all=go_all[,c(1,2,3,9,7)]    #只需要1,2,3,9,7列的数据
go_all$geneID <- str_replace_all(go_all$geneID,"/",",")     #将geneID列的基因名用逗号替换/
names(go_all)=c("Category","ID","term","Genes","adj_pval")  #重新命名列名
gene=data.frame(ID=gene,logFC=deg$logFC)
circ <- circle_dat(go_all,gene)

画圈图

GOCircle(circ, nsub = 10)
#参数nsub表示需要展示的GO Term数，可自己设置

1.png

#另一种画法
process=head(go_all[,3])
chord <- chord_dat(circ,gene,process)
#png
png(filename = "Chord.png",width = 1000,height = 1000)
GOChord(chord, space = 0.02, gene.order = 'logFC', 
        gene.space = 0.25, gene.size = 5)
dev.off()

2.png

部分代码参考：

https://www.jianshu.com/p/48ac98098760