#install.packages("colorspace")
#install.packages("stringi")
#install.packages("ggplot2")

#if (!requireNamespace("BiocManager", quietly = TRUE))
#    install.packages("BiocManager")
#BiocManager::install("DOSE")
#BiocManager::install("clusterProfiler")
#BiocManager::install("enrichplot")


library("clusterProfiler")
library("org.Rn.eg.db")
library("enrichplot")
library("ggplot2")

pvalueFilter=0.05                   #p值过滤条件
qvalueFilter=0.05                   #矫正后的p值过滤条件

setwd("D:\\biowolf\\geoSurvival\\16.GO")            #设置工作目录
rt=read.table("id.txt",sep="\t",header=T,check.names=F)           #读取id.txt文件
rt=rt[is.na(rt[,"entrezID"])==F,]                                 #去除基因id为NA的基因
gene=rt$entrezID
geneFC=rt$logFC
names(geneFC)=gene

colorSel="qvalue"
if(qvalueFilter>0.05){
	colorSel="pvalue"
}

#GO富集分析
kk=enrichGO(gene = gene,OrgDb = org.Hs.eg.db, pvalueCutoff =1, qvalueCutoff = 1, ont="all", readable =T)
GO=as.data.frame(kk)
GO=GO[(GO$pvalue<pvalueFilter & GO$qvalue<qvalueFilter),]
write.table(GO,file="GO.txt",sep="\t",quote=F,row.names = F)                 #保存富集结果
showNum=30
if(nrow(GO)<30){
	showNum=nrow(GO)
}

pdf(file="barplot.pdf",width = 11,height = 7)
barplot(kk, drop = TRUE, showCategory =showNum,color = colorSel)
dev.off()
		
#气泡图
pdf(file="bubble.pdf",width = 11,height = 7)
dotplot(kk,showCategory = showNum, orderBy = "GeneRatio", color = colorSel)
dev.off()