读取gene symbol
library(clusterProfiler)
library(org.Hs.eg.db)
input <- read.table("gene.csv",sep = ",",header = T)
把symbol转换为ENTREZID
genetransform <- bitr(input$target,
fromType = "SYMBOL",
toType = c("ENSEMBL","ENTREZID"),
OrgDb =org.Hs.eg.db )
#注意：此处物种是人类
GO富集分析
Go <- enrichGO(gene = genetransform$ENTREZID,
OrgDb = org.Hs.eg.db,
pvalueCutoff =0.05,
qvalueCutoff =0.05,
readable = TRUE)
head(Go)
将GO富集结果写出到文件
write.table(Go,file="GO RESULT.txt",sep="\t",
quote=F,row.names = F)
#把结果保存为R数据。
save(Go,file ="Go result.Rda" )
###################################################################
绘制柱状图
library(ggplot2)
library(org.Hs.eg.db)
library(clusterProfiler)
library(cowplot)
画图
barplot(Go,showCategory=20,color="pvalue")
导出图
tiff(file="Go image.tiff",width=35,height = 22,units = "cm",
compression = "lzw",bg="white",res=300)
barplot(Go,showCategory=20,color="pvalue")
dev.off()
####################################################################
绘制网络图
library(ggplot2)
library(org.Hs.eg.db)
library(clusterProfiler)
library(cowplot)
install.packages("ggnewscale")
library(ggnewscale)
cnetplot(Go,circular=T,colorEdge=T)
