R-基因-富集圈图/和弦图

原创于 2024-12-30 13:34:25 发布 · 869 阅读

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看到别人文章里面的GO和KEGG富集分析结果，画的一张图有通路有基因，于是，懒惰的本小卡拉弄了一个R脚本，满足自己的小好胜心！

一、文件准备

GO/KEGG富集分析结果文件，格式如下：

差异表达基因文件，格式如下：

二、R代码

getwd()

rm=list(ls)

getwd()
setwd("D:/Rcicrcleplot")

library(ggplot2)
library(circlize)
library(GOplot)
library(tidyverse)
library(dplyr)

list.files()

go<-read.csv("GO.csv",header=T,sep=",")
View(go)

DEG<-read.csv("DEG.csv",header=T,sep=",")
View(DEG)

go<- go[,c("ID","Count","Description","ONTOLOGY","pvalue","geneID")]
View(go)

pro<-DEG[,c("geneSymbol","log2FoldChange")]
View(pro)

go$GeneList<-gsub("/",",",go$geneID)
View(go)

go<- go[,c("ID","Count","Description","ONTOLOGY","pvalue","GeneList")]
View(go)

pro<-DEG[,c("geneSymbol","log2FoldChange")]
View(pro)

colnames(go)<-c( 'ID','ObservedGeneNum', 'term','category','adj_pval','genes')
View(go)

colnames(pro)<-c("ID","logFC")
View(pro)

#pro <- pro %>% filter(logFC > log2(1.2) | logFC < -log2(1.2))
#View(pro)

circ <- circle_dat(go,pro)
View(circ)
#write.table(circ,file="circ.xls",col.names=T,row.names=T,quote=F,sep="\t")

#head(go)
go <- go[order(go$ObservedGeneNum), ]
View(go)

gop<-go[1:5,]
gop <- go
View(gop)


###展示基因与GO Terms关系的圈图 (GOChord())###

chord <-chord_dat(data = circ, genes = pro,process = gop$term)
#write.table(chord,file="chord.xls",col.names=T,row.names=T,quote=F,sep="\t")

cols<- gop$term

pdf("cicrplot.pdf",width=15,height=16)

#GOChord(data, title, space, gene.order, gene.size,gene.space, nlfc = 1,lfc.col, lfc.min,lfc.max, ribbon.col, border.size, process.label, limit)
#data: 二进制矩阵
#title：标题
#space：基因对应方块之间的距离
#gene.order：基因排列顺序
#gene.size：基因标签大小
#nlfc：logFC 列的数目
#lfc.col：LFC颜色，定义模式：c(color for low values, color for the mid point, color for the highvalues)
#lfc.min：LFC最小值
#lfc.max：LFC最大值
#ribbon.col：向量定义基因与GO Term间条带颜色
#border.size:基因与GO Term间条带边框粗细
#process.label:GO Term 图例文字大小
#limit:c(3, 2)，两个数字；第一个参数筛选基因(保留至少存在于3个GO Term的基因),第二个参数筛选GO Term(保留至少包含2个基因的GO Term )

GOChord(chord,
           space = 0.02,
           gene.order = 'logFC',
           gene.space = 0.25,
           #border.size = NA ,
           gene.size = 5,
           ribbon.col=brewer.pal(5, "Set3"),
           #process.label = 15
           ) +
  guides(size = guide_legend("GO Terms", ncol = 2, byrow = T, 
                             override.aes = list(shape = 22, fill = brewer.pal(5, "Set3"), 
                                                 size = 8)))
dev.off()

###泡图(GOBubble())###
pdf("GOBubbleplot.pdf",width=15,height=16)
GOBubble(circ, labels = 3)
dev.off()

pdf("GOBubble_multipleplot_.pdf",width=15,height=16)
GOBubble(circ, 
         #title = 'Bubble plot', 
         colour =c('orange', 'darkred', 'gold'), 
         display = 'multiple', 
         labels = 3)
dev.off()

### 圈图展示基因富集分析结果(GOCircle())###
pdf("GOCircleplot_.pdf",width=10,height=11)
GOCircle(circ)
dev.off()

###基因与GO Term的热图(GOHeat) ###
#nlfc = 1：颜色对应l
#ogFC nlfc = 0：颜色对应每个基因注释了到了几个GO Term
pdf("GOHeat_plot_.pdf",width=8.5,height=8)
GOHeat(chord, nlfc = 1, fill.col = c('red', 'yellow','green'))
dev.off()


###聚类(GOCluster)###
#GOCluster()调用R内置函数hclust 根据功能分内进行层次聚类。
pdf("GOClusterterm_plot_.pdf",width=11,height=11)
GOCluster(circ, 
          gop$term, 
          clust.by = 'logFC',
          term.width = 2, 
          term.col = brewer.pal(length(gop$term), "Set3"))+
  guides(size = guide_legend("GO Terms", ncol = 2, byrow = T, 
                             override.aes = list(shape = 22, 
                                                 fill = brewer.pal(length(gop$term), "Set3"), 
                                                 size = 8)))
dev.off()