富集分析制作氣泡圖

###自定義作氣泡圖

x<-read.csv(file.choose(),stringsAsFactors = F)

#篩選p<0.05

x<-x[x$PValue<0.05,]

x_go=x[,1:5]

xbp=x_go[grep("BP",x_go$Category),]

xcc=x_go[grep("CC",x_go$Category),]

xmf=x_go[grep("MF",x_go$Category),]

xkegg=x_go[grep("KEGG",x_go$Category),]

xbp$Term=gsub(".*\\~","",xbp$Term)#Biological Process

xcc$Term=gsub(".*\\~","",xcc$Term)#Cell Component

xmf$Term=gsub(".*\\~","",xmf$Term)#Molecular Function

xkegg$Term=gsub(".*\\:","",xkegg$Term)#KEGG pathway

#加載ggplot2

library(ggplot2)

make_GO_bubble<-function(go_data,term_name){

? #選擇top10的數(shù)據(jù)（count）

? GO_DATA=go_data[order(go_data$Count,decreasing = T),]

? GO_DATA=head(GO_DATA,10)

? # 四維數(shù)據(jù)的展示

? p = ggplot(GO_DATA,aes(X.,Term))

? bubble=p+ geom_point(aes(size=Count,color=-log10(PValue)))

? # 自定義漸變顏色

? bubble =bubble+ scale_colour_gradient(low="green",high="red")

? # 改變圖片的樣式（主題）

? pr=bubble + theme_test(base_size = 16,base_rect_size = 1)

? pr=pr+labs(x="Rich factor",y=term_name,title="Enrichment of DEGs")

? return(pr) }?

#BP

make_GO_bubble(xbp,term_name="Biological Process")#HEIGHT 550

make_GO_bubble(xcc,term_name = "Cell Component")

make_GO_bubble(xmf,term_name = "Molecular Function")

make_GO_bubble(xkegg,term_name = "KEGG pathway")