go和kegg通路富集分析视频教程和代码分享

go和kegg通路富集分析

go和kegg通路富集分析视频教程

go和kegg富集分析函数构建

go_kegg_enrich

if(!dir.exists( save.dir)){        

dir.create( save.dir,recursive=T) #如果save.dir路径不存在，就创建该路径        

}        

#keytypes( org.Hs.eg.db) #查看org.Hs.eg.db数据库中各种数据类型        

#将gene_symbol转换成entrenzid        

gene.trans

#head( gene.trans)        

#1 GO分析        

All

#head( All,1)        

if( nrow( All)>0){        

All1

#dim( All1)        

all.go.file

all.go.file1

saveRDS(All,file=all.go.file1)        

write.csv( All1,file=all.go.file)        

#save(All,file = 'All.rda')        

#All

#如果要单独绘制BP，CC，MF，把ont="ALL"修改成自己想要的类型即可        

#top.number

for(top.number in show.top.number.list){        

if( top.number

width=12/1.5        

height=10/1.5        

}else{        

width=12*( top.number/20)        

height=10*( top.number/20)        

}        

#2 画图，气泡图        

#2.1 气泡图，显示前n项，标题为“Enrichment GO Up-Gene”        

all.go.dotplot.pdf

all.go.dotplot.png

plot.title

p

#scale_color_gradient(low = "red", high = "blue")+        

#theme_bw()        

ggsave(all.go.dotplot.pdf,plot=p,width = width,height = height)        

ggsave(all.go.dotplot.png,plot=p,width = width,height = height,dpi=300)        

#2.2 柱状图，显示前20项，标题为“Enrichment GO Top20”        

#save.dir

all.go.barplot.pdf

all.go.barplot.png

plot.title

p1

#scale_color_gradient(low = "red", high = "blue")+        

#theme_bw()        

ggsave(all.go.barplot.pdf,plot=p1,width = width,height = height)        

ggsave(all.go.barplot.png,plot=p1,width = width,height = height,dpi=300)        

# 2.3 BP,MF,CC分别分面显示(要加载DOSE包)        

all.go.facet.dotplot.pdf

all.go.facet.dotplot.png

plot.title

p1

theme_bw()        

p1        

ggsave(all.go.facet.dotplot.pdf,p1,width = width,height = height)        

ggsave(all.go.facet.dotplot.png,p1,width = width,height = height,dpi=300)        

}        

#三个单独出图        

id

go.types

#go.type

for(go.type in go.types){        

sub.go

if( nrow( sub.go)>0){        

sub.go.file

write.csv(as.data.frame(sub.go),file=sub.go.file)        

#write.csv(as.data.frame(sub.go),file="target_genes",go.type,"enrich_go_res.csv",sep=",")        

for(top.number in show.top.number.list){        

if( top.number

width=12/1.5        

height=10/1.5        

}else{        

width=12*( top.number/20)        

height=10*( top.number/20)        

}        

plot.title

p10

scale_color_gradient(low = "red", high = "blue")+        

theme_bw()        

sub.go.pdf

sub.go.png

ggsave(sub.go.pdf,p10,width = width,height = height)        

ggsave(sub.go.png,p10,width = width,height = height,dpi=300)        

}        

}else{        

print(paste0("No gene has been enriched in GO ",go.type," enrich analysis"))        

}        

}        

}else{        

print("No gene has been enriched in GO enrich analysis")        

}        

####kegg分析####        

#1KEGG分析        

id

KEGG

if(!is.null(KEGG)){        

if( nrow( KEGG)>0){        

#2 画图，第一种做法，气泡图，设置字体大小        

#3 画图，第二种做法，柱状图        

#4 画图，第三种做法，泡泡图        

#dotplot(color="pvalue",KEGG,showCategory=10,title="Enrichment KEGG Top10")        

kegg.res.file

write.csv(as.data.frame(KEGG),file=kegg.res.file)        

all.kegg.file1

saveRDS( KEGG,file=all.kegg.file1)        

#4.1 调节标题，字体，泡泡大小        

for(top.number in show.top.number.list){        

if( top.number

width=12/1.5        

height=10/1.5        

}else{        

width=12*( top.number/20)        

height=10*( top.number/20)        

}        

plot.title

p2

scale_color_gradient(low = "red", high = "blue")+        

theme_bw()        

kegg.dotplot.pdf

kegg.dotplot.png

ggsave(kegg.dotplot.pdf,p2,width = width,height = height)        

ggsave(kegg.dotplot.png,p2,width = width,height = height,dpi=300)        

}        

}        

}else{        

print("No gene has been enriched in KEGG enrich analysis")        

}        

}

利用构建的go和Kegg函数进行通路富集分析

go.kegg.enrich.analysis=T        

if(go.kegg.enrich.analysis){        

diff.res.file

diff.res

gene.symbol.list

save.name.prefix

show.top.number.list

go_kegg_enrich(gene.symbol.list=gene.symbol.list,save.dir=data.dir,go.org=go.org,kegg.org=kegg.org,save.name.prefix=save.name.prefix,show.top.number.list)        

}