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GEO数据挖掘(三)使用DAVID数据库进行GO、KEGG富集分析
2022-07-06 16:33:00 【游戏编程】
首先整理好前面已经处理好的差异基因数据,部分基因截图如下:
打开DAVID网站: https://david.ncifcrf.gov/home.jsp
点击Start Analysis进入下一页面。
依次真好箭头所指内容,最后点击提交。
点击箭头处开始分析。
点击Chart进入下载页面
Ctrl+A进行全选再复制到一个TXT文件,然后用excel就可以打开了。
打开后会发现Term这一列前面有GO数据自己的一个编号,点击分列
这样就分开了,接下来画一个气泡图
rm(list = ls())options(stringsAsFactors = F)library(ggplot2)data=read.csv("./go_bp.csv")data$GeneRatio <- data$Count / data$List.Totaldata <- data[order(-data$PValue),]data$pathway <- factor(data$Term,levels=data$Term)#画图p = ggplot(data,aes(GeneRatio,pathway))p=p + geom_point()+theme(axis.text.x = element_text(colour="black",size=1)) p=p + geom_point(aes(size=Count))pbubble = p+ geom_point(aes(color=PValue,size=Count))pr = pbubble+scale_color_gradient(low="red",high = "green")pr = pr+labs(color=expression(PValue),size="Count", x="GeneRatio",y="")pr + theme_bw()
同理也可以做出KEGG的图,当然这里需要去除掉PValue大于0.05的Term,这里只作演示就没有去掉了,这里可以根据自己需要去选择自己想要展示的Term。
作者:生信开荒牛
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