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Geo data mining (III) enrichment analysis of go and KEGG using David database
2022-07-07 00:05:00 【Game programming】
First, sort out the previously processed differential gene data , Some gene screenshots are as follows :
open DAVID Website : https://david.ncifcrf.gov/home.jsp
Click on Start Analysis Go to the next page .
In turn, what the arrow refers to , Finally, click Submit .
Click the arrow to start the analysis .
Click on Chart Go to download page
Ctrl+A Select all and copy to a TXT file , And then use excel You can open it .
Open it and you'll find Term There is GO A number of the data itself , Click to sort
This separates , Next, draw a bubble chart
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)# drawing 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()
Similarly, you can also make KEGG Graph , Of course, it needs to be removed PValue Greater than 0.05 Of Term, It's not removed here just for demonstration , Here you can choose what you want to show according to your needs Term.
author : Shengxin kaihuang cattle
Game programming , A game development favorite ~
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