富集分析经常做，之前只知道GO term有从上到下的层次关系，今天才知道KEGG pathway也有类似的分层关系。
起因是我准备更新一下自己的kegg富集结果展示图，之前一直画的这种图，略显朴素了。
正好搜到了这张图，还挺好看的（主要是
配色很清新）
https://doi.org/10.1016/j.phymed.2021.153714
这张图并不难（等有空把代码整理出来发给大家），可是这个kegg pathway annotation我真没见过呀！去官网看了看，能找到，但没法下载
https://www.genome.jp/kegg/pathway.html
在朋友圈求助后，费了很大劲才把这个问题解决。中间好几个小伙伴都很热心地给了我帮助，感谢他们！
以下是我整理的KEGG pathway annotation文件的网盘链接，用到的代码和数据也在里面，想改善一下kegg富集图的朋友可以看看。
链接：https://pan.baidu.com/s/18pwYZGGZSuk2_LGW8_nQFQ
提取码：ihyn
(PS: 觉得有用可以给我本期推送的第1篇推文点个赞呀，谢谢了！)
最终能得到这个表格
整理这个文件的思路如下
- 浏览器打开这个网页(https://www.genome.jp/kegg/pathway.html)，然后查看网页源代码（一般是鼠标右键），就能看到这个：
先不要被它吓到，后面的信息提取都是基于这些字符串
然后复制粘贴到一个文本文件
kegg_html.txt，删掉前188行左右，后17行左右（删掉的这些行明显不含有用信息），得到kegg_html_copy.txt。然后运行我编写的代码
pre.R就能得到最终表格了
library(tidyverse)
tmp1=readLines("kegg_html_copy.txt")
tmp2=c()
for (li in 1:length(tmp1)) {
if(str_detect(tmp1[li],">[0-9]")) {
tmp2=append(tmp2,tmp1[li])
}
}
###
big_anno=""
small_anno=""
final_lines=c()
for (li in 1:length(tmp2)) {
if (str_detect(tmp2[li],">[0-9]\\. ")) {
tmp_anno=str_extract(tmp2[li],">.*<")
tmp_anno=str_split(tmp_anno,"\\. ")[[1]][2]
tmp_anno=str_split(tmp_anno,"<")[[1]][1]
big_anno=tmp_anno
} else if (str_detect(tmp2[li],">[0-9]\\.[0-9]{1,2} ")) {
tmp_anno2=str_extract(tmp2[li],">.*<")
tmp_anno2=str_replace(tmp_anno2,"^>[0-9]\\.[0-9]{1,2} ","")
tmp_anno2=str_split(tmp_anno2,"<")[[1]][1]
small_anno=tmp_anno2
} else if (str_detect(tmp2[li],">[0-9]{5}")){
element1=str_extract(tmp2[li],">[0-9]{5}")
element1=str_split(element1,">")[[1]][2]
if (!str_detect(tmp2[li],"hsa\\+pathogen")) {
element2=str_extract(tmp2[li],"pathway\\/[a-zA-Z]{2,4}[0-9]{5}")
element2=str_split(element2,"\\/")[[1]][2]
element3=str_extract(tmp2[li],"pathway.*?<") #非贪婪匹配
element3=str_extract(element3,">.*<")
element3=str_split(element3,">")[[1]][2]
element3=str_split(element3,"<")[[1]][1]
} else {
element2="organism:hsa+pathogen"
element3=str_extract(tmp2[li],"hsa\\+pathogen.*?<") #非贪婪匹配
element3=str_extract(element3,">.*<")
element3=str_split(element3,">")[[1]][2]
element3=str_split(element3,"<")[[1]][1]
}
tmp_line=paste(as.character(element1),element2,element3,big_anno,small_anno,sep = ";")
final_lines=append(final_lines,tmp_line)
}else{
print(tmp2[li])
}
}
###
final_df=as.data.frame(final_lines)
colnames(final_df)="V1"
final_df=final_df%>%apply(1, function(x){as.data.frame(str_split(x,";")[[1]])})
final_df=as.data.frame(final_df)
final_df=as.data.frame(t(final_df))
rownames(final_df)=NULL
colnames(final_df)=NULL
colnames(final_df)=c("ID","Pathway Identifier","Pathway","big annotion","small annotion")
###
library(xlsx)
write.xlsx(final_df,file = "kegg_info.xlsx",col.names = T,row.names = F)
