kegg在线链接图的颜色设置 2021-07-08

转载，留待以后学习。
这是生信菜鸟团成员的帖子，发现可以自动注释，真是大好，作为生信初学者，无疑是利器，还可以有代码可改！
只剩赞了！
原文链接放在最后，尊重作者原创！
一般来说， 有了kegg的ID，就可以直接去官网查看具体的通路图片，但是需要把差异基因给标注上去，就有点麻烦了，我以前做过类似的工作，结果没有做笔记，这次相当于重新造了个轮子，好惨！

简单的KEGG图片，看下面的url：

http://www.genome.jp/kegg-bin/show_pathway?hsa03040

http://www.genome.jp/kegg-bin/show_pathway?hsa05168

可以看出来只需要变化KEGG的ID即可。

如果要做下面的这个，上调基因用红色表示，下调基因用绿色表示：

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clipboard

需要重新理解kegg的API规则，比如：http://www.kegg.jp/kegg/docs/weblink.html

我就造出了下面的links：

http://www.genome.jp/kegg-bin/show_pathway?map=hsa04115&multi_query=CDKN1A+red%2Cblue%0DSESN3+red%2Cblue%0DIGFBP3+blue%2Cred%0DFAS+red%2Cblue%0DCD82+red%2Cblue%0DGADD45B+blue%2Cred%0DSERPINB5+red%2Cblue%0DZMAT3+blue%2Cred%0DCCNB3+red%2Cblue%0D

http://www.genome.jp/kegg-bin/show_pathway?map=hsa04151&multi_query=CDKN1A+red%2Cblue%0DLAMC3+red%2Cblue%0DCOL1A2+blue%2Cred%0DCREB1+blue%2Cred%0DEGF+red%2Cblue%0DFGFR3+blue%2Cred%0DGHR+red%2Cblue%0DGNG11+red%2Cblue%0DITGA2+red%2Cblue%0DITGA3+red%2Cblue%0DITGAV+red%2Cblue%0DLAMB3+red%2Cblue%0DMYC+blue%2Cred%0DPCK2+blue%2Cred%0DPPP2R5C+blue%2Cred%0DLPAR5+blue%2Cred%0DGNB4+blue%2Cred%0DSGK1+blue%2Cred%0DCREB3L2+blue%2Cred%0DTEK+red%2Cblue%0DTHBS2+blue%2Cred%0DPDGFD+blue%2Cred%0DOSMR+red%2Cblue%0D

当然，肯定不是手动的啦！！！

代码很简单

this_keggID 就是 04115 等等的KEGG的ID，数字格式的哦！

this_kegg_has_geneID <- kegg2GeneID_list[[this_keggID]] ## 拿到这个KEGG的所有基因

this_kegg_has_geneSymbol <- unique(geneAnno(this_kegg_has_geneID)$symbol) ## 把基因的entrez ID转换为gene 的symbol ，其中geneAnno是我自定义的！

跟我们的显著上下调基因取交集，其中diff_gene_list是以symbol为标记的

this_kegg_has_geneSymbol_diff <- intersect(this_kegg_has_geneSymbol,diff_gene_list)

UP GENE: DHX8+red%2Cblue%0D ##自己定义调色规则

DOWN GENE:DHX8+blue%2Cred%0D

color = ifelse(vcx15_DEG[this_kegg_has_geneSymbol_diff,]$logFC >0 ,'red%2Cblue%0D','blue%2Cred%0D')

根据交集的基因来拼接调色字符串咯

kegg_suffix <- paste0(paste(this_kegg_has_geneSymbol_diff,color,sep='+'),collapse = '')

再把link给拼起来。

href=paste0("http://www.genome.jp/kegg-bin/show_pathway?map=hsa",

this_keggID,"&multi_query=", kegg_suffix)

整个过程做成一个循环就好啦！！

我开发的R包有集成这个功能：https://github.com/jmzeng1314/humanid

https://github.com/jmzeng1314/humanid/blob/master/R/add_kegg_up_down_link.R
http://www.bio-info-trainee.com/2061.html