KEGG_cnetplot绘制基因—通路图（展示想要的通路）——R

以KEGG富集结果为例

首先进行KEGG富集分析

library(clusterProfiler)
de_ekp <- enricher(gene,
                   TERM2GENE = pathway2gene,
                   TERM2NAME = pathway2name,
                   pvalueCutoff = 1,
                   qvalueCutoff = 1)

1、展示前5个通路

cnetplot(de_ekp, 
         foldChange =foldchange, 
         showCategory = 5,
         node_label = "all", # category | gene | all | none
         colorEdge = TRUE)

foldchange如何获得呢
x数据

在这里插入图片描述

 foldchange = x$log2Fold_change
names(foldchange) <- x$symbol

foldchange


2、展示特定的通路

y <- c("Fatty acid biosynthesis","Fatty acid metabolism","PPAR signaling pathway","Insulin signaling pathway","Fatty acid degradation","Glucagon signaling pathway","Insulin resistance")
# 把想要展示的通路名称赋值给y#
cnetplot(de_ekp, 
         foldChange =foldchange, 
         showCategory = y,
         node_label = "all", # category | gene | all | none
         colorEdge = TRUE)

更改颜色

p1 <- cnetplot(de_ekp, 
          foldChange =log2(foldchange), 
          showCategory = y,
          node_label = "all", # category | gene | all | none
          ##circular = TRUE,#
          colorEdge = TRUE)
          
 p1+scale_color_gradientn(colours = c("green","blue", "red"))

更改颜色资料：
https://support.bioconductor.org/p/p133748/