可视化—KEGG富集图中如何展示特定的通路

原创

sheldor没耳朵

发布于 2024-11-01 15:40:31

980

发布于 2024-11-01 15:40:31

文章被收录于专栏：R语言可视化

可视化—KEGG富集图中如何展示特定的通路

kegg富集的结果默认是按照pValue值展示前几条的通路

如

#绘制前10条通路
p1 <- barplot(kk, showCategory=10)

那如何在途中展示特定的通路呢，则需要我们提前对KEGG的结果进行筛选

注：示例数据，无意义

rm(list = ls()) 
load( file =  'step1.Rdata' )

#2.3 pathway----
library(patchwork)
library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(clusterProfiler)
library(ggplot2)
library(stringr)
target_intersect <- c(target_intersect,"LRRK1")
unique(target_intersect)#14

#2.3.1 KEGG----
gene_target_case_entr=
  as.character(na.omit(AnnotationDbi::select
                       (org.Hs.eg.db,keys = target_intersect,
                         columns = 'ENTREZID',keytype = 'SYMBOL')[,2]))
kk <- enrichKEGG(gene= gene_target_case_entr,
                 organism     = 'hsa',
                 #universe     = gene_all,
                 pvalueCutoff = 1,
                 qvalueCutoff =1)
kk <- setReadable(kk,
                   OrgDb = org.Hs.eg.db,
                   keyType = "ENTREZID")
#绘制前10条通路
p1 <- barplot(kk, showCategory=10)

如果我们要展示特定通路，需要提前筛选，如我只关注炎症和免疫反应相关的通路（查资料且保证原始k k@result中有对应通路）。

#显示特定的通路
selected_pathways <- c(
  "B cell receptor signaling pathway",
  "T cell receptor signaling pathway",
  "Fc epsilon RI signaling pathway",
  "PD-L1 expression and PD-1 checkpoint pathway in cancer",
  "Th1 and Th2 cell differentiation",
  "IL-17 signaling pathway",
  "Th17 cell differentiation",
  "MAPK signaling pathway",
  "PI3K-Akt signaling pathway",
  "Ras signaling pathway"
)
kk_filtered <- kk@result %>%
  filter(Description %in% selected_pathways)
## 转换为 enrichResult 对象，以便绘图
kk_filtered <- new("enrichResult", result = kk_filtered)
# 绘制条形图
p1 <- barplot(kk_filtered, showCategory = length(selected_pathways))
ggsave(plot = p1,path = "plot/",
       'Kegg_plot_修.pdf',width = 9,height = 6)

write.csv(kk,file="table/kegg_result.csv",
          quote = F,row.names = F)