2018年SCI论文--整合GEO数据挖掘完整复现 七 ：DAVID在线工具进行KEGG富集分析

论文地址

DAVID官网

KEGG富集分析和GO富集分析方法一致，具体步骤见我上篇文章DAVID在线工具进行GO富集分析，这里主要展示可视化结果

获得KEGG富集分析结果

1.输入文件为所有差异表达基因列表
2.选择GO富集分析结果时，我们点击“Pathways (1 selected)”下拉选项，选择“KEGG_PATHWAY”选项，最后保存为"kegg_pathway.txt"文件

气泡图

setwd("./3.DAVID_GO_KEGG/KEGG")
rt = read.table(file = 'kegg_pathway.txt',sep = '\t',header = T,quote = '')
keggSig = rt[rt$PValue < 0.05,]
library(tidyr)
keggSig = separate(keggSig, Term, sep = ":",
                 into = c("ID", "Term"))

library(ggplot2)
ggplot(keggSig,aes(x=Fold.Enrichment,y=Term)) + 
  geom_point(aes(size=Count,color=-1*log10(PValue)))+
  scale_colour_gradient(low="green",high="red")+
  labs(
    color=expression(-log[10](P.value)),
    size="Gene number",
    x="Fold enrichment"
    # y="Pathway name",
    # title="Pathway enrichment")
  )+
  theme_bw()+
  theme(
    axis.text.y = element_text(size = rel(1.3)),
    axis.title.x = element_text(size=rel(1.3)),
    axis.title.y = element_blank()
  )
ggsave('plot.pdf',width = 7,height = 4)

cytoscape软件绘制代谢通路网络图

软件下载地址，配置环境为java8，软件会自动下载安装java8,如果装了java9需要卸载后再安装，cytoscape教学视频

准备输入文件

network data

library(tidyr)
  separate_keggSig = separate_rows(keggSig,Genes)
  network_data = separate_keggSig[,c('ID','Genes')]
  colnames(network_data)[2] = 'Name'
  write.table(network_data,
              file = 'network_data.txt',
              sep = '\t',
              quote = F,
              row.names = F,
              col.names = T)
              

table data

uniGene = unique(network_data$Name)
  allSign = read.table(file = 'allSign.xls',sep = '\t',header = T,quote = '')
  pathway_gene = allSign[match(uniGene,allSign$Name),]
  pathway_gene$status = ifelse(pathway_gene$logFC > 0,'up','down')
  
  df = data.frame(Name = keggSig[,2],status = rep('id',nrow(keggSig)))
  table_data = rbind(df,pathway_gene[,c(1,3)])
  write.table(table_data,
              file = 'table_data.txt',
              sep = '\t',
              quote = F,
              row.names = F,
              col.names = T)

输入network文件

输入table文件

默认设置就好

设置风格、颜色

手动调整、保存图片

这个比较花时间，适合边听歌边画，还挺有意思的，哈哈

下面就是成品了，还是挺难看的，果然没有艺术细胞，一般图片保存为pdf格式，也可以保存为cys文件，方便再次在cytoscape中打开

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