环境加载
注意这里面一些参数现在我还没有完全运行好,因此需要注意。
# 清空变量
remove(list = ls())
# 加载所需R包
library(clusterProfiler)
library(ggplot2)
加载GSEA结果,以便用于后续可视化
load(file = "data/gsea_result.Rda")
气泡图
########## 气泡图:dotplot ##########
tiff(file="figures/GSEA_GO_dotplot.tiff",
width = 35,height = 22,units ="cm",
compression="lzw",bg="white",res=300)
dotplot(gsego, showCategory=30) + ggtitle("dotplot for GSEA")
dev.off()
dotplot(gsekk, showCategory=30)
dotplot(gsegmt, showCategory=30)
网络图
########## 网络图:cnetplot ##########
tiff(file="figures/GSEA_KEGG_cnetplot.tiff",
width = 35,height = 22,units ="cm",
compression="lzw",bg="white",res=300)
cnetplot(gsekk, categorySize="pvalue", foldChange=geneList)
dev.off()
cnetplot(gsekk, foldChange=geneList)
cnetplot(gsekk, foldChange=geneList, circular = TRUE