直接上操作吧
##先下载一个注释数据库
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("org.Mm.eg.db")
library(clusterProfiler)
library(DOSE)
library(org.Mm.eg.db)
library(stringr)
##筛选数据
deseq2.sig <- subset(res, padj < 0.05 & abs(log2FoldChange) > 1)
##BP（Biological Process）, CC（Cellular Component）两个角度定义
ego_cc<-enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Mm.eg.db,
keyType = 'ENSEMBL',
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.01,
qvalueCutoff = 0.05)
ego_bp<-enrichGO(gene = gene.df$ENSEMBL,
OrgDb = org.Mm.eg.db,
keyType = 'ENSEMBL',
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.01,
qvalueCutoff = 0.05)
然后就可以画图了，我们这里用ego_bp来画
barplot(ego_bp,showCategory = 18,title="The GO_BP enrichment analysis of all DEGs ")+
scale_size(range=c(2, 12))+
scale_x_discrete(labels=function(ego_bp) str_wrap(ego_bp,width = 25))
目前就先写到GO吧。
匆匆学习终究还是只得皮毛，权做日后复习只用，希望日后继续把这个坑填完
