可以看到,在新版的clusterProfiler包中,是已经包含了KEGG通路的分类信息的: category:为level A,总共有7大类 subcategory:为level B,为7大类下面的更加细分一点的类别 ID:为level C,为第三大类别,也即KEGG Pathway数据库中最详细的一层,就是通路本身。 现在绘图吧: 代码语言:javascript 代码运行次数:0 复制 Clou...
category:为level A,总共有7大类 subcategory:为level B,为7大类下面的更加细分一点的类别 ID:为level C,为第三大类别,也即KEGG Pathway数据库中最详细的一层,就是通路本身。 现在绘图吧: # 选取每个 category 类别中的top5通路进行绘图 library(dplyr) dat_top5 <- dat %>% group_by(category) %>% s...
RichFactor = Count / as.numeric(sub("/\\d+", "", BgRatio))) #计算Fold Enrichment（富集倍数...
(Enrichment_KEGG2@result$subcategory))) head(Enrichment_KEGG2@result[,1:3]) # category subcategory ID #hsa04060 Environmental Information Processing Signaling molecules and interaction hsa04060 #hsa04061 Environmental Information Processing Signaling molecules and interaction hsa04061 #hsa05323 Human ...
showCategory=20) p2 #使用ggplot2包做个性化调整; #设置x轴范围,避免点的溢出绘图区; p3<-p2+scale_x_continuous(limits = c(0.025, 0.1), breaks= c(0.025,0.05,0.075, 0.10), label= c("0.025","0.05","0.075","0.10")) p3 #geneid转换: ...
showCategory=20) p2 #使用ggplot2包做个性化调整; #设置x轴范围,避免点的溢出绘图区; p3<-p2+scale_x_continuous(limits = c(0.025, 0.1), breaks= c(0.025,0.05,0.075, 0.10), label= c("0.025","0.05","0.075","0.10")) p3 #geneid转换: ...
KEGG物种信息及缩写汇总 我们经常做KEGG分析时,需要根据物种缩写去搜索相应的数据库,本文根据官方的列表进行分享,方便检索:
if( nrow( sub.go)>0){ sub.go.file write.csv(as.data.frame(sub.go),file=sub.go.file) #write.csv(as.data.frame(sub.go),file="target_genes",go.type,"enrich_go_res.csv",sep=",") for(top.number in show.top.number.list){ ...
GO_all <- enrichGO(gene = gene_list_for_GO_KEGG$SYMBOL,ont = 'All' , keyType = 'SYMBOL', OrgDb = 'org.Hs.eg.db', pvalueCutoff = 0.05) dotplot(GO_all, title = 'Top10 GO terms of each sub-class', showCategory = 10, color = 'p.adjust', split='ONTOLOGY')+ facet_grid(...
Tapping a row in the table view either pushes the subcategories of that category onto the navigation stack if the row represents a subcategory, or it toggles the enabled/disabled state of an organism if the row represents an organism. The set of enabled organisms is then posted as a ...