> #install.packages("colorspace")
> #install.packages("stringi")
> #source("http://bioconductor.org/biocLite.R")
> #biocLite("DOSE")
> #biocLite("clusterProfiler")
> #biocLite("pathview")
>
> setwd("C:\\Users\\sdkj\\Desktop\\HYZtcmsp\\13.GO")
> library("clusterProfiler")
Registered S3 method overwritten by 'enrichplot':
method from
fortify.enrichResult DOSE
clusterProfiler v3.14.2 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
> library("org.Hs.eg.db")
> rt=read.table("id.txt",sep="\t",header=T,check.names=F)
> rt=rt[is.na(rt[,"entrezID"])==F,]
>
> cor=rt$logFC
> gene=rt$entrezID
> names(cor)=gene
>
> #GO富集分析
> kk <- enrichGO(gene = gene,OrgDb = org.Hs.eg.db, pvalueCutoff =0.05, qvalueCutoff = 0.05)
> write.table(kk,file="GO.txt",sep="\t",quote=F,row.names = F)
>
> #柱状图
> tiff(file="barplot.tiff",width = 35,height = 20,units ="cm",compression="lzw",bg="white",res=600)
> barplot(kk, drop = TRUE, showCategory =20)
Error in farver::decode_colour(colors, alpha = TRUE, to = "lab", na_value = "transparent") :
参数没有用(na_value = "transparent")
> dev.off()
null device
1
>
> #点图
> tiff(file="dotplot.tiff",width = 35,height = 20,units ="cm",compression="lzw",bg="white",res=600)
> dotplot(kk,showCategory = 20)
Error in farver::decode_colour(colors, alpha = TRUE, to = "lab", na_value = "transparent") :
参数没有用(na_value = "transparent")
> dev.off()
null device
1
>
>
>
>
参数没有用是啥意思？
