Reading KEGG annotation online:
fail to download KEGG data... Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... 此外: Warning message: In utils::download.file(url, quiet = TRUE, method = method, ...) : URL 'http://rest.kegg.jp/link/hsa/pathway': status was 'Couldn't connect to server'
KEGG=as.data.frame(kk) Error in h(simpleError(msg, call)) : 在为'as.data.frame'函数选择方法时评估'x'参数出了错: 找不到对象'kk' KEGG$geneID=as.character(sapply(KEGG$geneID,function(x)paste(rt$Gene[match(strsplit(x,"/")[[1]],as.character(rt$entrezID))],collapse="/"))) Error in h(simpleError(msg, call)) : 在为'sapply'函数选择方法时评估'X'参数出了错: 找不到对象'KEGG' KEGG=KEGG[(KEGG$pvalue<pvalueFilter & KEGG$qvalue<qvalueFilter),] 错误: 找不到对象'KEGG'
保存富集结果
write.table(KEGG,file="KEGG.txt",sep="\t",quote=F,row.names = F) Error in is.data.frame(x) : 找不到对象'KEGG'
定义显示Term数目
showNum=20 if(nrow(KEGG)<showNum){
- showNum=nrow(KEGG)
- } Error in h(simpleError(msg, call)) : 在为'nrow'函数选择方法时评估'x'参数出了错: 找不到对象'KEGG'
柱状图
pdf(file="barplot.pdf",width = 9,height = 7) barplot(kk, drop = TRUE, showCategory = showNum, color = colorSel) Error in barplot(kk, drop = TRUE, showCategory = showNum, color = colorSel) : 找不到对象'kk' dev.off() null device 1
气泡图
pdf(file="bubble.pdf",width = 9,height = 10) dotplot(kk, showCategory = showNum, orderBy = "GeneRatio",color = colorSel) Error in h(simpleError(msg, call)) : 在为'dotplot'函数选择方法时评估'object'参数出了错: 找不到对象'kk' dev.off() null device 1
绘制通路图
keggId="hsa05163" #选择通路，进行通路图绘制(需要修改) geneFC=rep(1,length(gene)) names(geneFC)=gene pv.out=pathview(gene.data = geneFC, pathway.id = keggId, species = "hsa", out.suffix = "pathview") Info: Downloading xml files for hsa05163, 1/1 pathways.. Warning: Download of hsa05163 xml file failed! This pathway may not exist! Info: Downloading png files for hsa05163, 1/1 pathways.. Warning: Download of hsa05163 png file failed! This pathway may not exist! Warning: Failed to download KEGG xml/png files, hsa05163 skipped! Warning message: In download.file(xml.url, xml.target, quiet = T) : InternetOpenUrl失败:’无法与服务器建立连接'
