cpd.data 指的药物分子的名称向量。 Pathway.id指的是在KEGG中的ID。 kegg.native默认是TRUE输出完整pathway的png格式文件,反之输出仅是输入的基因列表的pdf文件。 Map.null默认是TRUE,当使用FALSE时其pdf的文件图像会更漂亮 Split.group 主要是在kegg.native为FALSE的时候会起到一定的作用,主要是将在同一个反应的...
p <- pathview(gene.data = gse16873.d[, 1], cpd.data = sim.cpd.data, pathway.id ="00640", species = "hsa", out.suffix = "gse16873.cpd", keys.align = "y", kegg.native = T, key.pos = "topright") 我们还生成了相同pathway和数据的Graphviz视图。Graphviz视图更好地显示了层次结构。
cpd_name) match.df <- rbind(match.df,match.ver) } if(length(hsa_compound)==0){ match.df <- rbind(match.df,c(hsa_path[i,"pathID"],path_name,"","")) } } rownames(match.df) <- match.df[,1] colnames(match.df) <- c("Pathway_ID","Pathway_Name","Compound_ID","...
p<-pathview(gene.data=gse16873.d[,1],cpd.data=sim.cpd.data,pathway.id="00640",species="hsa",out.suffix="gse16873.cpd",keys.align="y",kegg.native=F,key.pos="bottomright",sign.pos="topright",cpd.lab.offset=-0.8)
示例,查询hsa:10458和ece:Z5100两个基因对应的 ncbi protein id http://rest.kegg.jp/conv/ncbi-proteinid/hsa:10458+ece:Z5100 代码语言:javascript 代码运行次数:0 运行 AI代码解释 hsa:10458ncbi-proteinid:NP_059345ece:Z5100ncbi-proteinid:AAG58814 ...
例: 检索编号为C01290的compound:http://rest./get/cpd:C01290 检索人类编号为05130的pathway图:http://rest./get/hsa05130/image 5. Conv: 把KEGG的标识符转化为其他标识符 使用方法: 例: 把将KEGGID 转化为NCBI Protein ID:http://rest./conv/ncbi-proteinid/hsa:10458 ece:Z5100 ...
可以提供1个药物的ID, 也可以一次提供多个,多个ID 用+连接 示例: 查询和D005664这种药物存在相互作用的记录 http://rest./ddi/D00564 dr:D00564 cpd:C00304 P unclassified dr:D00564 cpd:C01946 P unclassified dr:D00564 cpd:C04931 P unclassified dr:D00564 cpd:C05849 P unclassified ...
pathway.id = "00640", species = "hsa", out.suffix = "gse16873.cpd", keys.align = "y", kegg.native = T, key.pos = "topright") keys.align = "y"控制color bar对齐方式,key.pos = "topright"则是对应color bar在图上的位置(主要有bottomleft,bottomright,topleft以及topright) ...
Usage:bitr(geneID,fromType,toType,OrgDb,drop=TRUE)Arguments geneID input gene id fromType input idtypetoType output idtypeOrgDb annotation db drop drop NA or not # example:>x<-c("GPX3","GLRX","LBP","CRYAB","DEFB1","HCLS1","SOD2","HSPA2","ORM1","IGFBP1","PTHLH","GPC3","...