# # # R代码从装饰图案的KEGGgraphApp来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:loadtoy # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(KEGGgraph) toyKGML < -执行(“extdata / kgml-ed-toy。xml”,包= " KEGGgraph”) toyGraph <——parseKGML2Graph (toyKGML genesOnly = FALSE) toyGraph节点(toyGraph) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:vistoy # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(Rgraphviz) nodeInfo < - getKEGGnodeData (toyGraph) nodeType < -酸式焦磷酸钠(nodeInfo方法)makeNodeRenderAttrs < -函数(g,标签=节点(g),形状=“椭圆”,填补= " # e0e0e0 ",…){房车< -列表(标签=标签、形状=形状、填充=填补,…)nA < - nodeRenderInfo (g)(我在seq (= rv)){如果(长度(rv[[我]])= = 1){房车[[我]]< -代表(rv[[我]],numNodes (g))其他}{如果(长度(rv[[我]])! = numNodes (g))停止("属性向量必须尽可能多的元素“g”节点。”)}的名字(rv[[我]])< -节点(g) nA[[名称(rv)[[我]]]]< - rv[[我]]}nodeRenderInfo (g) < - nA返回(g)} toyDrawn < - plotKEGGgraph (toyGraph) toyDrawnRefine <——makeNodeRenderAttrs (toyDrawn填补= ifelse (nodeType = =“基因”,“lightblue”、“橙色”),形状= ifelse (nodeType = =“基因”,“椭圆”、“矩形”))# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:vistoyReal # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # renderGraph (toyDrawnRefine) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:spiaLoad # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #如果(要求(SPIA)){数据(colorectalcancer、包=“SPIA”)}{加载其他(执行(“extdata / colorectalcancerSPIA。RData”,包= " KEGGgraph ")}头(上)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:spiaTrans # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(hgu133plus2.db) x < - hgu133plus2ENTREZID顶级美元ENTREZ < - unlist (as.list (x ($ ID]))前< -前[! is.na(顶部ENTREZ美元),]前< -前[!复制(最高ENTREZ美元),]号< -前(前adj.P美元。Val < 0.05,] DE_Colorectal号logFC美元的名字(DE_Colorectal) < - < - as.vector(一号ENTREZ美元)ALL_Colorectal <——顶级美元ENTREZ # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:remoteRetreval # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # tmp <——“hsa05210。xml”retrieveKGML (pathwayid = " 05210 ",有机体=“保险”,destfile = tmp) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:spiaPer # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # colFile < -执行(“extdata / hsa05210。xml”,包= " KEGGgraph”) g < - parseKGML2Graph (colFile) deKID < - translateGeneID2KEGGID(名字(DE_Colorectal)) allKID < - translateGeneID2KEGGID (ALL_Colorectal) isDiffExp < -节点(g) % % deKID sprintf (“% % % 2.2 f基因差异表达”,意味着(isDiffExp) * 100) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:spiaVis # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(RColorBrewer)库(org.Hs.eg.db)图书馆(RBGL)图书馆(网格)ar < - 20关口< -牧师(colorRampPalette(布鲁尔。RdBu)朋友(6)(ar)) logfcs < - DE_Colorectal[匹配(节点(g), deKID)]的名字(logfcs) < -节点(g) logfcs [is.na (logfcs)] < - 0 incol <——圆((logfcs + 2) * 5);incol (incol > ar) < - ar未被发现的<——!节点(g) % % allKID logcol <——关口(incol);logcol (logfcs = = 0) < -“darkgrey”;logcol[被]< -“黄色”名称(logcol) < -名称(logfcs) nA <——makeNodeAttrs (g, fillcolor = logcol标签= ",宽度= 10,身高= 1.2)标准(mar = c (3、5 0 5), mgp = c(0, 0, 0))布局(垫=矩阵(c(代表(1,8),2),ncol = 1, byrow = TRUE))情节(g,“点”,nodeAttrs = nA)图像(as.matrix (seq (ar)),坳=关口,yaxt =“n”, xaxt =“n”)多行文字(“下调”,一边= 1 = 0 = 1行)多行文字(“老年病”,一边= 1 = 1 = 1行)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:spiaSingleNode # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # gDeg <度(g) gIsSingle < - gDeg [[1]] + gDeg[[2]] = = 0选项(数字= 3)gGeneID < - translateKEGGID2GeneID(节点(g)) gSymbol < -酸式焦磷酸钠(gGeneID,函数(x) mget (x, org.Hs。egSYMBOL ifnotfound = NA) [[1]]) isUp < - logfcs > 0 isDown < - logfcs < 0 singleUp < isUp & gIsSingle singleDown <——isDown & gIsSingle # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:spiaSub # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ups < -节点(g) [logfcs > 0] upn < -独特(unlist(社区(g, ups, return.self = TRUE))) upSub < - subKEGGgraph (upn g) upNeighbor < -节点(upSub)(酸式焦磷酸钠(社区(upSub,节点(upSub)),长度)> 0]upNeighbor < - setdiff (upNeighbor,节点(g)[被])upSub < - subKEGGgraph (upNeighbor upSub) upSubGID < - translateKEGGID2GeneID(节点(upSub)) upSymbol < - gSymbol [upSubGID] upnA < - makeNodeAttrs (upSub fillcolor = logcol节点(upSub),标签= upSymbol fixedsize = TRUE,宽度= 10,身高= 10,字体= 20)情节(upSub,“点”,nodeAttrs = upnA)