### R代码来自Vignette Source'Kegggraphapp.rnw'####################################################################################kegggraph”）toygraph <-parsekgml2grapl（toykgml，genesonly = false）toygraph节点（toygraph）############################################################### ###代码块数字2：vistoy ########################################################makEnoderenderattrs < - function（g，label = nodes（g），shape =“椭圆”，fill =“＃e0e0e0”，...）{rv < - list（label = label = label，shape = shape = shape，fill = fill = fill,。。[i]]，numnodes（g））} else {if（length（rv [i]]）！= numnodes（g））stop（“属性向量必须具有与'g'具有nodes的元素一样多的元素。”）}名称（rv [[i]]）<-nodes（g）na [[名称（rv）[[[i]]]] <-rv [[i]} noderenderInfo（g）<-na return（g）} toydrawn <-plotkegggraph（toygraph）toydrawnrefine <-makenoderenderattrs（toydrawn，toydrawn，toydrawn，fill = ifelse = ifelse（nodeType）（nodeType）==“ gene”，“ lightblue”，“橙色”），shape = ifelse（nodeType ==“基因”，“椭圆”，“矩形”））#########################################################################################################＃##代码块编号4：Spiaload ######################################################### if(require(SPIA)) { data(colorectalcancer,package="SPIA") } else { load(system.file("extdata/colorectalcancerSPIA.RData", package="KEGGgraph")) } head(top) ################################################### ### code chunk number 5: spiaTrans ################################################### library(hgu133plus2.db) x <- hgu133plus2ENTREZID top$ENTREZ <- unlist(as.list(x[top$ID])) top <- top[!is.na(top$ENTREZ),] top <- top[!duplicated(top$ENTREZ),] tg1 <- top[top$adj.P.Val < 0.05,] DE_Colorectal <- tg1$logFC names(DE_Colorectal) <- as.vector(tg1$ENTREZ) ALL_Colorectal <- top$ENTREZ ################################################### ### code chunk number 6: remoteRetreval (eval = FALSE) ################################################### ## tmp <- "hsa05210.xml" ## retrieveKGML(pathwayid="05210", organism="hsa", destfile=tmp) ################################################### ### code chunk number 7: spiaPer ################################################### colFile <- system.file("extdata/hsa05210.xml", package="KEGGgraph") g <- parseKGML2Graph(colFile) deKID <- translateGeneID2KEGGID(names(DE_Colorectal)) allKID <- translateGeneID2KEGGID(ALL_Colorectal) isDiffExp <- nodes(g) %in% deKID sprintf("%2.2f%% genes differentially-expressed", mean(isDiffExp)*100) ################################################### ### code chunk number 8: spiaVis ################################################### library(RColorBrewer) library(org.Hs.eg.db) library(RBGL) library(grid) ar <- 20 cols <- rev(colorRampPalette(brewer.pal(6, "RdBu"))(ar)) logfcs <- DE_Colorectal[match(nodes(g), deKID)] names(logfcs) <- nodes(g) logfcs[is.na(logfcs)] <- 0 incol <- round((logfcs+2)*5); incol[incol>ar] <- ar undetected <- !nodes(g) %in% allKID logcol <- cols[incol]; logcol[logfcs==0] <- "darkgrey"; logcol[undetected] <- "yellow" names(logcol) <- names(logfcs) nA <- makeNodeAttrs(g, fillcolor=logcol, label="", width=10, height=1.2) par(mar=c(3,5,0,5), mgp=c(0,0,0)) layout(mat=matrix(c(rep(1,8),2), ncol=1, byrow=TRUE)) plot(g, "dot", nodeAttrs=nA) image(as.matrix(seq(1,ar)), col=cols, yaxt="n", xaxt="n") mtext("down-regulation", side=1, at=0, line=1) mtext("up-regulation", side=1, at=1, line=1) ################################################### ### code chunk number 9: spiaSingleNode ################################################### gDeg <- degree(g) gIsSingle <- gDeg[[1]] + gDeg[[2]] == 0 options(digits=3) gGeneID <- translateKEGGID2GeneID(nodes(g)) gSymbol <- sapply(gGeneID, function(x) mget(x, org.Hs.egSYMBOL, ifnotfound=NA)[[1]]) isUp <- logfcs > 0 isDown <- logfcs < 0 singleUp <- isUp & gIsSingle singleDown <- isDown & gIsSingle ################################################### ### code chunk number 10: spiaSub ################################################### ups <- nodes(g)[logfcs > 0] upNs <- unique(unlist(neighborhood(g, ups, return.self=TRUE))) upSub <- subKEGGgraph(upNs, g) upNeighbor <- nodes(upSub)[sapply(neighborhood(upSub, nodes(upSub)), length)>0] upNeighbor <- setdiff(upNeighbor, nodes(g)[undetected]) upSub <- subKEGGgraph(upNeighbor, upSub) upSubGID <- translateKEGGID2GeneID(nodes(upSub)) upSymbol <- gSymbol[upSubGID] upnA <- makeNodeAttrs(upSub, fillcolor=logcol[nodes(upSub)], label=upSymbol, fixedsize=TRUE, width=10, height=10, font=20) plot(upSub, "dot", nodeAttrs=upnA)