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R code for the Graph Lab
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<h1 class="documentFirstHeading">R code for the Graph Lab</h1>
<div class="documentDescription">This will be the actual code we use in the Lab.</div>
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<p>##############################</p><div id="mb_0">#####################<br /><br />### chunk number 1: load<br /><br />###################################################<br /><br />library('graph')<br /><br />library('Rgraphviz')<br /><br />library('RBGL')<br /><br />library('GO')<br /><br />library('GOstats')<br /><br />library('ALL')<br /><br />library('hgu95av2')<br /><br />library('genefilter')<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 2: 2<br /><br />###################################################<br /><br />myNodes <- c('s', 'p', 'q', 'r')<br /><br />myEdges <- list(s=list(edges=c('p', 'q')),<br /><br />         p=list(edges=c('p', 'q')),<br /><br />         q=list(edges=c('p', 'r')),<br /><br />         r=list(edges=c('s')))<br /><br />g <- new('graphNEL', nodes=myNodes, edgeL=myEdges, edgemode='directed')<br /><br />g<br /><br />plot(g)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 3: 3<br /><br />###################################################<br /><br />nodes(g)<br /><br />edges(g)<br /><br />degree(g)<br /><br />plot(g)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 4: grManip<br /><br />###################################################<br /><br />g1 = addNode("t", g)<br /><br />g2 = removeNode("p", g)<br /><br />g3 = addEdge("t", "s", g1, weights=pi/2)<br /><br />plot(g3)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 5: imca<br /><br />###################################################<br /><br />data("integrinMediatedCellAdhesion")<br /><br />IMCAGraph<br /><br />nodes(IMCAGraph)<br /><br />edges(IMCAGraph)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 6: exploreimca<br /><br />###################################################<br /><br />class(IMCAGraph)<br /><br />adj(IMCAGraph, "SOS")<br /><br />s = acc(IMCAGraph, "SOS")<br /><br />s<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 7: setop<br /><br />###################################################<br /><br />V <- letters[1:4]<br /><br />set.seed(4713)<br /><br />ug1 <- randomGraph(V, 1, .55)<br /><br />ug2 <- randomGraph(V, 1, .55)<br /><br />plot(ug1)<br /><br />plot(ug2)<br /><br />plot(complement(ug1))<br /><br />plot(intersection(ug1,ug2))<br /><br />plot(union(ug1,ug2))<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 8: graphrep<br /><br />###################################################<br /><br />ft = cbind(1:4, c(2,3,1,4))<br /><br />ft<br /><br />m = ftM2adjM(ft)<br /><br />g = ftM2graphNEL(ft)<br /><br />plot(g)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 9: gxl eval=FALSE<br /><br />###################################################<br /><br />## edit(file=system.file("GXL", "kmstEx.gxl", package="graph"))<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 10: rg<br /><br />###################################################<br /><br />re  = randomEGraph(paste(1:100), edges=50)<br /><br />plot(re, "neato")<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 11: cc<br /><br />###################################################<br /><br />cc = connComp(re)<br /><br />cc[1:5]<br /><br />table(listLen(cc))<br /><br />wh = which.max(listLen(cc))<br /><br />sg = subGraph(cc[[wh]], re)<br /><br />plot(sg, "neato")<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 12: igg<br /><br />###################################################<br /><br />get("GO:0003700", GOTERM)<br /><br />tfg = GOGraph("GO:0003700", GOMFPARENTS)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 13:<br /><br />###################################################<br /><br />plot(tfg)<br /><br />get("GO:0003677", GOTERM)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 14: nda<br /><br />###################################################<br /><br />nda = makeNodeAttrs(re)<br /><br />nda<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 15: colors<br /><br />###################################################<br /><br />colors = rainbow(length(cc))<br /><br />ord   = order(listLen(cc))<br /><br />for(i in seq(along=ord))<br /><br />  nda$fillcolor[cc[[ord[i]]]] = colors[i]<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 16: la<br /><br />###################################################<br /><br />la = agopen(re,  nodeAttrs=nda, layoutType="neato", name="whatever")<br /><br />la<br /><br />plot(la)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 17: la2<br /><br />###################################################<br /><br />nda$shape[cc[[4]]]="box"<br /><br />la2 = agopen(re,  nodeAttrs=nda, layoutType="neato", name="whatever")<br /><br />plot(la2)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 18:<br /><br />###################################################<br /><br />class(la)<br /><br />slotNames(la)<br /><br />AgEdge(la)<br /><br />slotNames(AgEdge(la)[[1]])<br /><br />AgEdge(la)[[1]]@color<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 19: all<br /><br />###################################################<br /><br />data(ALL)<br /><br />s1 = grep("^B", as.character(ALL$BT))<br /><br />s2 = which(as.character(ALL$mol) %in% c("BCR/ABL","NEG"))<br /><br />eset = ALL[, intersect(s1, s2)]<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 20: iqr<br /><br />###################################################<br /><br />n = nrow(pData(eset))<br /><br />q25 = rowQ(exprs(eset), n*0.25)<br /><br />q75 = rowQ(exprs(eset), n*0.75)<br /><br />iqr = q75-q25<br /><br />sel = (iqr>=median(iqr))<br /><br />eset = eset[sel, ]<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 21: tt<br /><br />###################################################<br /><br />tt = rowttests(eset, "mol")<br /><br />hist(tt$p.value, 200, col="orange")<br /><br />diffps =  geneNames(eset)[order(tt$p.value)[1:100]]<br /><br />diffps<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 22:<br /><br />###################################################<br /><br />diffll = unlist(mget(diffps, hgu95av2LOCUSID))<br /><br />diffll<br /><br />diffll = as.character(unique(diffll))<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 23: hyperg<br /><br />###################################################<br /><br />gGhyp = GOHyperG(diffll)<br /><br />hist(gGhyp$pv)<br /><br />goCats = names(which(gGhyp$pv<0.01))<br /><br /> mget(goCats, GOTERM)<br /><br /><br /><br /><br /><br />###################################################<br /><br />### chunk number 24: indGoG<br /><br />###################################################<br /><br />gGO = makeGOGraph(diffll, "MF")<br /><br />gGO<br /><br />natt = makeNodeAttrs(gGO, shape="ellipse", label=substr(nodes(gGO), 7, 10))<br /><br />natt$fillcolor[goCats]='red'<br /><br />lgGO = agopen(gGO, recipEdges="distinct", layoutType="dot", nodeAttrs=natt, name="")<br /><br />plot(lgGO)</div>
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