## ----label='Set server port', eval=TRUE--------------------------------------- library(RedeR) rdp <- RedPort() ## ----label='Main call', eval=FALSE-------------------------------------------- # calld(rdp) ## ----label='Add graph (not included)', eval=TRUE, include=FALSE--------------- library(igraph) g1 <- graph.lattice(c(5,5,5)) addGraph( rdp, g1, layout.kamada.kawai(g1) ) ## ----label='Add graph', eval=FALSE, results='hide'---------------------------- # library (igraph) # g1 <- graph.lattice(c(5,5,5)) # addGraph( rdp, g1, layout.kamada.kawai(g1) ) ## ----label='Get graph', eval=TRUE, results='hide'----------------------------- g2 <- getGraph(rdp) resetd(rdp) ## ----label='Build subgraphs', eval=TRUE, results='hide'----------------------- g3 <- barabasi.game(10) g4 <- barabasi.game(10) V(g3)$name<-paste("sn",1:10,sep="") V(g4)$name<-paste("sm",1:10,sep="") addGraph(rdp, g3, isNest =TRUE, gcoord=c(25,25), gscale=50) addGraph(rdp, g4, isNest =TRUE, gcoord=c(75,75), gscale=50) ## ----label='Get subgraph', eval=TRUE, results='hide'-------------------------- selectNodes(rdp,"N0") g5 <- getGraph(rdp, status= "selected") resetd(rdp) ## ----label='Build scale-free graph and send to the app', eval=TRUE, results='hide'---- g6 <- barabasi.game(500) addGraph(rdp, g6, gzoom=20) ## ----label='Start relax', eval=TRUE, results='hide'--------------------------- relax(rdp,p2=400,p5=30,ps=T) ## ----label='Workflow 1: get a dataframe and an interactome', eval=TRUE, results='hide'---- data(ER.limma) data(hs.inter) dt <- ER.limma gi <- hs.inter ## ----label='Workflow 1: extract a subgraph and set attributes to RedeR', eval=TRUE, results='hide'---- gt3 <- subg(g=gi, dat=dt[dt$degenes.t3!=0,], refcol=1) gt3 <- att.setv(g=gt3, from="Symbol", to="nodeAlias") gt3 <- att.setv(g=gt3, from="logFC.t3", to="nodeColor", breaks=seq(-2,2,0.4), pal=2) ## ----label='Workflow 1: extract another subgraph and set attributes to RedeR', eval=TRUE, results='hide'---- gt6 <- subg(g=gi, dat=dt[dt$degenes.t6!=0,], refcol=1) gt6 <- att.setv(g=gt6, from="Symbol", to="nodeAlias") gt6 <- att.setv(g=gt6, from="logFC.t6", to="nodeColor", breaks=seq(-2,2,0.4), pal=2) ## ----label='=Workflow 1: extract another subgraph and set attributes to RedeR', eval=TRUE, results='hide'---- gt12 <- subg(g=gi, dat=dt[dt$degenes.t12!=0,], refcol=1) gt12 <- att.setv(g=gt12, from="Symbol", to="nodeAlias") gt12 <- att.setv(g=gt12, from="logFC.t12", to="nodeColor", breaks=seq(-2,2,0.4), pal=2) ## ----label='=Workflow 1: customize subgraph names', eval=TRUE, results='hide'---- gt3$nestAlias <- "3h" gt6$nestAlias <- "6h" gt12$nestAlias <- "12h" ## ----label='Workflow 1: add subgraphs to the app', eval=TRUE, results='hide'---- N0 <- addGraph(rdp, gt3, gcoord=c(10,25), gscale=20, isNest=TRUE, theme='tm1', gzoom=30) N1 <- addGraph(rdp, gt6, gcoord=c(20,70), gscale=50, isNest=TRUE, theme='tm1', gzoom=30) N2 <- addGraph(rdp, gt12, gcoord=c(70,55), gscale=80, isNest=TRUE, theme='tm1', gzoom=30) ## ----label='Workflow 1: nest subgraphs', eval=TRUE, results='hide'------------ N3 <- nestNodes(rdp, nodes=V(gt3)$name, parent=N1, theme='tm2') N4 <- nestNodes(rdp, nodes=V(gt6)$name, parent=N2, theme='tm2') nestNodes(rdp, nodes=V(gt3)$name, parent=N4, theme='tm3') ## ----label='Workflow 1: assign edges to containers', eval=TRUE, results='hide'---- mergeOutEdges(rdp) ## ----label='Workflow 1: relax the network', eval=TRUE, results='hide'--------- relax(rdp,50,400) ## ----label='Workflow 1: add a color legend (other types are available)', eval=TRUE, results='hide'---- scl <- gt3$legNodeColor$scale leg <- gt3$legNodeColor$legend addLegend.color(rdp, colvec=scl, labvec=leg, title="node color (logFC)") ## ----label='Workflow 1: select a gene', eval=TRUE, results='hide'------------- selectNodes(rdp,"RET") ## ----label='Workflow 1: reset graph', eval=TRUE, results='hide'--------------- resetd(rdp) ## ----label='get a dataframe and an igraph object', eval=TRUE, results='hide'---- data(ER.deg) dt <- ER.deg$dat sg <- ER.deg$ceg ## ----label='Workflow 2: map the dataframe to the graph', eval=TRUE, results='hide'---- sg <- att.mapv(sg, dat=dt, refcol=1) ## ----label='Workflow 2: set attributes to RedeR', eval=TRUE, results='hide'---- sg <- att.setv(sg, from="Symbol", to="nodeAlias") sg <- att.setv(sg, from="logFC.t3", to="nodeColor", breaks=seq(-1,1,0.2), pal=2) sg <- att.setv(sg, from="ERbdist", to="nodeSize", nquant=10, isrev=TRUE, xlim=c(5,40,1)) ## ----label='Workflow 2: add graph to the app', eval=TRUE, results='hide'------ addGraph(rdp,sg) ## ----label='Workflow 2: compute hierarchical clustering', eval=TRUE, results='hide'---- hc <- hclust(dist(get.adjacency(sg, attr="weight"))) ## ----label='Workflow 2: map the hclust object onto the network', eval=TRUE, results='hide'---- nestID <- nesthc(rdp,hc, cutlevel=3, nmemb=5, cex=0.3, labels=V(sg)$nodeAlias) ## ----label='Workflow 2: assign edges to containers', eval=TRUE, results='hide'---- mergeOutEdges(rdp,nlev=2) ## ----label='Workflow 2: relax the network', eval=TRUE, results='hide'--------- relax(rdp) ## ----label='Workflow 2: add color legend', eval=TRUE, results='hide'---------- scl <- sg$legNodeColor$scale leg <- sg$legNodeColor$legend addLegend.color(rdp, colvec=scl, labvec=leg, title="diff. gene expression (logFC)") ## ----label='Workflow 2: add node size legend', eval=TRUE, results='hide'------ scl <- sg$legNodeSize$scale leg <- sg$legNodeSize$legend addLegend.size(rdp, sizevec=scl, labvec=leg, title="bd site distance (kb)") ## ----label='Workflow 2: reset graph', eval=TRUE, results='hide'--------------- resetd(rdp) ## ----label='Session information', eval=TRUE, echo=FALSE----------------------- sessionInfo()