#create Rgraphviz commands #create dot file for graphviz from ICLUST output #modified from ICLUST.graph to produce Rgraphviz output "ICLUST.rgraph" <- function(ic.results,out.file = NULL, min.size=1,short=FALSE,labels=NULL, size=c(8,6), node.font=c("Helvetica", 14), edge.font=c("Helvetica", 10), rank.direction=c("RL","TB","LR","BT"), digits=2,title="ICLUST",label.font=2, ...){ if(!requireNamespace('Rgraphviz')) {stop("I am sorry, you need to have the Rgraphviz package installed") #create several dummy functions to get around the "no visible global function definition" problem nodes <- function() {} addEdge <- function() {} subGraph <- function(){} } clusters <- as.matrix(ic.results$clusters) results <- ic.results$results rank.direction <- match.arg(rank.direction) #first some basic setup parameters #create the items as boxes #add the sign from the clusters num.var <- dim(clusters)[1] #how many variables? num.clust <- num.var - dim(clusters)[2] vars <- paste("V",1:num.var,sep="") clust <- paste("C",1:num.clust,sep="") clust.graph <- new("graphNEL",nodes=c(vars,clust),edgemode="directed") graph.shape <- c(rep("box",num.var),rep("ellipse",num.clust)) graph.rank <- c(rep("sink",num.var),rep("",num.clust)) names(graph.shape) <- nodes(clust.graph) names(graph.rank) <- nodes(clust.graph) edge.label <- rep("",num.clust*2) edge.name <- rep("",num.clust*2) names(edge.label) <- seq(1:num.clust*2) #show the cluster structure with ellipses for (i in 1:num.clust) {if(results[i,1]>0) { #avoid printing null results clust.graph <- addEdge(row.names(results)[i], results[i,1], clust.graph,1) edge.label[(i-1)*2+1] <- round(results[i,"r1"],digits) edge.name [(i-1)*2+1] <- paste(row.names(results)[i],"~", results[i,1],sep="") clust.graph <- addEdge(row.names(results)[i], results[i,2], clust.graph,1) edge.label[i*2] <- round(results[i,"r2"],digits) edge.name [i*2] <- paste(row.names(results)[i],"~", results[i,2],sep="") }} nAttrs <- list() #node attributes eAttrs <- list() #edge attributes if (!is.null(labels)) {var.labels <- c(labels,row.names(results)) #note how this combines variable labels with the cluster variables names(var.labels) <- nodes(clust.graph) nAttrs$label <- var.labels names(edge.label) <- edge.name node.font.size <- as.numeric(node.font[2]) n.font.size <- c(rep(label.font*node.font.size,length(labels)),rep(node.font.size,(length(var.labels)-length(labels)))) names(n.font.size) <- nodes(clust.graph) nAttrs$fontsize <- n.font.size } names(edge.label) <- edge.name e.font.size <- rep(6,num.clust*2) names(e.font.size) <- edge.name nAttrs$shape <- graph.shape eAttrs$fontsize <- e.font.size nAttrs$rank <- graph.rank eAttrs$label <- edge.label attrs <- list(node = list(shape = "ellipse", fixedsize = FALSE),graph=list(rankdir=rank.direction, fontsize=8,bgcolor="white" )) obs.var <- subGraph(vars,clust.graph) cluster.vars <- subGraph(clust,clust.graph) observed <- list(list(graph=obs.var,cluster=TRUE,attrs=c(rank="sink"))) plot(clust.graph, nodeAttrs = nAttrs, edgeAttrs = eAttrs, attrs = attrs,subGList=observed,main=title) if (!is.null(out.file)) { toDotty(clust.graph,out.file,nodeAttrs = nAttrs, edgeAttrs = eAttrs, attrs = attrs,subGList=observed) } } #test with Harman data sets #ic1 <- ICLUST(Harman74.cor$cov) #ic4 <- ICLUST(Harman74.cor$cov,nclusters=4) #ic8 <- ICLUST(Harman23.cor$cov) #ICLUST.rgraph(ic1) #ICLUST.rgraph(ic4) #ICLUST.rgraph(ic8,labels=colnames(Harman23.cor$cov))