Nothing
#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))
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