load rgl before graph 3d

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index af0b351..8407e31 100644 (file)
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -14,7 +14,7 @@
 #   dev.off()
 #}
 
-PlotDendroCut <- function(chd,filename,reso,clusternb) {   
+PlotDendroCut <- function(chd,filename,reso,clusternb) {
    h.chd <- as.hclust(chd)
    memb <- cutree(h.chd, k = clusternb)
    cent <- NULL
@@ -951,7 +951,7 @@ plot.spec <- function(spec, nb.word = 20) {
            vcex <- norm.vec(word.size[,i], 2, 3)
                text(-0.9, -0.5, cn[i], cex = 1, adj=0, srt=90, col='black')
            for (j in 1:length(word.size[,i])) {
-               yval <- yval-(strheight(word.to.plot[j,i],cex=vcex[j])+0.02)
+               yval <- yval-(strheight(word.to.plot[j,i],cex=vcex[j])+0.01)
                text(-0.9, yval, word.to.plot[j,i], cex = vcex[j], col = col, adj=0)
            }
        }
@@ -996,6 +996,7 @@ plot.alceste.graph <- function(rdata,nd=3,layout='fruke', chilim = 2) {
 
 make.simi.afc <- function(x,chitable,lim=0, alpha = 0.1, movie = NULL) {
     library(igraph)
+    library(rgl)
     chimax<-as.matrix(apply(chitable,1,max))
     chimax<-as.matrix(chimax[,1][1:nrow(x)])
     chimax<-cbind(chimax,1:nrow(x))
@@ -1192,19 +1193,20 @@ graphml.to.file <- function(graph.path) {
 graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
        require(igraph)
        g <- graph.simi$graph
-    print(graph.simi$eff)
+    #print(graph.simi$eff)
     if (!is.null(graph.simi$eff)) {
            V(g)$weight <- graph.simi$eff
     } else {
         V(g)$weight <- graph.simi$label.cex
     }
-       layout <- layout.norm(graph.simi$layout,-5,5,-5,5,-5,5)
-       print(layout)
+       layout <- layout.norm(graph.simi$layout,-10,10,-10,10,-10,10)
+       #print(layout)
        V(g)$x <- layout[,1]
        V(g)$y <- layout[,2]
        if (ncol(layout) == 3) {
                V(g)$z <- layout[,3]
        }
+    E(g)$weight <- graph.simi$we.width
        if (community) {
                member <- graph.simi$communities$membership
                col <- rainbow(max(member))
@@ -1218,7 +1220,7 @@ graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, commun
                v.colors <- col2rgb(color)
                V(g)$r <- v.colors[1,]
                V(g)$g <- v.colors[2,]
-               V(g)$b <- v.colors[3,]          
+               V(g)$b <- v.colors[3,]
        }
        if (!is.null(sweight)) {
                V(g)$sweight <- sweight
@@ -1238,6 +1240,7 @@ graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, commun
 graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
        require(igraph)
        g <- graph
+    layout <- layout.norm(layout,-5,5,-5,5,-5,5)
        V(g)$x <- layout[,1]
        V(g)$y <- layout[,2]
        if (ncol(layout) == 3) {