X-Git-Url: http://iramuteq.org/git?a=blobdiff_plain;f=Rscripts%2FRgraph.R;h=e758cfb2fedc4132b2c665f12139075eecbef52a;hb=c038ef7892cf106654fcd0d35389584513b2ec1d;hp=dacd7a81d98d2afc18b869bb2fd9cdb78194c1fd;hpb=dbd43dfa2a70c764332cf4694e22f29ca14b3539;p=iramuteq

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index dacd7a8..e758cfb 100644
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -680,12 +680,12 @@ plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro
         colcloud <- rainbow(length(sum.cl))
         colcloud <- del.yellow(colcloud)
     }
-    label.ori<-tree[[2]]
+	label.ori<-tree$tip.label
     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
-	    tree[[2]]<-paste('classe ',tree[[2]])
-    }
+	    tree$tip.label<-paste('classe ',tree$tip.label)
+	}
 	par(mar=c(2,1,0,1))
 	plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.5, y.lim=c(-0.3,tree$Nnode))
 	par(mar=c(0,0,0,0))
@@ -748,12 +748,12 @@ plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendr
         colcloud <- rainbow(length(sum.cl))
     }
     par(mar=c(0,0,0,0))
-    label.ori<-tree[[2]]
+	label.ori<-tree$tip.label
     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
-	    tree[[2]]<-paste('classe ',tree[[2]])
-    }
+	    tree$tip.label<-paste('classe ',tree$tip.label)
+	}
 	plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     for (i in rev(tree.order)) {
         par(mar=c(0,0,1,0),cex=0.9)
@@ -799,11 +799,11 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
         }
     }
 	par(mar=c(0,0,0,0),cex=1)
-	label.ori<-tree[[2]]
+	label.ori<-tree$tip.label
     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
-	    tree[[2]]<-paste('classe ',tree[[2]])
+	    tree$tip.label<-paste('classe ',tree$tip.label)
     }
 	plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     #cl.order <- as.numeric(label.ori)
@@ -862,11 +862,11 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
     }
     layout(matlay, widths=lay.width,TRUE)
 	par(mar=c(3,0,2,4),cex=1)
-	label.ori<-tree[[2]]
+	label.ori<-tree$tip.label
     if (!is.null(lab)) {
-        tree$tip.label <- lab[tree.order]
+        tree$tip.label <- lab
     } else {
-	    tree[[2]]<-paste('classe ',tree[[2]])
+	    tree$tip.label<-paste('classe ',tree$tip.label)
     }
     to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
     if (!bw) {
@@ -1164,10 +1164,12 @@ graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, commun
     } else {
         V(g)$weight <- graph.simi$label.cex
     }
-	V(g)$x <- graph.simi$layout[,1]
-	V(g)$y <- graph.simi$layout[,2]
-	if (ncol(graph.simi$layout) == 3) {
-		V(g)$z <- graph.simi$layout[,3]
+	layout <- layout.norm(graph.simi$layout,-5,5,-5,5,-5,5)
+	print(layout)
+	V(g)$x <- layout[,1]
+	V(g)$y <- layout[,2]
+	if (ncol(layout) == 3) {
+		V(g)$z <- layout[,3]
 	}
 	if (community) {
 		member <- graph.simi$communities$membership
@@ -1215,6 +1217,13 @@ graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, co
 	if (!is.null(sweight)) {
 		V(g)$sweight <- sweight
 	}
+	if (is.null(V(g)$weight)) {
+		if (!is.null(sweight)) {
+			V(g)$weight <- sweight
+		} else {
+			V(g)$weight <- 1
+		}
+	}
 	df <- get.data.frame(g, what='both')
 	if (!is.null(nodesfile)) {
 		write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)