compatibility with ape > 5.0

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index dacd7a8..12938bf 100644 (file)
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -799,11 +799,11 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
         }
     }
        par(mar=c(0,0,0,0),cex=1)
         }
     }
        par(mar=c(0,0,0,0),cex=1)

-       label.ori<-tree[[2]]
+       label.ori<-tree$tip.label

     if (!is.null(lab)) {
         tree$tip.label <- lab
     } else {
     if (!is.null(lab)) {
         tree$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)
     }
        plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
     #cl.order <- as.numeric(label.ori)


@@ -1164,10 +1164,12 @@ graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, commun
     } else {
         V(g)$weight <- graph.simi$label.cex
     }
     } 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
        }
        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)$sweight <- sweight
        }
        if (!is.null(sweight)) {
                V(g)$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$vertices, nodesfile, sep='\t', row.names=FALSE)
        df <- get.data.frame(g, what='both')
        if (!is.null(nodesfile)) {
                write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)