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0a5b07d
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compatibility with ape > 5.0
author
Pierre Ratinaud
<ratinaud@univ-tlse2.fr>
Thu, 3 May 2018 16:31:24 +0000
(18:31 +0200)
committer
Pierre Ratinaud
<ratinaud@univ-tlse2.fr>
Thu, 3 May 2018 16:31:24 +0000
(18:31 +0200)
Rscripts/Rgraph.R
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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)