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$Nnode))
par(mar=c(0,0,0,0))
colcloud <- rainbow(length(sum.cl))
}
par(mar=c(0,0,0,0))
- label.ori<-tree[[2]]
+ label.ori<-tree$tip.label
if (!is.null(lab)) {
tree$tip.label <- lab
} else {
- tree[[2]]<-paste('classe ',tree[[2]])
- }
+ tree$tip.label<-paste('classe ',tree$tip.label)
+ }
plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
for (i in rev(tree.order)) {
par(mar=c(0,0,1,0),cex=0.9)
}
}
par(mar=c(0,0,0,0),cex=1)
- label.ori<-tree[[2]]
+ label.ori<-tree$tip.label
if (!is.null(lab)) {
tree$tip.label <- lab
} else {
- tree[[2]]<-paste('classe ',tree[[2]])
+ tree$tip.label<-paste('classe ',tree$tip.label)
}
plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
#cl.order <- as.numeric(label.ori)
}
layout(matlay, widths=lay.width,TRUE)
par(mar=c(3,0,2,4),cex=1)
- label.ori<-tree[[2]]
+ label.ori<-tree$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) {
} 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$membership
if (!is.null(sweight)) {
V(g)$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)