> I wrote a few methods for plotting phylogenetic trees in ggplot, might
> come in handy (though for now only applicable for objects class
> "phylo" not "multiphylo"). Based on plot methods from ape
> package:

> #################
> #---LIBRARIES---#
> #################
> library(ape)
> library(ggplot2)

> #####################
> #---FORTIFY.PHYLO---#
> #####################
> fortify.phylo <- function(phylo) {

> Ntip <- length(phylo$tip.label)
> Nnode <- phylo$Nnode
> Nedge <- dim(phylo$edge)[1]
> z <- reorder(phylo, order = "pruningwise")
> yy <- numeric(Ntip + Nnode)
> TIPS <- phylo$edge[phylo$edge[, 2] <= Ntip, 2]
> yy[TIPS] <- 1:Ntip

> ans1 <- .C("node_height_clado", as.integer(Ntip), as.integer(Nnode),
> as.integer(z$edge[, 1]), as.integer(z$edge[,2]), as.integer(Nedge),
> double(Ntip + Nnode), as.double(yy), DUP = FALSE, PACKAGE = "ape")

>         yy <- ans1[[7]]

> ans2 <- .C("node_depth_edgelength", as.integer(Ntip),
> as.integer(Nnode), as.integer(z$edge[, 1]), as.integer(z$edge[, 2]),
> as.integer(Nedge), as.double(z$edge.length), double(Ntip + Nnode), DUP
> = FALSE, PACKAGE = "ape")

>         xx <- ans2[[7]]

>     edge <- phylo$edge
>     nodes <- (Ntip + 1):(Ntip + Nnode)
>     x0v <- xx[nodes]
>     y0v <- y1v <- numeric(Nnode)
>     NodeInEdge1 <- vector("list", Nnode)

>     for (i in nodes) {
>         ii <- i - Ntip
>         j <- NodeInEdge1[[ii]] <- which(edge[, 1] == i)
>         tmp <- range(yy[edge[j, 2]])
>         y0v[ii] <- tmp[1]
>         y1v[ii] <- tmp[2] }

>     x0h <- xx[edge[, 1]]
>     x1h <- xx[edge[, 2]]
>     y0h <- yy[edge[, 2]]

> lineh <- data.frame(x=x1h, y=y0h, xend=x0h, yend=y0h)
> linev <- data.frame(x=x0v, y=y1v, xend=x0v, yend=y0v)
> x <- rbind(linev, lineh)

> return(x)
> }

> ###################
> #---LABEL.PHYLO---#
> ###################
> label.phylo <- function(phylo) {

> Ntip <- length(phylo$tip.label)
> Nnode <- phylo$Nnode
> Nedge <- dim(phylo$edge)[1]
> z <- reorder(phylo, order = "pruningwise")
> yy <- numeric(Ntip + Nnode)
> TIPS <- phylo$edge[phylo$edge[, 2] <= Ntip, 2]
> yy[TIPS] <- 1:Ntip

> ans1 <- .C("node_height_clado", as.integer(Ntip), as.integer(Nnode),
> as.integer(z$edge[, 1]), as.integer(z$edge[,2]), as.integer(Nedge),
> double(Ntip + Nnode), as.double(yy), DUP = FALSE, PACKAGE = "ape")

>         yy <- ans1[[7]]

> ans2 <- .C("node_depth_edgelength", as.integer(Ntip),
> as.integer(Nnode), as.integer(z$edge[, 1]), as.integer(z$edge[, 2]),
> as.integer(Nedge), as.double(z$edge.length), double(Ntip + Nnode), DUP
> = FALSE, PACKAGE = "ape")

>         xx <- ans2[[7]]

> data.frame(x=xx[1:Ntip], y=yy[1:Ntip], label=phylo$tip.label)
> }

> ###############
> #---EXAMPLE---#
> ###############
> data(bird.orders)
> x <- bird.orders
> #x<-read.nexus(treefile.tree)

> xlim=35

> p <- ggplot(data=x)
> p <- p + geom_segment(aes(x=x,y=y,xend=xend,yend=yend), colour="blue",alpha=1)
> p <- p + geom_text(data=label.phylo(x), aes(x=x, y=y, label=label),hjust=0, family=3, vjust=0.5, size=3) + xlim(0, xlim)
> theme <- theme_update(
>                            axis.text.y = theme_blank(),
>                            axis.ticks = theme_blank(),
>                            axis.title.x = theme_blank(),
>                            axis.title.y = theme_blank(),
>                            legend.position = "none"
>                       )
> p <- p + theme_set(theme)
> print(p)

> --
> while(!succeed) { try(); }

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