##' plots simultaneously a whole phylogenetic tree and a portion of it. 
 ##'
 ##' 
 ##' @title gzoom
 ##' @param phy phylo object
 ##' @param focus selected tips
 ##' @param subtree logical
 ##' @param widths widths
 ##' @return a list of ggplot object
 ##' @importFrom ggplot2 xlim
 ##' @importFrom ggplot2 scale_color_manual
 ##' @importFrom ape drop.tip
 ##' @author ygc
 ##' @examples
 ##' require(ape)
 ##' data(chiroptera)
 ##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
 gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
     if (is.character(focus)) {
         focus <- which(phy$tip.label %in% focus)
     }
 
     group_name <- "focus"
     phy <- gfocus(phy, focus, group_name)
 
     foc <- attr(phy, group_name)
     ## foc should +1 since the group index start from 0
     cols <- c("black", "red")[foc+1]
 
     p1 <- ggtree(phy, color=cols)
     
     subtr <- drop.tip(phy, phy$tip.label[-focus],
                       subtree=subtree, rooted=TRUE)
     
     p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)
     p2 <- p2 + xlim(0, max(p2$data$x)*1.2)

     multiplot(p1, p2, ncol=2, widths=widths) 

     
     invisible(list(p1=p1, p2=p2))
 }
 
 gzoom.ggplot <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
     node <- MRCA(tree_view, focus)
     cpos <- get_clade_position(tree_view, node)
     p2 <- with(cpos, tree_view+
                      xlim(xmin, xmax+xmax_adjust)+
                      ylim(ymin, ymax))

     multiplot(tree_view, p2, ncol=2, widths=widths)

     invisible(list(p1=tree_view, p2=p2))
 }
 
 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 ##' @param xmax_adjust adjust xmax (xlim[2])
 setMethod("gzoom", signature(object="gg"),
           function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
               gzoom.ggplot(object, focus, widths, xmax_adjust)
           })
 
 
 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 setMethod("gzoom", signature(object="apeBootstrap"),
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
               gzoom.phylo(get.tree(object), focus, subtree, widths)
           })
 
 

 ##' zoom selected subtree
 ##'
 ##' 
 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 setMethod("gzoom", signature(object="beast"),
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
               gzoom.phylo(get.tree(object), focus, subtree, widths)
           })
 

 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 setMethod("gzoom", signature(object="codeml"),
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
               gzoom.phylo(get.tree(object), focus, subtree, widths)
           })
 

 
 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 setMethod("gzoom", signature(object="nhx"),
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
               gzoom.phylo(get.tree(object), focus, subtree, widths)
           })
 
 
 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 setMethod("gzoom", signature(object="paml_rst"),
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
               gzoom.phylo(get.tree(object), focus, subtree, widths)
           })
 
 
 ##' @rdname gzoom-methods
 ##' @exportMethod gzoom
 setMethod("gzoom", signature(object="phylo"),
           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
               gzoom.phylo(object, focus, subtree, widths)
           })