##' drawing phylogenetic tree from phylo object
 ##'

 ##'

 ##' @title ggtree

 ##' @inheritParams geom_tree

 ##' @param tr phylo object

 ##' @param open.angle open angle, only for 'fan' layout

 ##' @param mrsd most recent sampling date
 ##' @param as.Date logical whether using Date class in time tree

 ##' @param yscale y scale

 ##' @param yscale_mapping yscale mapping for category variable

 ##' @param ladderize logical (default \code{TRUE}). Should the tree be re-organized to have a 'ladder'
 ##' aspect?
 ##' @param right logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
 ##' right-hand side? See \code{\link[ape]{ladderize}} for more information. 

 ##' @param branch.length variable for scaling branch, if 'none' draw cladogram

 ##' @param root.position position of the root node (default = 0)

 ##' @return tree
 ##' @importFrom ggplot2 ggplot
 ##' @importFrom ggplot2 xlab
 ##' @importFrom ggplot2 ylab
 ##' @importFrom ggplot2 annotate
 ##' @importFrom ggplot2 scale_x_reverse

 ##' @importFrom ggplot2 ylim

 ##' @importFrom ggplot2 coord_flip
 ##' @importFrom ggplot2 coord_polar
 ##' @export
 ##' @author Yu Guangchuang

 ##' @seealso \code{\link[ape]{ladderize}}

 ##' @examples
 ##' require(ape)
 ##' tr <- rtree(10)
 ##' ggtree(tr)

 ggtree <- function(tr,

                    mapping        = NULL,
                    layout         = "rectangular",

                    open.angle     = 0,

                    mrsd           = NULL,
                    as.Date        = FALSE,
                    yscale         = "none",

                    yscale_mapping = NULL,

                    ladderize      = TRUE,
                    right          = FALSE,
                    branch.length  = "branch.length",

                    root.position  = 0,

                    ...) {

     # Check if layout string is valid.

     layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular",
                             "radial", "unrooted", "equal_angle", "daylight"))
 

     if (layout == "unrooted") {
         layout <- "daylight"
         message('"daylight" method was used as default layout for unrooted tree.')
     }
 

     if(yscale != "none") {
         ## for 2d tree

         layout <- "slanted"

     }

     if (is.null(mapping)) {

         mapping <- aes_(~x, ~y)

     } else {

         mapping <- modifyList(aes_(~x, ~y), mapping)

     }

 
     p <- ggplot(tr,

                 mapping       = mapping,

                 layout        = layout,

                 mrsd          = mrsd,
                 as.Date       = as.Date,

                 yscale        = yscale,

                 yscale_mapping= yscale_mapping,

                 ladderize     = ladderize,
                 right         = right,
                 branch.length = branch.length,

                 root.position = root.position,

                 ...)

 
     if (is(tr, "multiPhylo")) {
         multiPhylo <- TRUE
     } else {
         multiPhylo <- FALSE
     }

     p <- p + geom_tree(layout=layout, multiPhylo=multiPhylo, ...)
 
 
     p <- p + theme_tree()

     if (layout == "circular" || layout == "radial") {

         p <- p + layout_circular()

         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6

         ## and also have some space for tree scale (legend)

         p <- p + ylim(0, NA)

     } else if (layout == "fan") {

         p <- p + layout_fan(open.angle)

     }

     class(p) <- c("ggtree", class(p))
 

     return(p)
 }