@@ -1,5 +1,6 @@

 # ggtree 1.17.1

++ `root.position` parameter for `fortify` and `ggtree` (2019-05-27, Mon)

 + `geom_facet`, a geom layer version of `facet_plot` (2019-05-23, Thu)

 + update `scale_x_ggtree`, now we can use `gheatmap() + scale_x_ggtree()` (2019-05-22, Wed)

 + extend `xlim_expand` to work with `ggplot2` (2019-05-20, Tue)

@@ -19,7 +19,8 @@ geom_rootedge <- function(rootedge = NULL, ...) {

         position = "identity",

         show.legend = NA,

         params = list(rootedge = rootedge, ...),

-        check.aes = FALSE

+        check.aes = FALSE,

+        inherit.aes = FALSE

     )

 }

@@ -32,7 +33,9 @@ StatRootEdge <- ggproto("StatRootEdge", Stat,

                             if (is.null(rootedge)) {

                                 rootedge <- d$branch.length

                             }

-                            if (is.null(rootedge) || is.na(rootedge)) {

+                            if (is.null(rootedge)) {

+                                xend <- d$x

+                            } else if (is.na(rootedge)) {

                                 xend <- d$x

                             } else {

                                 xend <- d$x - rootedge

@@ -30,7 +30,7 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

-        mapping <- modifyList(mapping, default_aes)

+        mapping <- modifyList(default_aes, mapping)

     }

     if (layout %in% c("rectangular", "fan", "circular")) {

@@ -14,6 +14,7 @@

 ##' @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

@@ -41,6 +42,7 @@ ggtree <- function(tr,

                    ladderize      = TRUE,

                    right          = FALSE,

                    branch.length  = "branch.length",

+                   root.position  = 0,

                    ...) {

     # Check if layout string is valid.

@@ -71,6 +73,7 @@ ggtree <- function(tr,

                 ladderize     = ladderize,

                 right         = right,

                 branch.length = branch.length,

+                root.position = root.position,

                 ...)

     if (is(tr, "multiPhylo")) {

@@ -14,6 +14,7 @@ fortify.phylo <- function(model, data,

                           mrsd          = NULL,

                           as.Date       = FALSE,

                           yscale        = "none",

+                          root.position = 0,

                           ...) {

     x <- as.phylo(model) ## reorder.phylo(get.tree(model), "postorder")

@@ -39,7 +40,7 @@ fortify.phylo <- function(model, data,

         ypos <- getYcoord(x)

         N <- Nnode(x, internal.only=FALSE)

-        xypos <- tibble::data_frame(node=1:N, x=xpos, y=ypos)

+        xypos <- tibble::data_frame(node=1:N, x=xpos + root.position, y=ypos)

         df <- as_tibble(model) %>%

             mutate_(isTip = ~(! node %in% parent))

@@ -11,7 +11,7 @@

 ggtree(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", ...)

+  branch.length = "branch.length", root.position = 0, ...)

 }

 \arguments{

 \item{tr}{phylo object}

@@ -38,6 +38,8 @@ right-hand side? See \code{\link[ape]{ladderize}} for more information.}

 \item{branch.length}{variable for scaling branch, if 'none' draw cladogram}

+\item{root.position}{position of the root node (default = 0)}

+

 \item{...}{additional parameter}

 }

 \value{