@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.13.0

+Version: 1.13.0.001

 Authors@R: c(

 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

@@ -1,3 +1,12 @@

+# ggtree 1.13.0.001

+

++ compatible with ggplot2 2.2.1.9000 (2018-05-02, Wed)

+  - incorporate newly introduce parameter `linejoin` and `arrow.fill` in `geom_segment`

+

+# ggtree 1.12.0

+

++ Bioconductor 3.7 release (2018-05-01, Tue)

+

 # ggtree 1.11.6

 + reexport `treeio::read.iqtree` & `treeio::read.astral`(2018-04-17, Tue)

@@ -121,7 +121,7 @@ geom_cladelabel <- function(node, label,

     }

-    

+

     list(

       layer_bar,

       layer_text

@@ -168,7 +168,7 @@ stat_cladeBar <- function(mapping=NULL, data=NULL,

                           node, offset, align, extend,  ...,

                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

-  

+

     default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, xend=~x, yend=~y)

     if (is.null(mapping)) {

         mapping <- default_aes

@@ -69,7 +69,7 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

                              "alpha", "angle", "fontface", "group", "lineheight", "size", "vjust")

     # ignore angle

-    arg_list_geom_curve <- c( "curvature", "ncp", "arrow", "lineend",

+    arg_list_geom_curve <- c( "curvature", "ncp", "arrow", "arrow.fill", "lineend",

                               "alpha", "group", "linetype")

@@ -121,7 +121,6 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

     args_stat_cladeBar2$inherit.aes <- inherit.aes

     args_stat_cladeBar2$na.rm       <- na.rm

-

     if (!is.null(color)) {

         if (length(color) > 2) {

           stop("color should be of length 1 or 2")

@@ -189,7 +188,8 @@ stat_cladeText2 <- function(mapping=NULL, data=NULL,

 stat_cladeBar2 <- function(mapping=NULL, data=NULL,

                            geom="curve", position="identity",

                            node, offset, align, ...,

-                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

+                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE,

+                           arrow=NULL, arrow.fill=NULL) {

   default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, xend=~x, yend=~y)

   if (is.null(mapping)) {

     mapping <- default_aes

@@ -209,6 +209,8 @@ stat_cladeBar2 <- function(mapping=NULL, data=NULL,

                     offset=offset,

                     align=align,

                     na.rm=na.rm,

+                    arrow = arrow,

+                    arrow.fill = arrow.fill,

                     ...)

   )

@@ -31,12 +31,13 @@ geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {

 ##' @param data data

 ##' @param stat Name of stat to modify data

 ##' @param position position

-##' @param arrow arrow

 ##' @param lineend lineend

 ##' @param na.rm logical

 ##' @param show.legend logical

 ##' @param inherit.aes logical

 ##' @param nudge_x horizontal adjustment of x

+##' @param arrow specification for arrow heads, as created by arrow().

+##' @param arrow.fill fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.

 ##' @param ... additional parameter

 ##' @importFrom ggplot2 layer

 ##' @export

@@ -45,9 +46,9 @@ geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {

 ##' @return add segment layer

 ##' @author Guangchuang Yu

 geom_segment2 <- function(mapping = NULL, data = NULL, stat = "identity",

-                         position = "identity", arrow = NULL, lineend = "butt",

+                         position = "identity", lineend = "butt",

                          na.rm = FALSE, show.legend = NA, inherit.aes = TRUE,

-                         nudge_x = 0,

+                         nudge_x = 0, arrow = NULL, arrow.fill = NULL,

                          ...) {

     default_aes <- aes_(node=~node)

@@ -85,13 +86,14 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,

                                  data[which(data$subset),]

                              },

-                             draw_panel = function(data, panel_scales, coord, arrow = NULL,

-                                                   lineend = "butt", na.rm = FALSE, nudge_x = 0) {

+                             draw_panel = function(data, panel_params, coord, arrow = NULL, arrow.fill = NULL,

+                                                   lineend = "butt", linejoin = "round", na.rm = FALSE, nudge_x = 0) {

                                  data$x <- data$x + nudge_x

                                  ## data$x <- data$x - sapply(data$label, function(x) convertWidth(grobWidth(textGrob(x, gp=gpar(fontsize=.04* .pt))), "native", TRUE))

-                                 GeomSegment$draw_panel(data, panel_scales, coord, arrow,

-                                                        lineend, na.rm)

+                                 GeomSegment$draw_panel(data = data, panel_params = panel_params, coord = coord,

+                                                        arrow = arrow, arrow.fill = arrow.fill,

+                                                        lineend = lineend, linejoin = linejoin, na.rm = na.rm)

                              }

                              )

@@ -7,12 +7,14 @@

 ##' @param curvature A numeric value giving the amount of curvature.

 ##' Negative values produce left-hand curves,

 ##' positive values produce right-hand curves, and zero produces a straight line.

+##' @param arrow specification for arrow heads, as created by arrow().

+##' @param arrow.fill fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.

 ##' @param ... additional parameter

 ##' @return ggplot layer

 ##' @export

 ##' @importFrom ggplot2 GeomCurve

 ##' @author Guangchuang Yu

-geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {

+geom_taxalink <- function(taxa1, taxa2, curvature=0.5, arrow = NULL, arrow.fill = NULL, ...) {

     position = "identity"

     show.legend = NA

     na.rm = TRUE

@@ -31,6 +33,8 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {

                         taxa2 = taxa2,

                         curvature = curvature,

                         na.rm = na.rm,

+                        arrow = arrow,

+                        arrow.fill = arrow.fill,

                         ...),

           check.aes = FALSE

           )

@@ -5,8 +5,9 @@

 \title{geom_segment2}

 \usage{

 geom_segment2(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", arrow = NULL, lineend = "butt", na.rm = FALSE,

-  show.legend = NA, inherit.aes = TRUE, nudge_x = 0, ...)

+  position = "identity", lineend = "butt", na.rm = FALSE,

+  show.legend = NA, inherit.aes = TRUE, nudge_x = 0, arrow = NULL,

+  arrow.fill = NULL, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

@@ -17,8 +18,6 @@ geom_segment2(mapping = NULL, data = NULL, stat = "identity",

 \item{position}{position}

-\item{arrow}{arrow}

-

 \item{lineend}{lineend}

 \item{na.rm}{logical}

@@ -29,6 +28,10 @@ geom_segment2(mapping = NULL, data = NULL, stat = "identity",

 \item{nudge_x}{horizontal adjustment of x}

+\item{arrow}{specification for arrow heads, as created by arrow().}

+

+\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}

+

 \item{...}{additional parameter}

 }

 \value{

@@ -4,7 +4,8 @@

 \alias{geom_taxalink}

 \title{geom_taxalink}

 \usage{

-geom_taxalink(taxa1, taxa2, curvature = 0.5, ...)

+geom_taxalink(taxa1, taxa2, curvature = 0.5, arrow = NULL,

+  arrow.fill = NULL, ...)

 }

 \arguments{

 \item{taxa1}{taxa1, can be label or node number}

@@ -15,6 +16,10 @@ geom_taxalink(taxa1, taxa2, curvature = 0.5, ...)

 Negative values produce left-hand curves,

 positive values produce right-hand curves, and zero produces a straight line.}

+\item{arrow}{specification for arrow heads, as created by arrow().}

+

+\item{arrow.fill}{fill color to usse for the arrow head (if closed). `NULL` means use `colour` aesthetic.}

+

 \item{...}{additional parameter}

 }

 \value{