@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.1.18

+Version: 1.1.19

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -27,11 +27,8 @@ export(expand)

 export(flip)

 export(geom_aline)

 export(geom_nodepoint)

-export(geom_point2)

 export(geom_rootpoint)

-export(geom_segment2)

 export(geom_text)

-export(geom_text2)

 export(geom_tiplab)

 export(geom_tippoint)

 export(geom_tree)

@@ -118,35 +115,27 @@ importFrom(ape,which.edge)

 importFrom(ape,write.tree)

 importFrom(colorspace,rainbow_hcl)

 importFrom(ggplot2,"%+replace%")

-importFrom(ggplot2,GeomPoint)

-importFrom(ggplot2,GeomSegment)

-importFrom(ggplot2,GeomText)

 importFrom(ggplot2,aes)

 importFrom(ggplot2,aes_string)

 importFrom(ggplot2,annotate)

 importFrom(ggplot2,annotation_custom)

 importFrom(ggplot2,coord_flip)

 importFrom(ggplot2,coord_polar)

-importFrom(ggplot2,draw_key_path)

-importFrom(ggplot2,draw_key_point)

-importFrom(ggplot2,draw_key_text)

 importFrom(ggplot2,element_blank)

 importFrom(ggplot2,element_line)

 importFrom(ggplot2,element_rect)

 importFrom(ggplot2,element_text)

 importFrom(ggplot2,fortify)

+importFrom(ggplot2,geom_point)

 importFrom(ggplot2,geom_rect)

 importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

 importFrom(ggplot2,geom_tile)

 importFrom(ggplot2,ggplot)

 importFrom(ggplot2,ggplotGrob)

-importFrom(ggplot2,ggproto)

 importFrom(ggplot2,guide_legend)

 importFrom(ggplot2,guides)

 importFrom(ggplot2,labs)

-importFrom(ggplot2,layer)

-importFrom(ggplot2,position_nudge)

 importFrom(ggplot2,scale_color_manual)

 importFrom(ggplot2,scale_fill_discrete)

 importFrom(ggplot2,scale_fill_gradient)

@@ -162,6 +151,7 @@ importFrom(ggplot2,ylab)

 importFrom(ggplot2,ylim)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,rgb)

+importFrom(grid,editGrob)

 importFrom(grid,gpar)

 importFrom(grid,linesGrob)

 importFrom(grid,rasterGrob)

@@ -1,120 +1,46 @@

-

 ##' add tip point

 ##'

 ##' 

 ##' @title geom_tippoint

-##' @inheritParams geom_point2

+##' @param mapping aes mapping

+##' @param ... additional parameter

 ##' @return tip point layer

 ##' @export

 ##' @author Guangchuang Yu

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

-                       position = "identity", na.rm = FALSE,

-                          show.legend = NA, inherit.aes = TRUE, ...) {

+geom_tippoint <- function(mapping = NULL, ...) {

     isTip <- NULL

-    self_mapping <- aes(subset = isTip)

-    if (is.null(mapping)) {

-        mapping <- self_mapping

-    } else {

-        mapping %<>% modifyList(self_mapping)

-    }

-    geom_point2(mapping, data, stat, position, na.rm, show.legend, inherit.aes, ...)    

+    geom_point(mapping, subset=.(isTip), ...)

 }

 ##' add node point

 ##'

 ##' 

 ##' @title geom_nodepoint

-##' @inheritParams geom_point2

+##' @param mapping aes mapping

+##' @param ... additional parameter

 ##' @return node point layer

 ##' @export

 ##' @author Guangchuang Yu

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

-                       position = "identity", na.rm = FALSE,

-                       show.legend = NA, inherit.aes = TRUE, ...) {

+geom_nodepoint <- function(mapping = NULL,  ...) {

     isTip <- NULL

-    self_mapping <- aes(subset = !isTip)

-    if (is.null(mapping)) {

-        mapping <- self_mapping

-    } else {

-        mapping %<>% modifyList(self_mapping)

-    }

-    geom_point2(mapping, data, stat, position, na.rm, show.legend, inherit.aes, ...)    

+    geom_point(mapping, subset=.(!isTip), ...)

 }

+

 ##' add root point

 ##'

 ##' 

 ##' @title geom_rootpoint

-##' @inheritParams geom_point2

+##' @param mapping aes mapping

+##' @param ... additional parameter

 ##' @return root point layer

+##' @importFrom ggplot2 geom_point

 ##' @export

 ##' @author Guangchuang Yu

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

-                           position = "identity", na.rm = FALSE,

-                           show.legend = NA, inherit.aes = TRUE, ...) {

+geom_rootpoint <- function(mapping = NULL,  ...) {

     isTip <- node <- parent <- NULL

-    self_mapping <- aes(subset = (node == parent))

-    if (is.null(mapping)) {

-        mapping <- self_mapping

-    } else {

-        mapping %<>% modifyList(self_mapping)

-    }

-    geom_point2(mapping, data, stat, position, na.rm, show.legend, inherit.aes, ...)

+    geom_point(mapping, subset=.(node == parent), ...)

 }

-##' geom_point2 support aes(subset) via setup_data

-##'

-##' 

-##' @title geom_point2

-##' @param mapping aes mapping

-##' @param data data

-##' @param stat stat

-##' @param position position

-##' @param na.rm logical

-##' @param show.legend logical

-##' @param inherit.aes logical

-##' @param ... addktional parameter

-##' @importFrom ggplot2 layer

-##' @export

-##' @seealso

-##' \link[ggplot2]{geom_point}

-##' @return point layer

-##' @author Guangchuang Yu

-geom_point2 <- function(mapping = NULL, data = NULL, stat = "identity",

-                       position = "identity", na.rm = FALSE,

-                       show.legend = NA, inherit.aes = TRUE, ...) {

-  layer(

-    data = data,

-    mapping = mapping,

-    stat = stat,

-    geom = GeomPointGGtree,

-    position = position,

-    show.legend = show.legend,

-    inherit.aes = inherit.aes,

-    params = list(

-      na.rm = na.rm,

-      ...

-    )

-  )

-}

-

-##' @importFrom ggplot2 ggproto

-##' @importFrom ggplot2 GeomPoint

-##' @importFrom ggplot2 draw_key_point

-GeomPointGGtree <- ggproto("GeomPointGGtree", GeomPoint,

-                           setup_data = function(data, params) {

-                               data[data$subset,]

-                           },

-                           

-                           draw_panel = function(data, panel_scales, coord, na.rm = FALSE){

-                               GeomPoint$draw_panel(data, panel_scales, coord, na.rm)

-                           },

-                           

-                           draw_key = draw_key_point,

-                           

-                           required_aes = c("x", "y"),

-                           default_aes = aes(shape = 19, colour = "black", size = 1.5, fill = NA,

-                               alpha = NA, stroke = 0.5)

-                           )

@@ -11,75 +11,14 @@

 ##' @author Yu Guangchuang

 geom_aline <- function(mapping=NULL, linetype="dotted", size=1, ...) {

     x <- y <- isTip <- NULL

-    dot_mapping <- aes(xend=x+diff(range(x))/200, x=max(x), yend=y, subset=isTip)

+    dot_mapping <- aes(xend=x+diff(range(x))/200, x=max(x), yend=y)

     if (!is.null(mapping)) {

         dot_mapping <- modifyList(dot_mapping, mapping)

     }

-    geom_segment2(dot_mapping,

-                  linetype=linetype,

-                  size=size, ...)

+    geom_segment(mapping,

+                 subset=.(isTip),

+                 linetype=linetype,

+                 size=size, ...)

 }

-

-

-##' geom_segment2 support aes(subset) via setup_data

-##'

-##' 

-##' @title geom_segment2

-##' @param mapping aes mapping 

-##' @param data data

-##' @param stat stat

-##' @param position position

-##' @param arrow arrow

-##' @param lineend lineend

-##' @param na.rm logical

-##' @param show.legend logical

-##' @param inherit.aes logical

-##' @param ... additional parameter

-##' @importFrom ggplot2 layer

-##' @export

-##' @seealso

-##' \link[ggplot2]{geom_segment}

-##' @return add segment layer

-##' @author Guangchuang Yu

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

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

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

-                         ...) {

-  layer(

-    data = data,

-    mapping = mapping,

-    stat = stat,

-    geom = GeomSegmentGGtree,

-    position = position,

-    show.legend = show.legend,

-    inherit.aes = inherit.aes,

-    params = list(

-      arrow = arrow,

-      lineend = lineend,

-      na.rm = na.rm,

-      ...

-    )

-  )

-}

-

-##' @importFrom ggplot2 GeomSegment

-##' @importFrom ggplot2 draw_key_path

-GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,

-                          setup_data = function(data, params) {

-                              data[data$subset,]

-                          },

-                          

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

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

-

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

-                                                     lineend, na.rm)

-                          },

-                          

-                          required_aes = c("x", "y", "xend", "yend"),

-                          default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = NA),

-                          

-                          draw_key = draw_key_path

-                          )

@@ -1,42 +1,3 @@

-##' geom_text2 support aes(subset) via setup_data

-##'

-##' 

-##' @title geom_text2

-##' @inheritParams geom_text

-##' @return text layer

-##' @importFrom ggplot2 layer

-##' @importFrom ggplot2 position_nudge

-##' @export

-##' @seealso

-##' \link[ggplot2]{geom_text}

-##' @author Guangchuang Yu

-geom_text2 <- function(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", parse = FALSE, show.legend = NA, inherit.aes = TRUE,

-  ..., nudge_x = 0, nudge_y = 0, check_overlap = FALSE)

-{

-  if (!missing(nudge_x) || !missing(nudge_y)) {

-    if (!missing(position)) {

-      stop("Specify either `position` or `nudge_x`/`nudge_y`", call. = FALSE)

-    }

-

-    position <- position_nudge(nudge_x, nudge_y)

-  }

-

-  layer(

-    data = data,

-    mapping = mapping,

-    stat = stat,

-    geom = GeomTextGGtree,

-    position = position,

-    show.legend = show.legend,

-    inherit.aes = inherit.aes,

-    params = list(

-      parse = parse,

-      check_overlap = check_overlap,

-      ...

-    )

-  )

-}

 ##' text annotations

 ##' @export

@@ -47,12 +8,7 @@ geom_text2 <- function(mapping = NULL, data = NULL, stat = "identity",

 ##' @param stat The statistical transformation to use on the data for this layer

 ##' @param position The position adjustment to use for overlapping points on this layer

 ##' @param parse if TRUE, the labels will be passd into expressions

-##' @param show.legend logical

-##' @param inherit.aes logical

 ##' @param ... other arguments passed on to 'layer'

-##' @param nudge_x horizontal adjustment

-##' @param nudge_y vertical adjustment

-##' @param check_overlap if TRUE, text that overlaps previous text in the same layer will not be plotted

 ##' @source

 ##' This is just the imported function

 ##' from the ggplot2 package. The documentation you should

@@ -62,24 +18,3 @@ geom_text2 <- function(mapping = NULL, data = NULL, stat = "identity",

 ##' \link[ggplot2]{geom_text}

 geom_text <- ggplot2::geom_text

-

-##' @importFrom ggplot2 GeomText

-##' @importFrom ggplot2 draw_key_text

-GeomTextGGtree <- ggproto("GeomTextGGtree", GeomText,

-                          setup_data = function(data, params) {

-                              data[data$subset,]

-                          },

-                          

-                          draw_panel = function(data, panel_scales, coord, parse = FALSE,

-                              na.rm = FALSE, check_overlap = FALSE) {

-                              GeomText$draw_panel(data, panel_scales, coord, parse,

-                                                  na.rm, check_overlap)

-                          },

-

-                          required_aes = c("x", "y", "label"),

-                          

-                          default_aes = aes(colour = "black", size = 3.88, angle = 0, hjust = 0.5,

-                              vjust = 0.5, alpha = NA, family = "", fontface = 1, lineheight = 1.2),

-                          

-                          draw_key = draw_key_text

-                          )

@@ -40,10 +40,12 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dott

     } 

     list(

-        geom_text2(mapping=text_mapping, 

-                   hjust = hjust, ...),

+        geom_text(mapping=text_mapping,

+                  subset=.(isTip),

+                  hjust = hjust, ...),

         if (!is.null(dot_mapping))

-            geom_segment2(mapping=dot_mapping,

+            geom_segment(mapping=dot_mapping,

+                         subset=.(isTip),

                           linetype = linetype,

                           size = linesize, ...)

         )

@@ -9,6 +9,7 @@

 ##' @param width width of subview, [0,1]

 ##' @param height height of subview, [0,1]

 ##' @return ggplot object

+##' @importFrom grid editGrob

 ##' @importFrom ggplot2 annotation_custom

 ##' @importFrom ggplot2 ggplotGrob

 ##' @export

@@ -16,11 +17,20 @@

 subview <- function(mainview, subview, x, y, width=.1, height=.1) {

     xrng <- mainview$data$x %>% range %>% diff

     yrng <- mainview$data$y %>% range %>% diff

-   

+

+    grob <- ggplotGrob(subview)

     mainview + annotation_custom(

-        ggplotGrob(subview),

+        editGrob(grob, name=paste(grob$name, annotation_id())),

         xmin = x - width*xrng,

         xmax = x + width*xrng,

         ymin = y - height*yrng,

         ymax = y + height*yrng)

 }

+

+annotation_id <- local({

+  i <- 1

+  function() {

+    i <<- i + 1

+    i

+  }

+})

@@ -4,26 +4,12 @@

 \alias{geom_nodepoint}

 \title{geom_nodepoint}

 \usage{

-geom_nodepoint(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", na.rm = FALSE, show.legend = NA,

-  inherit.aes = TRUE, ...)

+geom_nodepoint(mapping = NULL, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

-\item{data}{data}

-

-\item{stat}{stat}

-

-\item{position}{position}

-

-\item{na.rm}{logical}

-

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

-\item{...}{addktional parameter}

+\item{...}{additional parameter}

 }

 \value{

 node point layer

deleted file mode 100644

@@ -1,40 +0,0 @@

-% Generated by roxygen2 (4.1.1): do not edit by hand

-% Please edit documentation in R/geom_point.R

-\name{geom_point2}

-\alias{geom_point2}

-\title{geom_point2}

-\usage{

-geom_point2(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", na.rm = FALSE, show.legend = NA,

-  inherit.aes = TRUE, ...)

-}

-\arguments{

-\item{mapping}{aes mapping}

-

-\item{data}{data}

-

-\item{stat}{stat}

-

-\item{position}{position}

-

-\item{na.rm}{logical}

-

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

-\item{...}{addktional parameter}

-}

-\value{

-point layer

-}

-\description{

-geom_point2 support aes(subset) via setup_data

-}

-\author{

-Guangchuang Yu

-}

-\seealso{

-\link[ggplot2]{geom_point}

-}

-

@@ -4,26 +4,12 @@

 \alias{geom_rootpoint}

 \title{geom_rootpoint}

 \usage{

-geom_rootpoint(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", na.rm = FALSE, show.legend = NA,

-  inherit.aes = TRUE, ...)

+geom_rootpoint(mapping = NULL, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

-\item{data}{data}

-

-\item{stat}{stat}

-

-\item{position}{position}

-

-\item{na.rm}{logical}

-

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

-\item{...}{addktional parameter}

+\item{...}{additional parameter}

 }

 \value{

 root point layer

deleted file mode 100644

@@ -1,44 +0,0 @@

-% Generated by roxygen2 (4.1.1): do not edit by hand

-% Please edit documentation in R/geom_segment.R

-\name{geom_segment2}

-\alias{geom_segment2}

-\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, ...)

-}

-\arguments{

-\item{mapping}{aes mapping}

-

-\item{data}{data}

-

-\item{stat}{stat}

-

-\item{position}{position}

-

-\item{arrow}{arrow}

-

-\item{lineend}{lineend}

-

-\item{na.rm}{logical}

-

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

-\item{...}{additional parameter}

-}

-\value{

-add segment layer

-}

-\description{

-geom_segment2 support aes(subset) via setup_data

-}

-\author{

-Guangchuang Yu

-}

-\seealso{

-\link[ggplot2]{geom_segment}

-}

-

@@ -10,9 +10,7 @@ read for the geom_text function can be found here: \link[ggplot2]{geom_text}

 }

 \usage{

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

-  position = "identity", parse = FALSE, show.legend = NA,

-  inherit.aes = TRUE, ..., nudge_x = 0, nudge_y = 0,

-  check_overlap = FALSE)

+  position = "identity", parse = FALSE, ...)

 }

 \arguments{

 \item{mapping}{the aesthetic mapping}

@@ -26,17 +24,7 @@ only needed if you want to override he plot defaults.}

 \item{parse}{if TRUE, the labels will be passd into expressions}

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

 \item{...}{other arguments passed on to 'layer'}

-

-\item{nudge_x}{horizontal adjustment}

-

-\item{nudge_y}{vertical adjustment}

-

-\item{check_overlap}{if TRUE, text that overlaps previous text in the same layer will not be plotted}

 }

 \description{

 text annotations

deleted file mode 100644

@@ -1,48 +0,0 @@

-% Generated by roxygen2 (4.1.1): do not edit by hand

-% Please edit documentation in R/geom_text.R

-\name{geom_text2}

-\alias{geom_text2}

-\title{geom_text2}

-\usage{

-geom_text2(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", parse = FALSE, show.legend = NA,

-  inherit.aes = TRUE, ..., nudge_x = 0, nudge_y = 0,

-  check_overlap = FALSE)

-}

-\arguments{

-\item{mapping}{the aesthetic mapping}

-

-\item{data}{A layer specific dataset -

-only needed if you want to override he plot defaults.}

-

-\item{stat}{The statistical transformation to use on the data for this layer}

-

-\item{position}{The position adjustment to use for overlapping points on this layer}

-

-\item{parse}{if TRUE, the labels will be passd into expressions}

-

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

-\item{...}{other arguments passed on to 'layer'}

-

-\item{nudge_x}{horizontal adjustment}

-

-\item{nudge_y}{vertical adjustment}

-

-\item{check_overlap}{if TRUE, text that overlaps previous text in the same layer will not be plotted}

-}

-\value{

-text layer

-}

-\description{

-geom_text2 support aes(subset) via setup_data

-}

-\author{

-Guangchuang Yu

-}

-\seealso{

-\link[ggplot2]{geom_text}

-}

-

@@ -4,26 +4,12 @@

 \alias{geom_tippoint}

 \title{geom_tippoint}

 \usage{

-geom_tippoint(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", na.rm = FALSE, show.legend = NA,

-  inherit.aes = TRUE, ...)

+geom_tippoint(mapping = NULL, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

-\item{data}{data}

-

-\item{stat}{stat}

-

-\item{position}{position}

-

-\item{na.rm}{logical}

-

-\item{show.legend}{logical}

-

-\item{inherit.aes}{logical}

-

-\item{...}{addktional parameter}

+\item{...}{additional parameter}

 }

 \value{

 tip point layer

@@ -289,7 +289,7 @@ With _`collapse`_ function, user can collapse a selected clade.

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

 cp <- ggtree(tree) %>% collapse(node=21)

-cp + geom_point2(aes(subset=(node == 21)), size=5, shape=23, fill="steelblue")

+cp + geom_point(subset=.(node == 21), size=5, shape=23, fill="steelblue")

 ```

 ## expand collapsed clade

@@ -401,8 +401,8 @@ With _`groupOTU`_ and _`groupClade`_, it's easy to highlight selected taxa and e

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

 ggtree(tree, aes(color=group, linetype=group)) +

-    geom_text2(aes(label=label, subset=(group==2)), hjust = -.5) +

-        geom_text2(aes(label=label, subset=(group==1)), hjust = -.5, color="blue")

+    geom_text(aes(label=label), subset=.(group==2), hjust = -.5) +

+        geom_text(aes(label=label), subset=.(group==1), hjust = -.5, color="blue")

 ```