@@ -43,6 +43,7 @@ export(geom_point2)

 export(geom_range)

 export(geom_rootpoint)

 export(geom_segment2)

+export(geom_taxalink)

 export(geom_text2)

 export(geom_tiplab)

 export(geom_tippoint)

@@ -153,6 +154,7 @@ importFrom(ape,reorder.phylo)

 importFrom(ape,which.edge)

 importFrom(ape,write.tree)

 importFrom(ggplot2,"%+replace%")

+importFrom(ggplot2,GeomCurve)

 importFrom(ggplot2,GeomPoint)

 importFrom(ggplot2,GeomRect)

 importFrom(ggplot2,GeomSegment)

@@ -9,8 +9,6 @@

 ##' @export

 ##' @author Guangchuang Yu

 geom_range <- function(range="height_0.95_HPD", ...) {

-

-    stat = "range"

     position = "identity"

     show.legend = NA

     na.rm = TRUE

new file mode 100644

@@ -0,0 +1,55 @@

+##' link between taxa

+##'

+##' 

+##' @title geom_taxalink

+##' @param taxa1 taxa1, can be label or node number

+##' @param taxa2 taxa2, can be label or node number

+##' @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 ... additional parameter

+##' @return ggplot layer

+##' @export

+##' @importFrom ggplot2 GeomCurve

+##' @author Guangchuang Yu

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

+    position = "identity"

+    show.legend = NA

+    na.rm = TRUE

+    inherit.aes = FALSE    

+

+    mapping <- aes_(x=~x, y=~y, node=~node, label=~label)

+

+    layer(stat=StatTaxalink,

+          mapping=aes_(x=~x, y=~y, node=~node, label=~label),

+          geom=GeomCurve,

+          position='identity',

+          show.legend=show.legend,

+          inherit.aes = inherit.aes,

+          params = list(taxa1 = taxa1,

+                        taxa2 = taxa2,

+                        curvature = curvature,

+                        na.rm = na.rm,

+                        ...)

+          )

+}

+

+

+StatTaxalink <- ggproto("StatTaxalink", Stat,

+                        compute_group = function(self, data, scales, params, taxa1, taxa2) {

+                            node <- data$node

+                            label <- data$label

+                            node1 <- which(taxa1 == label | taxa1 == node)

+                            node2 <- which(taxa2 == label | taxa2 == node)

+                            x <- data$x

+                            y <- data$y

+                            

+                            data.frame(x = x[node1],

+                                       xend = x[node2],

+                                       y = y[node1],

+                                       yend = y[node2])

+                            

+                        },

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

+                        )

+

new file mode 100644

@@ -0,0 +1,29 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_taxalink.R

+\name{geom_taxalink}

+\alias{geom_taxalink}

+\title{geom_taxalink}

+\usage{

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

+}

+\arguments{

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

+

+\item{taxa2}{taxa2, can be label or node number}

+

+\item{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.}

+

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

+}

+\value{

+ggplot layer

+}

+\description{

+link between taxa

+}

+\author{

+Guangchuang Yu

+}

+