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

 Package: ggtree

 Type: Package

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

-Version: 1.3.14

+Version: 1.3.15

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -40,6 +40,7 @@ export(geom_cladelabel)

 export(geom_hilight)

 export(geom_nodepoint)

 export(geom_point2)

+export(geom_range)

 export(geom_rootpoint)

 export(geom_segment2)

 export(geom_text2)

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.3.15

+------------------------

+ o geom_range for adding range of HPD to present uncertainty of evolutionary inference <2016-04-01, Fri>

+ 

 CHANGES IN VERSION 1.3.14

 ------------------------

  o geom_tiplab works with NA values, compatible with collapse <2016-03-05, Sat>

@@ -108,9 +112,9 @@ CHANGES IN VERSION 1.3.1

    + see https://github.com/hadley/ggplot2/issues/1380

  o matching beast stats with tree using internal node number instead of label <2015-10-20, Tue>

-CHANGES IN VERSION 1.3.0

+CHANGES IN VERSION 1.2.0

 ------------------------

- o BioC 3.3 branch

+ o BioC 3.2 released

 CHANGES IN VERSION 1.1.21

 ------------------------

@@ -1,30 +1,2 @@

-add_range <- function(p, ...) {

-    df <- p$data

-    rr <- gsub("\\[", "", df$height_range)

-    rr <- gsub("\\]", "", rr)

-    rr2 <- strsplit(rr, split=',') %>% do.call('rbind', .)

-    rr2 <- matrix(as.numeric(rr2), ncol=2, byrow=FALSE)

-    ## if (!is.null(mrsd)) {

-    ##     mrsd %<>% as.Date

-    ##     date <- Date2decimal(mrsd)

-    ##     rr2 <- rr2 + date - max(rr2)

-    ##     if (asDate) {

-    ##         rr2 <- decimal2Date(rr2)

-    ##     }

-    ## }

-    rr2 <- rr2 + df$x - df$height

-    p + geom_segment2(x=rr2[,1], xend=rr2[,2], y=df$y, yend=df$y, ...)

-}

-## add range of height, only work with beast and only for height

-## when I have an idea of implementing such feature for all range

-## I will export it and make it usable for all users.

-##

-##

-## file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")

-## beast <- read.beast(file)

-## p <- ggtree(beast)

-## add_range(p, color='firebrick', size=2, alpha=.3)

-##

-## p <- ggtree(beast, mrsd='2013-01-01') + theme_tree2()

-## add_range(p, color='firebrick', size=2, alpha=.3)

+

@@ -17,7 +17,7 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5) {

     stat = "hilight"

     position = "identity"

     show.legend = NA

-    na.rm = FALSE

+    na.rm = TRUE

     inherit.aes = FALSE

     default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, branch.length=~branch.length)

new file mode 100644

@@ -0,0 +1,58 @@

+##' bar of range (HPD, range etc) to present uncertainty of evolutionary inference

+##'

+##' 

+##' @title geom_range

+##' @param range range, e.g. "height_0.95_HPD"

+##' @param ... additional parameter, e.g. color, size, alpha

+##' @return ggplot layer

+##' @importFrom ggplot2 aes_string

+##' @export

+##' @author Guangchuang Yu

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

+

+    stat = "range"

+    position = "identity"

+    show.legend = NA

+    na.rm = TRUE

+    inherit.aes = FALSE    

+

+    if (range == "height_0.95_HPD") {

+        branch.length = "height"

+    } else {

+        branch.length = "branch.length"

+    }

+    default_aes <- aes_(x=~x, y=~y)

+    mapping <- modifyList(default_aes, aes_string(branch.length=branch.length, label=range))

+        

+    layer(

+        stat = StatRange,

+        mapping = mapping,

+        data = NULL,

+        geom = GeomSegment,

+        position = position,

+        show.legend=show.legend,

+        inherit.aes = inherit.aes,

+        params = list(na.rm = na.rm, ...)

+    )

+    

+}

+

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

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

+                         ## label is actually the range

+                         

+                         df <- data[!is.na(data[,"label"]),]

+                         rr <- gsub("\\[", "", df[,"label"])

+                         rr <- gsub("\\]", "", rr)

+                         rr2 <- strsplit(rr, split=',') %>% do.call('rbind', .)

+                         rr2 <- matrix(as.numeric(rr2), ncol=2, byrow=FALSE)

+                         rr2 <- rr2 + df$x - df$branch

+                         data.frame(x = rr2[,1],

+                                    xend = rr2[,2],

+                                    y = df$y,

+                                    yend = df$y)

+                     },

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

+                     )

+

+

new file mode 100644

@@ -0,0 +1,23 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_range.R

+\name{geom_range}

+\alias{geom_range}

+\title{geom_range}

+\usage{

+geom_range(range = "height_0.95_HPD", ...)

+}

+\arguments{

+\item{range}{range, e.g. "height_0.95_HPD"}

+

+\item{...}{additional parameter, e.g. color, size, alpha}

+}

+\value{

+ggplot layer

+}

+\description{

+bar of range (HPD, range etc) to present uncertainty of evolutionary inference

+}

+\author{

+Guangchuang Yu

+}

+