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

 Package: ggtree

 Type: Package

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

-Version: 0.99.18

+Version: 0.99.19

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -25,6 +25,7 @@ export(geom_tippoint)

 export(geom_tree)

 export(get.fields)

 export(get.offspring.tip)

+export(get.path)

 export(get.phylopic)

 export(get.placements)

 export(get.subs)

@@ -32,6 +33,8 @@ export(get.tipseq)

 export(get.tree)

 export(get.treeinfo)

 export(get.treetext)

+export(getNodeNum)

+export(getRoot)

 export(ggplotGrob)

 export(ggtree)

 export(gplot)

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

+CHANGES IN VERSION 0.99.19

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

+ o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu>

+ 

 CHANGES IN VERSION 0.99.18

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

  o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>

@@ -250,6 +250,15 @@ get.offspring.tip <- function(tr, node) {

     clade$tip.label

 }

+

+##' calculate total number of nodes

+##'

+##' 

+##' @title getNodeNum

+##' @param tr phylo object

+##' @return number 

+##' @author Guangchuang Yu

+##' @export

 getNodeNum <- function(tr) {

     Ntip <- length(tr[["tip.label"]])

     Nnode <- tr[["Nnode"]]

@@ -328,6 +337,14 @@ getNodeName <- function(tr) {

     return(nodeName)

 }

+##' get the root number 

+##'

+##' 

+##' @title getRoot

+##' @param tr phylo object

+##' @return root number

+##' @export

+##' @author Guangchuang Yu

 getRoot <- function(tr) {

     edge <- tr[["edge"]]

     ## 1st col is parent,

@@ -349,6 +366,16 @@ get.trunk <- function(tr) {

     return(get.path(tr, root, i))

 }

+##' path from start node to end node

+##'

+##' 

+##' @title get.path

+##' @param phylo phylo object

+##' @param from start node

+##' @param to end node

+##' @return node vectot

+##' @export

+##' @author Guangchuang Yu

 get.path <- function(phylo, from, to) {

     anc_from <- getAncestor(phylo, from)

     anc_from <- c(from, anc_from)

@@ -109,7 +109,8 @@ fortify.beast <- function(model, data,

                           yscale    = "none",

                           ladderize = TRUE,

                           right     =FALSE,

-                          ndigits   = NULL, ...) {

+                          ndigits   = NULL,

+                          time_scale = FALSE, ...) {

     phylo <- get.tree(model)

     df    <- fortify(phylo, layout=layout,

@@ -187,10 +188,19 @@ fortify.beast <- function(model, data,

     df <- cbind(df, stats)

     df <- scaleY(phylo, df, yscale, layout, ...)

+    if (time_scale) {

+        df <- scaleX_by_time(df)

+    }

+    

     return(df)

 }

-

+scaleX_by_time <- function(df) {

+    time <- with(df, gsub(".*_(\\d+\\.\\d+)", "\\1", label[isTip]))

+    latest <- which.max(time)

+    df$x <- df$x + as.numeric(time[latest]) - max(df$x)

+    return(df)

+}

 ##' @method fortify codeml

 ##' @export

@@ -607,5 +607,5 @@ Begin trees;

 		298 'V01086_A_Victoria_3_1975_H3N2_1975.50',

 		299 'X05907_A_England_321_1977_H3N2_1977.50'

 		;

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+tree TREE1 = [&R] 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