@@ -1,8 +1,6 @@

 .git

 .Rhistory

 R/.Rhistory

-

-Makefile

 Makefile

 TODO.md

 README.md

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

 Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-Version: 1.5.6

+Version: 1.5.7

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.

@@ -23,6 +23,7 @@ Suggests:

     Biostrings,

     colorspace,

     EBImage,

+    emojifont,

     knitr,

     rmarkdown,

     scales,

@@ -85,6 +85,7 @@ export(merge_tree)

 export(msaplot)

 export(multiplot)

 export(nodebar)

+export(nodeid)

 export(nodepie)

 export(open_tree)

 export(phyPML)

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 1.5.7

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

+ o geom_strip now only accept node id as input and support labeling strip <2016-07-27, Wed>

+ o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed> 

+ 

 CHANGES IN VERSION 1.5.6

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

  o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>

@@ -43,14 +43,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     if (geom == "text") {

         ## no fill parameter

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, angle=angle, family=family,

+                                    align=align, size=fontsize, barextend=barextend, angle=angle, family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, ...)

     } else {

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, angle=angle, fill=fill,family=family,

+                                    align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, ...)

@@ -65,9 +65,9 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

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

                            geom="text", position="identity",

-                           taxa1, taxa2, label, offset, align, ...,

+                           taxa1, taxa2, label, offset, align, barextend, ...,

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

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

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

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

@@ -86,6 +86,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       label=label,

                       offset=offset,

                       align=align,

+                      barextend=barextend,

                       na.rm=na.rm,

                       ...)

           )

@@ -96,7 +97,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

                           geom="segment", position="identity",

                           taxa1, taxa2, offset, align, barextend, ...,

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

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

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

     if (is.null(mapping)) {

         mapping <- default_aes

     } else {

@@ -123,8 +124,8 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

 StatStripText <- ggproto("StatStripText", Stat,

                          compute_group = function(self, data, scales, params, taxa1, taxa2,

-                                                  label, offset, align) {

-                             df <- get_striplabel_position(data, taxa1, taxa2, offset, align, adjustRatio = 1.03)

+                                                  label, offset, align, barextend) {

+                             df <- get_striplabel_position(data, taxa1, taxa2, offset, align, barextend, adjustRatio = 1.03)

                              df$y <- mean(c(df$y, df$yend))

                              df$label <- label

                              return(df)

@@ -167,6 +168,9 @@ get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {

 ## used in geom_strip, geom_taxalink

 taxa2node <- function(data, taxa) {

+    if (! 'label' %in% colnames(data))

+        data$label <- NA

+

     idx <- with(data, which(taxa == label | taxa == node))

     if (length(idx) == 0) {

@@ -1,3 +1,30 @@

+##' convert tip or node label(s) to internal node number

+##'

+##' 

+##' @title nodeid

+##' @param x tree object or graphic object return by ggtree

+##' @param label tip or node label(s)

+##' @return internal node number

+##' @export

+##' @author Guangchuang Yu

+nodeid <- function(x, label) {

+    if (is(x, "gg")) 

+        return(nodeid.gg(x, label))

+    

+    nodeid.tree(x, label)

+}

+

+nodeid.tree <- function(tree, label) {

+    tr <- get.tree(tree)

+    lab <- c(tr$tip.label, tr$node.label)

+    match(label, lab)

+}

+

+nodeid.gg <- function(p, label) {

+    p$data$node[match(label, p$data$label)]

+}

+    

+

 reroot_node_mapping <- function(tree, tree2) {

     root <- getRoot(tree)

@@ -31,7 +31,6 @@ library("ggplot2")

 library("ggtree")

 ```

-

 # Layers that allows subsetting

 `Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s). 

@@ -182,7 +182,7 @@ ggtree(tree) +

 `geom_cladelabel` is designed for labelling Monophyletic (Clade) while there are related taxa that are not form a clade. `ggtree` provides `geom_strip` to add a strip/bar to indicate the association with optional label (see [the issue](https://github.com/GuangchuangYu/ggtree/issues/52)).

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

-ggtree(tree) + geom_tiplab() + geom_strip('E', 'G', barsize=2, color='red') + geom_strip('F', 'L', barsize=2, color='blue')

+ggtree(tree) + geom_tiplab() + geom_strip(5, 7, barsize=2, color='red') + geom_strip(6, 12, barsize=2, color='blue')

 ```

 # taxa connection