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

 Package: ggtree

 Type: Package

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

-Version: 1.5.5

+Version: 1.5.6

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -27,6 +27,7 @@ export("%>%")

 export(.)

 export(Date2decimal)

 export(MRCA)

+export(StatBalance)

 export(StatHilight)

 export(add_colorbar)

 export(annotation_image)

@@ -38,6 +39,7 @@ export(download.phylopic)

 export(expand)

 export(flip)

 export(geom_aline)

+export(geom_balance)

 export(geom_cladelabel)

 export(geom_hilight)

 export(geom_label2)

@@ -67,6 +69,7 @@ export(get.treeinfo)

 export(get.treetext)

 export(getNodeNum)

 export(getRoot)

+export(get_balance_position)

 export(get_clade_position)

 export(get_heatmap_column_position)

 export(get_taxa_name)

@@ -108,6 +111,7 @@ export(rtree)

 export(scaleClade)

 export(scale_color)

 export(scale_x_ggtree)

+export(stat_balance)

 export(stat_hilight)

 export(subview)

 export(theme_inset)

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

+CHANGES IN VERSION 1.5.6

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

+ o geom_balance contributed by Justin Silverman <2016-06-22, Wed>

+   + see https://github.com/GuangchuangYu/ggtree/pull/64

+

 CHANGES IN VERSION 1.5.5

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

  o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>

@@ -1,24 +1,6 @@

-##' read newick tree

+

 ##' @export

-##' @rdname read.tree

-##' @param file file name

-##' @param text alternatively, using newick text

-##' @param tree.names if read several trees, specify their names

-##' @param skip number of lines of the input file to skip

-##' @param comment.char a single character,

-##'                     the remaining of the line after this character is ignored.

-##' @param keep.multi if 'TRUE' and 'tree.names = NULL'

-##'                   then single trees are returned in 'multiPhylo' format

-##'                   with any name that is present. Default is 'FALSE'

-##' @param ... further arguments to be passed to 'scan()'.

-##' @source

-##' This is just the imported function

-##' from the ape package. The documentation you should

-##' read for the read.tree function can be found here: \link[ape]{read.tree}

-##'

-##' @seealso

-##' \link[ape]{read.tree}

-read.tree <- ape::read.tree

+ape::read.tree

 ##' generate random tree

new file mode 100644

@@ -0,0 +1,208 @@

+#' highlights the two direct descendant clades of an internal node

+#' 

+#' Particularly useful when studying neighboring clades. Note that balances that

+#' correspond to multichotomies will not be displayed.

+#' 

+#' @title geom_balance

+#' @param node selected node (balance) to highlight

+#' @param fill color fill

+#' @param color color to outline highlights and divide balance

+#' @param alpha alpha (transparency)

+#' @param extend extend xmax of the rectangle

+#' @param extendto extend xmax to extendto

+#' @return ggplot2

+#' @export

+#' @importFrom ggplot2 aes_

+#' @importFrom ggplot2 GeomRect

+#' @author Justin Silverman

+#' @references J. Silverman, et al. \emph{A phylogenetic transform enhances

+#'   analysis of compositional microbiota data}. (in preparation)

+geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend=0, extendto=NULL) {

+  

+  data = NULL

+  stat = "balance"

+  position = "identity"

+  show.legend = NA

+  na.rm = TRUE

+  inherit.aes = FALSE

+  

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

+  mapping <- default_aes

+  

+  l1 <- layer(

+    stat=StatBalance,

+    data = data,

+    mapping = mapping,

+    geom = GeomRect,

+    position = position,

+    show.legend=show.legend,

+    inherit.aes = inherit.aes,

+    params = list(node=node,

+                  fill=fill,

+                  color=color,

+                  alpha=alpha,

+                  extend=extend,

+                  extendto=extendto,

+                  direction=1, 

+                  na.rm = na.rm)

+  )

+  l2 <- layer(

+    stat=StatBalance,

+    data = data,

+    mapping = mapping,

+    geom = GeomRect,

+    position = position,

+    show.legend=show.legend,

+    inherit.aes = inherit.aes,

+    params = list(node=node,

+                  fill=fill,

+                  color=color,

+                  alpha=alpha,

+                  extend=extend,

+                  extendto=extendto,

+                  direction=2,

+                  na.rm = na.rm)

+  )

+  return(c(l1,l2))

+}

+

+#' stat_balance

+#'

+#'

+#' @title stat_balance

+#' @param mapping aes mapping

+#' @param data data

+#' @param geom geometric object

+#' @param position position

+#' @param node node number

+#' @param show.legend show legend

+#' @param inherit.aes logical

+#' @param fill fill color

+#' @param color color to outline highlights and divide balance

+#' @param alpha transparency

+#' @param extend extend xmax of the rectangle

+#' @param extendto extend xmax to extendto

+#' @param ... additional parameter

+#' @return layer

+#' @importFrom ggplot2 layer

+#' @export

+stat_balance <- function(mapping=NULL, data=NULL, geom="rect",

+                         position="identity",  node, 

+                         show.legend=NA, inherit.aes=FALSE,

+                         fill, color, alpha, extend=0, extendto=NULL,

+                         ...) {

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

+  if (is.null(mapping)) {

+    mapping <- default_aes

+  } else {

+    mapping <- modifyList(mapping, default_aes)

+  }

+  

+  l1 <- layer(

+    stat=StatBalance,

+    data = data,

+    mapping = mapping,

+    geom = geom,

+    position = position,

+    show.legend=show.legend,

+    inherit.aes = inherit.aes,

+    params = list(node=node,

+                  fill=fill,

+                  color=color,

+                  alpha=alpha,

+                  extend=extend,

+                  extendto=extendto,

+                  direction=1,

+                  ...)

+  )

+  l2 <- layer(

+    stat=StatBalance,

+    data = data,

+    mapping = mapping,

+    geom = geom,

+    position = position,

+    show.legend=show.legend,

+    inherit.aes = inherit.aes,

+    params = list(node=node,

+                  fill=fill,

+                  color=color,

+                  alpha=alpha,

+                  extend=extend,

+                  extendto=extendto,

+                  direction=2,

+                  ...)

+  )

+  return(c(l1,l2))

+}

+

+##' StatBalance

+##' @rdname ggtree-ggproto

+##' @format NULL

+##' @usage NULL

+##' @importFrom ggplot2 Stat

+##' @export

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

+                       compute_group = function(self, data, scales, params, node, extend, extendto, direction) {

+                         df <- get_balance_position_(data, node, direction)

+                         

+                         df$xmax <- df$xmax + extend

+                         if (!is.null(extendto) && !is.na(extendto)) {

+                           if (extendto < df$xmax) {

+                             warning("extendto is too small, keep the original xmax value...")

+                           } else {

+                             df$xmax <- extendto

+                           }

+                         }

+                         return(df)

+                       },

+                       required_aes = c("x", "y", "branch.length")

+)

+

+

+#' get position of balance (xmin, xmax, ymin, ymax)

+#'

+#'

+#' @title get_balance_position

+#' @param treeview tree view

+#' @param node selected node

+#' @param direction either (1 for 'up' or 2 for 'down') 

+#' @return data.frame

+#' @export

+#' @author Justin Silverman

+get_balance_position <- function(treeview, node, direction) {

+  get_balance_position_(treeview$data, node, direction)

+}

+

+get_balance_position_ <- function(data, node, direction) {

+  ch <- tryCatch(getChild.df(data, node), error=function(e) NULL)

+  

+  if (length(ch) < 2 || is.null(ch)){

+    stop('balance cannot be a tip')

+  } else if (length(ch) > 2){

+    stop('balance has >2 direct child nodes, can use ape::multi2di to convert to binary tree')

+  }

+  

+  i <- match(node, data$node)

+  sp <- tryCatch(get.offspring.df(data, ch[direction]), error=function(e) ch[direction])

+  sp.all <- get.offspring.df(data, i)

+  sp.df <- data[match(sp, data$node),]

+  sp.all.df <- data[match(sp.all, data$node),]

+  n.df <- data[i,]

+  

+  # X direction is uniform for both children, but y is only based on range of

+  # one of the two children (direction)

+  x <- sp.all.df$x

+  y <- sp.df$y

+  #x.n <- n.df$x

+

+  if ("branch.length" %in% colnames(data)) {

+   xmin <- min(x)-data[i, "branch.length"]/2

+  } else {

+   xmin <- min(sp.df$branch)

+  }

+  #xmin <- x.n

+  data.frame(xmin=xmin,

+             xmax = max(x),

+             ymin=min(y)-0.5,

+             ymax=max(y)+0.5)

+}

\ No newline at end of file

@@ -31,20 +31,25 @@ mask <- function(tree_object, field, site, mask_site=FALSE) {

     }

     field_data <- sapply(field_data, gsub, pattern="\n", replacement="/")

+

+    x <- field_data[field_data != ""]

+    x <- x[!is.na(x)]

+    pos <- strsplit(x, " / ") %>% unlist %>%

+        gsub("^[a-zA-Z]+", "", . ) %>%

+        gsub("[a-zA-Z]\\s*$", "", .) %>%

+        as.numeric

     if (mask_site == FALSE) {

-        x <- field_data[field_data != ""]

-        x <- x[!is.na(x)]

-        pos <- strsplit(x, " / ") %>% unlist %>%

-            gsub("^[a-zA-Z]+", "", . ) %>%

-                gsub("[a-zA-Z]\\s*$", "", .) %>%

-                    as.numeric

         pos2 <- 1:max(pos)

         pos2 <- pos2[-site]

         site <- pos2

     }

+    site <- site[site %in% pos]

+    

     for (i in seq_along(field_data)) {

+        if (is.na(field_data[i]))

+            next

         for (j in seq_along(site)) {

             pattern <- paste0("/*\\s*[a-zA-Z]", site[j], "[a-zA-Z]\\s*")

             field_data[i] <- gsub(pattern, "",  field_data[i])

@@ -1,3 +1,4 @@

+

 filename <- function(file) {

     ## textConnection(text_string) will work just like a file

     ## in this case, just set the filename as ""

@@ -27,9 +27,9 @@ Please cite the following article when using `ggtree`:

 ```

 G Yu, D Smith, H Zhu, Y Guan, TTY Lam,

-ggtree: an R package for visualization and annotation of phylogenetic tree 

-		with different types of meta-data.

-Methods in Ecology and Evolution, submitted

+ggtree: an R package for visualization and annotation of phylogenetic trees 

+        with their covariates and other associated data.

+Methods in Ecology and Evolution, revised

 ```

 ## License ##

@@ -50,7 +50,7 @@ To view the vignette of `ggtree` installed in your system, start `R` and enter:

 vignette("ggtree", package = "ggtree")

 ```

-More documents can be found in <http://guangchuangyu.github.io/tags/ggtree>.

+More documents can be found in <https://guangchuangyu.github.io/ggtree>.

 ## Bugs/Feature requests ##

@@ -2,7 +2,7 @@ citHeader("To cite ggtree in publications use:")

 citEntry(

     entry  = "article",

-    title  = "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data",

+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",

     author = personList(

         as.person("Guangchuang Yu"),

         as.person("David Smith"),

@@ -10,7 +10,7 @@ citEntry(

         as.person("Yi Guan"),

         as.person("Tommy Tsan-Yuk Lam")

         ),

-    year    = "submitted",

+    year    = "revised",

     journal = "Methods in Ecology and Evolution",

     volume  = "",

     issue   = "",

@@ -20,7 +20,7 @@ citEntry(

     PMID    = "",

     url     = "", 

     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",

-        "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.",

-        "Methods in Ecology and Evolution submitted")

+        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",

+        "Methods in Ecology and Evolution revised")

 )

new file mode 100644

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

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_balance.R

+\name{geom_balance}

+\alias{geom_balance}

+\title{geom_balance}

+\usage{

+geom_balance(node, fill = "steelblue", color = "white", alpha = 0.5,

+  extend = 0, extendto = NULL)

+}

+\arguments{

+\item{node}{selected node (balance) to highlight}

+

+\item{fill}{color fill}

+

+\item{color}{color to outline highlights and divide balance}

+

+\item{alpha}{alpha (transparency)}

+

+\item{extend}{extend xmax of the rectangle}

+

+\item{extendto}{extend xmax to extendto}

+}

+\value{

+ggplot2

+}

+\description{

+highlights the two direct descendant clades of an internal node

+}

+\details{

+Particularly useful when studying neighboring clades. Note that balances that

+correspond to multichotomies will not be displayed.

+}

+\author{

+Justin Silverman

+}

+\references{

+J. Silverman, et al. \emph{A phylogenetic transform enhances

+  analysis of compositional microbiota data}. (in preparation)

+}

+

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_balance.R

+\name{get_balance_position}

+\alias{get_balance_position}

+\title{get_balance_position}

+\usage{

+get_balance_position(treeview, node, direction)

+}

+\arguments{

+\item{treeview}{tree view}

+

+\item{node}{selected node}

+

+\item{direction}{either (1 for 'up' or 2 for 'down')}

+}

+\value{

+data.frame

+}

+\description{

+get position of balance (xmin, xmax, ymin, ymax)

+}

+\author{

+Justin Silverman

+}

+

@@ -1,10 +1,13 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/geom_hilight.R

+% Please edit documentation in R/geom_balance.R, R/geom_hilight.R

 \docType{data}

-\name{StatHilight}

+\name{StatBalance}

+\alias{StatBalance}

 \alias{StatHilight}

-\title{StatHilight}

+\title{StatBalance}

 \description{

+StatBalance

+

 StatHilight

 }

 \keyword{datasets}

deleted file mode 100644

@@ -1,39 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ape.R

-\name{read.tree}

-\alias{read.tree}

-\title{read newick tree}

-\source{

-This is just the imported function

-from the ape package. The documentation you should

-read for the read.tree function can be found here: \link[ape]{read.tree}

-}

-\usage{

-read.tree(file = "", text = NULL, tree.names = NULL, skip = 0,

-  comment.char = "#", keep.multi = FALSE, ...)

-}

-\arguments{

-\item{file}{file name}

-

-\item{text}{alternatively, using newick text}

-

-\item{tree.names}{if read several trees, specify their names}

-

-\item{skip}{number of lines of the input file to skip}

-

-\item{comment.char}{a single character,

-the remaining of the line after this character is ignored.}

-

-\item{keep.multi}{if 'TRUE' and 'tree.names = NULL'

-then single trees are returned in 'multiPhylo' format

-with any name that is present. Default is 'FALSE'}

-

-\item{...}{further arguments to be passed to 'scan()'.}

-}

-\description{

-read newick tree

-}

-\seealso{

-\link[ape]{read.tree}

-}

-

new file mode 100644

@@ -0,0 +1,16 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/ape.R

+\docType{import}

+\name{reexports}

+\alias{read.tree}

+\alias{reexports}

+\title{Objects exported from other packages}

+\description{

+These objects are imported from other packages. Follow the links

+below to see their documentation.

+

+\describe{

+  \item{ape}{\code{\link[ape]{read.tree}}}

+}}

+\keyword{internal}

+

new file mode 100644

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

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_balance.R

+\name{stat_balance}

+\alias{stat_balance}

+\title{stat_balance}

+\usage{

+stat_balance(mapping = NULL, data = NULL, geom = "rect",

+  position = "identity", node, show.legend = NA, inherit.aes = FALSE,

+  fill, color, alpha, extend = 0, extendto = NULL, ...)

+}

+\arguments{

+\item{mapping}{aes mapping}

+

+\item{data}{data}

+

+\item{geom}{geometric object}

+

+\item{position}{position}

+

+\item{node}{node number}

+

+\item{show.legend}{show legend}

+

+\item{inherit.aes}{logical}

+

+\item{fill}{fill color}

+

+\item{color}{color to outline highlights and divide balance}

+

+\item{alpha}{transparency}

+

+\item{extend}{extend xmax of the rectangle}

+

+\item{extendto}{extend xmax to extendto}

+

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

+}

+\value{

+layer

+}

+\description{

+stat_balance

+}

+

new file mode 100644

@@ -0,0 +1,13 @@

+context('geom_balance')

+

+test_that('geom_balance gives proper errors if called on non-binary node', {

+  tr <- ape::read.tree(text="(t2:0.1280947195,(t4:0.2642134866,(t3:0.9758362926,(t1:0.3494729637,t5:0.189841171,t6:0.189841171):0.7222939907):0.3401968146):0.5143072554);")

+  

+  # Note: For some reason while ggplot will give warning and properly does not show

+  # the problematic geom, the output of the function is not recognized as a warning. 

+  # This is not crutial but it makes adding unit tests more difficult. 

+  #expect_warning(ggtree(tr)+geom_balance(10), '>2 direct child nodes')

+  #expect_warning(ggtree(tr)+geom_balance(3), 'balance cannot be a tip') 

+  

+  expect_true(is.ggplot(ggtree(tr)+geom_balance(9))) # should plot appropriately

+})

\ No newline at end of file

@@ -45,8 +45,8 @@ If you use `ggtree` in published research, please cite:

 ```

 G Yu, D Smith, H Zhu, Y Guan, TTY Lam,

-ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.

-revised.

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

+Methods in Ecology and Evolution, revised.

 ```

 # Introduction

@@ -169,10 +169,19 @@ ggtree(tree, layout="circular") + geom_hilight(node=21, fill="steelblue", alpha=

 Another way to highlight selected clades is setting the clades with different colors and/or line types as demonstrated in [Tree Manipulation](treeManipulation.html#groupclade) vignette.

+# Highlight balances

+In addition to _`geom_hilight`_, `ggtree` also implements _`geom_balance`_

+which is designed to highlight neighboring subclades of a given internal node. 

+

+```{r fig.width=4, fig.height=5, fig.align='center', warning=FALSE}

+ggtree(tree) + 

+  geom_balance(node=16, fill='steelblue', color='white', alpha=0.6, extend=1) +

+  geom_balance(node=19, fill='darkgreen', color='white', alpha=0.6, extend=1)

+```

 # labelling associated taxa (Monophyletic, Polyphyletic or Paraphyletic)

-`geom_cladelabel` is designed to 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)).

+`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')