1. ggtree
  2. Commit 13e3fd30125b69aff4b714595a57c3ef58e4b778
Browse code

update citation info

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118925 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 24/06/2016 06:22:28
Showing 18 changed files
DESCRIPTION
History View file @ 13e3fd3
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: ggtree
2 2 
 Type: Package
3 3 
 Title: a phylogenetic tree viewer for different types of tree annotations
4 
-Version: 1.5.5
4 
+Version: 1.5.6
5 5 
 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
6 6 
 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
7 7 
 Description: ggtree extends the ggplot2 plotting system which implemented the
NAMESPACE
History View file @ 13e3fd3
... ... 
@@ -27,6 +27,7 @@ export("%>%")
27 27 
 export(.)
28 28 
 export(Date2decimal)
29 29 
 export(MRCA)
30 
+export(StatBalance)
30 31 
 export(StatHilight)
31 32 
 export(add_colorbar)
32 33 
 export(annotation_image)
... ... 
@@ -38,6 +39,7 @@ export(download.phylopic)
38 39 
 export(expand)
39 40 
 export(flip)
40 41 
 export(geom_aline)
42 
+export(geom_balance)
41 43 
 export(geom_cladelabel)
42 44 
 export(geom_hilight)
43 45 
 export(geom_label2)
... ... 
@@ -67,6 +69,7 @@ export(get.treeinfo)
67 69 
 export(get.treetext)
68 70 
 export(getNodeNum)
69 71 
 export(getRoot)
72 
+export(get_balance_position)
70 73 
 export(get_clade_position)
71 74 
 export(get_heatmap_column_position)
72 75 
 export(get_taxa_name)
... ... 
@@ -108,6 +111,7 @@ export(rtree)
108 111 
 export(scaleClade)
109 112 
 export(scale_color)
110 113 
 export(scale_x_ggtree)
114 
+export(stat_balance)
111 115 
 export(stat_hilight)
112 116 
 export(subview)
113 117 
 export(theme_inset)
NEWS
History View file @ 13e3fd3
... ... 
@@ -1,3 +1,8 @@
1 
+CHANGES IN VERSION 1.5.6
2 
+------------------------
3 
+ o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
4 
+   + see https://github.com/GuangchuangYu/ggtree/pull/64
5 
+
1 6 
 CHANGES IN VERSION 1.5.5
2 7 
 ------------------------
3 8 
  o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>
R/ape.R
History View file @ 13e3fd3
... ... 
@@ -1,24 +1,6 @@
1 
-##' read newick tree
1 
+
2 2 
 ##' @export
3 
-##' @rdname read.tree
4 
-##' @param file file name
5 
-##' @param text alternatively, using newick text
6 
-##' @param tree.names if read several trees, specify their names
7 
-##' @param skip number of lines of the input file to skip
8 
-##' @param comment.char a single character,
9 
-##'                     the remaining of the line after this character is ignored.
10 
-##' @param keep.multi if 'TRUE' and 'tree.names = NULL'
11 
-##'                   then single trees are returned in 'multiPhylo' format
12 
-##'                   with any name that is present. Default is 'FALSE'
13 
-##' @param ... further arguments to be passed to 'scan()'.
14 
-##' @source
15 
-##' This is just the imported function
16 
-##' from the ape package. The documentation you should
17 
-##' read for the read.tree function can be found here: \link[ape]{read.tree}
18 
-##'
19 
-##' @seealso
20 
-##' \link[ape]{read.tree}
21 
-read.tree <- ape::read.tree
3 
+ape::read.tree
22 4
23 5
24 6 
 ##' generate random tree
R/geom_balance.R
History View file @ 13e3fd3
25 7 
new file mode 100644
... ... 
@@ -0,0 +1,208 @@
1 
+#' highlights the two direct descendant clades of an internal node
2 
+#'
3 
+#' Particularly useful when studying neighboring clades. Note that balances that
4 
+#' correspond to multichotomies will not be displayed.
5 
+#'
6 
+#' @title geom_balance
7 
+#' @param node selected node (balance) to highlight
8 
+#' @param fill color fill
9 
+#' @param color color to outline highlights and divide balance
10 
+#' @param alpha alpha (transparency)
11 
+#' @param extend extend xmax of the rectangle
12 
+#' @param extendto extend xmax to extendto
13 
+#' @return ggplot2
14 
+#' @export
15 
+#' @importFrom ggplot2 aes_
16 
+#' @importFrom ggplot2 GeomRect
17 
+#' @author Justin Silverman
18 
+#' @references J. Silverman, et al. \emph{A phylogenetic transform enhances
19 
+#'   analysis of compositional microbiota data}. (in preparation)
20 
+geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend=0, extendto=NULL) {
21 
+
22 
+  data = NULL
23 
+  stat = "balance"
24 
+  position = "identity"
25 
+  show.legend = NA
26 
+  na.rm = TRUE
27 
+  inherit.aes = FALSE
28 
+
29 
+  default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, branch.length=~branch.length)
30 
+  mapping <- default_aes
31 
+
32 
+  l1 <- layer(
33 
+    stat=StatBalance,
34 
+    data = data,
35 
+    mapping = mapping,
36 
+    geom = GeomRect,
37 
+    position = position,
38 
+    show.legend=show.legend,
39 
+    inherit.aes = inherit.aes,
40 
+    params = list(node=node,
41 
+                  fill=fill,
42 
+                  color=color,
43 
+                  alpha=alpha,
44 
+                  extend=extend,
45 
+                  extendto=extendto,
46 
+                  direction=1,
47 
+                  na.rm = na.rm)
48 
+  )
49 
+  l2 <- layer(
50 
+    stat=StatBalance,
51 
+    data = data,
52 
+    mapping = mapping,
53 
+    geom = GeomRect,
54 
+    position = position,
55 
+    show.legend=show.legend,
56 
+    inherit.aes = inherit.aes,
57 
+    params = list(node=node,
58 
+                  fill=fill,
59 
+                  color=color,
60 
+                  alpha=alpha,
61 
+                  extend=extend,
62 
+                  extendto=extendto,
63 
+                  direction=2,
64 
+                  na.rm = na.rm)
65 
+  )
66 
+  return(c(l1,l2))
67 
+}
68 
+
69 
+#' stat_balance
70 
+#'
71 
+#'
72 
+#' @title stat_balance
73 
+#' @param mapping aes mapping
74 
+#' @param data data
75 
+#' @param geom geometric object
76 
+#' @param position position
77 
+#' @param node node number
78 
+#' @param show.legend show legend
79 
+#' @param inherit.aes logical
80 
+#' @param fill fill color
81 
+#' @param color color to outline highlights and divide balance
82 
+#' @param alpha transparency
83 
+#' @param extend extend xmax of the rectangle
84 
+#' @param extendto extend xmax to extendto
85 
+#' @param ... additional parameter
86 
+#' @return layer
87 
+#' @importFrom ggplot2 layer
88 
+#' @export
89 
+stat_balance <- function(mapping=NULL, data=NULL, geom="rect",
90 
+                         position="identity",  node,
91 
+                         show.legend=NA, inherit.aes=FALSE,
92 
+                         fill, color, alpha, extend=0, extendto=NULL,
93 
+                         ...) {
94 
+  default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, branch.length=~branch.length)
95 
+  if (is.null(mapping)) {
96 
+    mapping <- default_aes
97 
+  } else {
98 
+    mapping <- modifyList(mapping, default_aes)
99 
+  }
100 
+
101 
+  l1 <- layer(
102 
+    stat=StatBalance,
103 
+    data = data,
104 
+    mapping = mapping,
105 
+    geom = geom,
106 
+    position = position,
107 
+    show.legend=show.legend,
108 
+    inherit.aes = inherit.aes,
109 
+    params = list(node=node,
110 
+                  fill=fill,
111 
+                  color=color,
112 
+                  alpha=alpha,
113 
+                  extend=extend,
114 
+                  extendto=extendto,
115 
+                  direction=1,
116 
+                  ...)
117 
+  )
118 
+  l2 <- layer(
119 
+    stat=StatBalance,
120 
+    data = data,
121 
+    mapping = mapping,
122 
+    geom = geom,
123 
+    position = position,
124 
+    show.legend=show.legend,
125 
+    inherit.aes = inherit.aes,
126 
+    params = list(node=node,
127 
+                  fill=fill,
128 
+                  color=color,
129 
+                  alpha=alpha,
130 
+                  extend=extend,
131 
+                  extendto=extendto,
132 
+                  direction=2,
133 
+                  ...)
134 
+  )
135 
+  return(c(l1,l2))
136 
+}
137 
+
138 
+##' StatBalance
139 
+##' @rdname ggtree-ggproto
140 
+##' @format NULL
141 
+##' @usage NULL
142 
+##' @importFrom ggplot2 Stat
143 
+##' @export
144 
+StatBalance <- ggproto("StatBalance", Stat,
145 
+                       compute_group = function(self, data, scales, params, node, extend, extendto, direction) {
146 
+                         df <- get_balance_position_(data, node, direction)
147 
+
148 
+                         df$xmax <- df$xmax + extend
149 
+                         if (!is.null(extendto) && !is.na(extendto)) {
150 
+                           if (extendto < df$xmax) {
151 
+                             warning("extendto is too small, keep the original xmax value...")
152 
+                           } else {
153 
+                             df$xmax <- extendto
154 
+                           }
155 
+                         }
156 
+                         return(df)
157 
+                       },
158 
+                       required_aes = c("x", "y", "branch.length")
159 
+)
160 
+
161 
+
162 
+#' get position of balance (xmin, xmax, ymin, ymax)
163 
+#'
164 
+#'
165 
+#' @title get_balance_position
166 
+#' @param treeview tree view
167 
+#' @param node selected node
168 
+#' @param direction either (1 for 'up' or 2 for 'down')
169 
+#' @return data.frame
170 
+#' @export
171 
+#' @author Justin Silverman
172 
+get_balance_position <- function(treeview, node, direction) {
173 
+  get_balance_position_(treeview$data, node, direction)
174 
+}
175 
+
176 
+get_balance_position_ <- function(data, node, direction) {
177 
+  ch <- tryCatch(getChild.df(data, node), error=function(e) NULL)
178 
+
179 
+  if (length(ch) < 2 || is.null(ch)){
180 
+    stop('balance cannot be a tip')
181 
+  } else if (length(ch) > 2){
182 
+    stop('balance has >2 direct child nodes, can use ape::multi2di to convert to binary tree')
183 
+  }
184 
+
185 
+  i <- match(node, data$node)
186 
+  sp <- tryCatch(get.offspring.df(data, ch[direction]), error=function(e) ch[direction])
187 
+  sp.all <- get.offspring.df(data, i)
188 
+  sp.df <- data[match(sp, data$node),]
189 
+  sp.all.df <- data[match(sp.all, data$node),]
190 
+  n.df <- data[i,]
191 
+
192 
+  # X direction is uniform for both children, but y is only based on range of
193 
+  # one of the two children (direction)
194 
+  x <- sp.all.df$x
195 
+  y <- sp.df$y
196 
+  #x.n <- n.df$x
197 
+
198 
+  if ("branch.length" %in% colnames(data)) {
199 
+   xmin <- min(x)-data[i, "branch.length"]/2
200 
+  } else {
201 
+   xmin <- min(sp.df$branch)
202 
+  }
203 
+  #xmin <- x.n
204 
+  data.frame(xmin=xmin,
205 
+             xmax = max(x),
206 
+             ymin=min(y)-0.5,
207 
+             ymax=max(y)+0.5)
208 
+}
0 209 
\ No newline at end of file
R/paml.R
History View file @ 13e3fd3
... ... 
@@ -31,20 +31,25 @@ mask <- function(tree_object, field, site, mask_site=FALSE) {
31 31 
     }
32 32
33 33 
     field_data <- sapply(field_data, gsub, pattern="\n", replacement="/")
34 
+
35 
+    x <- field_data[field_data != ""]
36 
+    x <- x[!is.na(x)]
37 
+    pos <- strsplit(x, " / ") %>% unlist %>%
38 
+        gsub("^[a-zA-Z]+", "", . ) %>%
39 
+        gsub("[a-zA-Z]\\s*$", "", .) %>%
40 
+        as.numeric
34 41
35 42 
     if (mask_site == FALSE) {
36 
-        x <- field_data[field_data != ""]
37 
-        x <- x[!is.na(x)]
38 
-        pos <- strsplit(x, " / ") %>% unlist %>%
39 
-            gsub("^[a-zA-Z]+", "", . ) %>%
40 
-                gsub("[a-zA-Z]\\s*$", "", .) %>%
41 
-                    as.numeric
42 43 
         pos2 <- 1:max(pos)
43 44 
         pos2 <- pos2[-site]
44 45 
         site <- pos2
45 46 
     }
46 47
48 
+    site <- site[site %in% pos]
49 
+
47 50 
     for (i in seq_along(field_data)) {
51 
+        if (is.na(field_data[i]))
52 
+            next
48 53 
         for (j in seq_along(site)) {
49 54 
             pattern <- paste0("/*\\s*[a-zA-Z]", site[j], "[a-zA-Z]\\s*")
50 55 
             field_data[i] <- gsub(pattern, "",  field_data[i])
R/utilities.R
History View file @ 13e3fd3
... ... 
@@ -1,3 +1,4 @@
1 
+
1 2 
 filename <- function(file) {
2 3 
     ## textConnection(text_string) will work just like a file
3 4 
     ## in this case, just set the filename as ""
README.md
History View file @ 13e3fd3
... ... 
@@ -27,9 +27,9 @@ Please cite the following article when using `ggtree`:
27 27
28 28 
 ```
29 29 
 G Yu, D Smith, H Zhu, Y Guan, TTY Lam,
30 
-ggtree: an R package for visualization and annotation of phylogenetic tree
31 
-		with different types of meta-data.
32 
-Methods in Ecology and Evolution, submitted
30 
+ggtree: an R package for visualization and annotation of phylogenetic trees
31 
+        with their covariates and other associated data.
32 
+Methods in Ecology and Evolution, revised
33 33 
 ```
34 34
35 35 
 ## License ##
... ... 
@@ -50,7 +50,7 @@ To view the vignette of `ggtree` installed in your system, start `R` and enter:
50 50 
 vignette("ggtree", package = "ggtree")
51 51 
 ```
52 52
53 
-More documents can be found in <http://guangchuangyu.github.io/tags/ggtree>.
53 
+More documents can be found in <https://guangchuangyu.github.io/ggtree>.
54 54
55 55
56 56 
 ## Bugs/Feature requests ##
inst/CITATION
History View file @ 13e3fd3
... ... 
@@ -2,7 +2,7 @@ citHeader("To cite ggtree in publications use:")
2 2
3 3 
 citEntry(
4 4 
     entry  = "article",
5 
-    title  = "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data",
5 
+    title  = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
6 6 
     author = personList(
7 7 
         as.person("Guangchuang Yu"),
8 8 
         as.person("David Smith"),
... ... 
@@ -10,7 +10,7 @@ citEntry(
10 10 
         as.person("Yi Guan"),
11 11 
         as.person("Tommy Tsan-Yuk Lam")
12 12 
         ),
13 
-    year    = "submitted",
13 
+    year    = "revised",
14 14 
     journal = "Methods in Ecology and Evolution",
15 15 
     volume  = "",
16 16 
     issue   = "",
... ... 
@@ -20,7 +20,7 @@ citEntry(
20 20 
     PMID    = "",
21 21 
     url     = "",
22 22 
     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
23 
-        "ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.",
24 
-        "Methods in Ecology and Evolution submitted")
23 
+        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.",
24 
+        "Methods in Ecology and Evolution revised")
25 25 
 )
26 26
man/geom_balance.Rd
History View file @ 13e3fd3
27 27 
new file mode 100644
... ... 
@@ -0,0 +1,40 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/geom_balance.R
3 
+\name{geom_balance}
4 
+\alias{geom_balance}
5 
+\title{geom_balance}
6 
+\usage{
7 
+geom_balance(node, fill = "steelblue", color = "white", alpha = 0.5,
8 
+  extend = 0, extendto = NULL)
9 
+}
10 
+\arguments{
11 
+\item{node}{selected node (balance) to highlight}
12 
+
13 
+\item{fill}{color fill}
14 
+
15 
+\item{color}{color to outline highlights and divide balance}
16 
+
17 
+\item{alpha}{alpha (transparency)}
18 
+
19 
+\item{extend}{extend xmax of the rectangle}
20 
+
21 
+\item{extendto}{extend xmax to extendto}
22 
+}
23 
+\value{
24 
+ggplot2
25 
+}
26 
+\description{
27 
+highlights the two direct descendant clades of an internal node
28 
+}
29 
+\details{
30 
+Particularly useful when studying neighboring clades. Note that balances that
31 
+correspond to multichotomies will not be displayed.
32 
+}
33 
+\author{
34 
+Justin Silverman
35 
+}
36 
+\references{
37 
+J. Silverman, et al. \emph{A phylogenetic transform enhances
38 
+  analysis of compositional microbiota data}. (in preparation)
39 
+}
40 
+
man/get_balance_position.Rd
History View file @ 13e3fd3
0 41 
new file mode 100644
... ... 
@@ -0,0 +1,25 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/geom_balance.R
3 
+\name{get_balance_position}
4 
+\alias{get_balance_position}
5 
+\title{get_balance_position}
6 
+\usage{
7 
+get_balance_position(treeview, node, direction)
8 
+}
9 
+\arguments{
10 
+\item{treeview}{tree view}
11 
+
12 
+\item{node}{selected node}
13 
+
14 
+\item{direction}{either (1 for 'up' or 2 for 'down')}
15 
+}
16 
+\value{
17 
+data.frame
18 
+}
19 
+\description{
20 
+get position of balance (xmin, xmax, ymin, ymax)
21 
+}
22 
+\author{
23 
+Justin Silverman
24 
+}
25 
+
man/ggtree-ggproto.Rd
History View file @ 13e3fd3
... ... 
@@ -1,10 +1,13 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/geom_hilight.R
2 
+% Please edit documentation in R/geom_balance.R, R/geom_hilight.R
3 3 
 \docType{data}
4 
-\name{StatHilight}
4 
+\name{StatBalance}
5 
+\alias{StatBalance}
5 6 
 \alias{StatHilight}
6 
-\title{StatHilight}
7 
+\title{StatBalance}
7 8 
 \description{
9 
+StatBalance
10 
+
8 11 
 StatHilight
9 12 
 }
10 13 
 \keyword{datasets}
man/read.tree.Rd
History View file @ 13e3fd3
11 14 
deleted file mode 100644
... ... 
@@ -1,39 +0,0 @@
1 
-% Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/ape.R
3 
-\name{read.tree}
4 
-\alias{read.tree}
5 
-\title{read newick tree}
6 
-\source{
7 
-This is just the imported function
8 
-from the ape package. The documentation you should
9 
-read for the read.tree function can be found here: \link[ape]{read.tree}
10 
-}
11 
-\usage{
12 
-read.tree(file = "", text = NULL, tree.names = NULL, skip = 0,
13 
-  comment.char = "#", keep.multi = FALSE, ...)
14 
-}
15 
-\arguments{
16 
-\item{file}{file name}
17 
-
18 
-\item{text}{alternatively, using newick text}
19 
-
20 
-\item{tree.names}{if read several trees, specify their names}
21 
-
22 
-\item{skip}{number of lines of the input file to skip}
23 
-
24 
-\item{comment.char}{a single character,
25 
-the remaining of the line after this character is ignored.}
26 
-
27 
-\item{keep.multi}{if 'TRUE' and 'tree.names = NULL'
28 
-then single trees are returned in 'multiPhylo' format
29 
-with any name that is present. Default is 'FALSE'}
30 
-
31 
-\item{...}{further arguments to be passed to 'scan()'.}
32 
-}
33 
-\description{
34 
-read newick tree
35 
-}
36 
-\seealso{
37 
-\link[ape]{read.tree}
38 
-}
39 
-
man/reexports.Rd
History View file @ 13e3fd3
40 0 
new file mode 100644
... ... 
@@ -0,0 +1,16 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/ape.R
3 
+\docType{import}
4 
+\name{reexports}
5 
+\alias{read.tree}
6 
+\alias{reexports}
7 
+\title{Objects exported from other packages}
8 
+\description{
9 
+These objects are imported from other packages. Follow the links
10 
+below to see their documentation.
11 
+
12 
+\describe{
13 
+  \item{ape}{\code{\link[ape]{read.tree}}}
14 
+}}
15 
+\keyword{internal}
16 
+
man/stat_balance.Rd
History View file @ 13e3fd3
0 17 
new file mode 100644
... ... 
@@ -0,0 +1,44 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/geom_balance.R
3 
+\name{stat_balance}
4 
+\alias{stat_balance}
5 
+\title{stat_balance}
6 
+\usage{
7 
+stat_balance(mapping = NULL, data = NULL, geom = "rect",
8 
+  position = "identity", node, show.legend = NA, inherit.aes = FALSE,
9 
+  fill, color, alpha, extend = 0, extendto = NULL, ...)
10 
+}
11 
+\arguments{
12 
+\item{mapping}{aes mapping}
13 
+
14 
+\item{data}{data}
15 
+
16 
+\item{geom}{geometric object}
17 
+
18 
+\item{position}{position}
19 
+
20 
+\item{node}{node number}
21 
+
22 
+\item{show.legend}{show legend}
23 
+
24 
+\item{inherit.aes}{logical}
25 
+
26 
+\item{fill}{fill color}
27 
+
28 
+\item{color}{color to outline highlights and divide balance}
29 
+
30 
+\item{alpha}{transparency}
31 
+
32 
+\item{extend}{extend xmax of the rectangle}
33 
+
34 
+\item{extendto}{extend xmax to extendto}
35 
+
36 
+\item{...}{additional parameter}
37 
+}
38 
+\value{
39 
+layer
40 
+}
41 
+\description{
42 
+stat_balance
43 
+}
44 
+
tests/testthat/test-geom_balance.R
History View file @ 13e3fd3
0 45 
new file mode 100644
... ... 
@@ -0,0 +1,13 @@
1 
+context('geom_balance')
2 
+
3 
+test_that('geom_balance gives proper errors if called on non-binary node', {
4 
+  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);")
5 
+
6 
+  # Note: For some reason while ggplot will give warning and properly does not show
7 
+  # the problematic geom, the output of the function is not recognized as a warning.
8 
+  # This is not crutial but it makes adding unit tests more difficult.
9 
+  #expect_warning(ggtree(tr)+geom_balance(10), '>2 direct child nodes')
10 
+  #expect_warning(ggtree(tr)+geom_balance(3), 'balance cannot be a tip')
11 
+
12 
+  expect_true(is.ggplot(ggtree(tr)+geom_balance(9))) # should plot appropriately
13 
+})
0 14 
\ No newline at end of file
vignettes/ggtree.Rmd
History View file @ 13e3fd3
... ... 
@@ -45,8 +45,8 @@ If you use `ggtree` in published research, please cite:
45 45
46 46 
 ```
47 47 
 G Yu, D Smith, H Zhu, Y Guan, TTY Lam,
48 
-ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data.
49 
-revised.
48 
+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.
49 
+Methods in Ecology and Evolution, revised.
50 50 
 ```
51 51
52 52 
 # Introduction
vignettes/treeAnnotation.Rmd
History View file @ 13e3fd3
... ... 
@@ -169,10 +169,19 @@ ggtree(tree, layout="circular") + geom_hilight(node=21, fill="steelblue", alpha=
169 169
170 170 
 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.
171 171
172 
+# Highlight balances
173 
+In addition to _`geom_hilight`_, `ggtree` also implements _`geom_balance`_
174 
+which is designed to highlight neighboring subclades of a given internal node.
175 
+
176 
+```{r fig.width=4, fig.height=5, fig.align='center', warning=FALSE}
177 
+ggtree(tree) +
178 
+  geom_balance(node=16, fill='steelblue', color='white', alpha=0.6, extend=1) +
179 
+  geom_balance(node=19, fill='darkgreen', color='white', alpha=0.6, extend=1)
180 
+```
172 181
173 182 
 # labelling associated taxa (Monophyletic, Polyphyletic or Paraphyletic)
174 183
175 
-`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)).
184 
+`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)).
176 185
177 186 
 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}
178 187 
 ggtree(tree) + geom_tiplab() + geom_strip('E', 'G', barsize=2, color='red') + geom_strip('F', 'L', barsize=2, color='blue')