@@ -1,15 +1,18 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization of tree and annotation data

-Version: 3.3.1

+Version: 3.3.1.900

 Authors@R: c(

-       person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

+       person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), 

+            comment = c(ORCID = "0000-0002-6485-8781")),

        person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

-       person("Shuangbin", "Xu",       email = "xshuangbin@163.com",      role = "aut", comment = c(ORCID="0000-0003-3513-5362")),

-       person("Yonghe", "Xia",         email = "xiayh17@gmail.com",       role = "ctb"),

-       person("Justin", "Silverman",   email = "jsilve24@gmail.com",      role = "ctb"),

+       person("Shuangbin", "Xu",       email = "xshuangbin@163.com",      role = "aut", 

+            comment = c(ORCID="0000-0003-3513-5362")),

+       person("Lin", " Li",            email = "williamlee2220@qq.com",   role = "ctb"),

        person("Bradley", "Jones",      email = "bjones@cfenet.ubc.ca",    role = "ctb"),

+       person("Justin", "Silverman",   email = "jsilve24@gmail.com",      role = "ctb"),

        person("Watal M.", "Iwasaki",   email = "heavy.watal@gmail.com",   role = "ctb"),

+       person("Yonghe", "Xia",         email = "xiayh17@gmail.com",       role = "ctb"),

        person("Ruizhu", "Huang",       email = "ruizhuRH@gmail.com",      role = "ctb")

        )

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

@@ -123,6 +123,7 @@ export(nodeid)

 export(nodelab)

 export(nodepie)

 export(open_tree)

+export(plot_list)

 export(range_format)

 export(read.tree)

 export(revts)

@@ -136,6 +137,7 @@ export(scale_color_subtree)

 export(scale_colour_manual)

 export(scale_colour_subtree)

 export(scale_fill_manual)

+export(scale_x_continuous)

 export(scale_x_ggtree)

 export(scale_x_range)

 export(set_hilight_legend)

@@ -161,6 +163,7 @@ importFrom(ape,ladderize)

 importFrom(ape,read.tree)

 importFrom(ape,reorder.phylo)

 importFrom(ape,rtree)

+importFrom(aplot,plot_list)

 importFrom(aplot,xrange)

 importFrom(dplyr,collapse)

 importFrom(dplyr,filter)

@@ -262,7 +265,6 @@ importFrom(methods,is)

 importFrom(methods,missingArg)

 importFrom(methods,setGeneric)

 importFrom(methods,setOldClass)

-importFrom(pillar,style_subtle)

 importFrom(rlang,.data)

 importFrom(rlang,abort)

 importFrom(rlang,as_name)

@@ -20,12 +20,15 @@

   - <https://www.rdocumentation.org/packages/phytools/versions/0.7-70/topics/cophylo> 

 + `fortify` method for `phyloseq` object should return a tidy data.frame

   - maybe we can defined another object (inherited from treedata?) and provide converter for `phyloseq`

-+ update ggtree man files

 + The `daylight` algorithm is quite slow compare to `ggraph` and needs to  be optimized

   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

 -->

+# ggtree 3.3.1.900

+

++ update man files (2022-03-23, Wed, #489)

+

 # ggtree 3.3.1

 + use graph layouts to visualize tree (2021-12-10, Fri, #460, #461)

@@ -110,8 +110,7 @@ scale_x_range <- function() {

 ##' tr <- rtree(10)

 ##' p <- ggtree(tr) + theme_tree2()

 ##' p2 <- revts(p) 

-##' p3 <- p2 + scale_x_continuous(labels=abs)

-##' plot_list(p, p2, p3, ncol=3, tag_levels="A")

+##' p2 + scale_x_continuous(labels=abs)

 ##' @author Guangchuang Yu

 revts <- function(treeview) {

     x <- treeview$data$x

@@ -191,7 +191,7 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

 ##' @inheritParams get_taxa_name

 ##' @return tree view

 ##' @export

-##' examples

+##' @examples

 ##' x <- rtree(15)

 ##' p <- ggtree(x) + geom_tiplab()

 ##' p1 <- collapse(p, 17)

@@ -300,10 +300,12 @@ rotate <- function(tree_view=NULL, node) {

 ##' @param node2 node number of clade 2. It should share a same parent node with node1

 ##' @return ggplot object

 ##' @export

+##' @examples

+##' set.seed(123)

 ##' x <- rtree(15)

 ##' p <- ggtree(x) + geom_tiplab() +

 ##'   geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")

-##' flip(p, 19, 20)   ## Depends on the condition of your tree

+##' flip(p, 23, 24)   ## Depends on the condition of your tree

 ##' @author Guangchuang Yu

 flip <- function(tree_view=NULL, node1, node2) {

     tree_view %<>% get_tree_view

@@ -31,6 +31,8 @@

 ##' @export

 ##' @author Yu Guangchuang

 ##' @examples

+##' tree <- rtree(10)

+##' ggplot(tree) + geom_tree()

 ##' @references

 ##' For demonstration of this function, please refer to chapter 4.2.1 of 

 ##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

@@ -22,8 +22,6 @@

 ##' For demonstration of this function, please refer to chapter 8.3 of 

 ##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

 ##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

-##' 

-

 geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

                        x = "node", reverse_x = FALSE, reverse_y = FALSE) {

     structure(list(insets = insets, width = width, height = height,

@@ -37,7 +35,6 @@ geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

 ##' @title inset

 ##' @rdname inset

 ##' @param tree_view tree view 

-##' @inheritParams geom_inset

 ##' @return tree view with insets

 ##' @importFrom yulab.utils get_fun_from_pkg

 ##' @export

@@ -13,7 +13,6 @@

 ##' @param height height ratio of sequence, defaults to 0.8

 ##' @return tree view

 ##' @export

-##' @importFrom colorspace rainbow_hcl

 ##' @importFrom treeio read.fasta

 ##' @importFrom ggplot2 geom_segment

 ##' @importFrom ggplot2 geom_rect

@@ -86,6 +86,10 @@ ggplot2::scale_color_manual

 ##' @export

 ggplot2::scale_fill_manual

+##' @importFrom ggplot2 scale_x_continuous

+##' @export

+ggplot2::scale_x_continuous

+

 ##' @importFrom ggplot2 margin

 ##' @export

 ggplot2::margin

@@ -97,3 +101,8 @@ grid::arrow

 ##' @importFrom grid unit

 ##' @export

 grid::unit

+

+

+##' @importFrom aplot plot_list

+##' @export

+aplot::plot_list

@@ -19,4 +19,3 @@ scale_x_ggtree <- function(breaks = waiver(), labels = waiver()) {

     structure(list(breaks = breaks, labels = labels), class="scale_ggtree")

 }

-

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

 as.polytomy(tree, feature, fun)

 }

 \arguments{

-\item{tree}{tree object}

+\item{tree}{tree object, 'phylo' object only}

 \item{feature}{selected feature}

@@ -9,7 +9,7 @@ pg \%<+\% data

 \arguments{

 \item{pg}{ggplot2 object}

-\item{data}{annotation data}

+\item{data}{annotation data that contains a column of “node” , or the first column of taxa labels}

 }

 \value{

 ggplot object with annotation data added

@@ -17,6 +17,9 @@ ggplot object with annotation data added

 \description{

 add annotation data to a tree

 }

+\details{

+This operator attaches annotation data to a ggtree graphic object

+}

 \examples{

 nwk <- system.file("extdata", "sample.nwk", package="treeio")

 tree <- read.tree(nwk)

@@ -11,17 +11,24 @@

 \item{node}{internal node number}

-\item{mode}{one of 'none', 'max', 'min' and 'mixed'}

+\item{mode}{one of 'none'(default), 'max', 'min' and 'mixed'. 'none' would simply collapse the clade as 'tip' and

+the rest will display a triangle, whose shape is determined by the farest/closest tip of the collapsed clade to indicate it}

-\item{clade_name}{set clade name. If clade_name = NULL, do nothing}

+\item{clade_name}{set a name for the collapsed clade. If clade_name = NULL, do nothing}

-\item{...}{additional parameters}

+\item{...}{additional parameters to set the color or transparency of the triangle}

 }

 \value{

 tree view

 }

 \description{

-collapse a clade

+collapse a selected clade, which can later be expanded with the 'expand()' fuction if necessary

+}

+\examples{

+x <- rtree(15)

+p <- ggtree(x) + geom_tiplab()

+p

+p1 <- collapse(p, node = 17, mode = "mixed", clade_name = "cclade", alpha = 0.8, color = "grey", fill = "light blue")

 }

 \seealso{

 expand

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

 expand(tree_view = NULL, node)

 }

 \arguments{

-\item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.}

+\item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object will be used.}

 \item{node}{internal node number to specify a clade. If NULL, using the whole tree}

 }

@@ -15,7 +15,13 @@ expand(tree_view = NULL, node)

 tree view

 }

 \description{

-expand collased clade

+expand collapsed clade

+}

+\examples{

+x <- rtree(15)

+p <- ggtree(x) + geom_tiplab()

+p1 <- collapse(p, 17)

+expand(p1, 17)

 }

 \seealso{

 collapse

@@ -9,13 +9,13 @@ facet_labeller(p, label)

 \arguments{

 \item{p}{facet_plot output}

-\item{label}{labels of facet panels}

+\item{label}{new labels of facet panels}

 }

 \value{

 ggplot object

 }

 \description{

-label facet_plot output

+function to relable selected panels created by 'geom_facet' or 'facet-plot'

 }

 \author{

 Guangchuang Yu

@@ -9,15 +9,22 @@ flip(tree_view = NULL, node1, node2)

 \arguments{

 \item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.}

-\item{node1}{node number of branch 1}

+\item{node1}{node number of clade 1. It should share a same parent node with node2}

-\item{node2}{node number of branch 2}

+\item{node2}{node number of clade 2. It should share a same parent node with node1}

 }

 \value{

-ggplot2 object

+ggplot object

 }

 \description{

-flip position of two selected branches

+exchange the position of 2 clades

+}

+\examples{

+set.seed(123)

+x <- rtree(15)

+p <- ggtree(x) + geom_tiplab() +

+  geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")

+flip(p, 23, 24)   ## Depends on the condition of your tree

 }

 \author{

 Guangchuang Yu

@@ -10,13 +10,13 @@ geom_hilight(data = NULL, mapping = NULL, node = NULL, type = "auto", ...)

 geom_highlight(data = NULL, mapping = NULL, node = NULL, type = "auto", ...)

 }

 \arguments{

-\item{data}{data.frame, The data to be displayed in this layer, default is NULL.}

+\item{data}{data.frame, The data to be displayed in this layer, defaults to NULL.}

-\item{mapping}{Set of aesthetic mappings, default is NULL.}

+\item{mapping}{Set of aesthetic mappings, defaults to NULL.}

 \item{node}{selected node to hilight, when data and mapping is NULL, it is required.}

-\item{type}{the type of layer, default is \code{auto}, meaning rectangular, circular,

+\item{type}{the type of layer, defaults to \code{auto}, meaning rectangular, circular,

 slanted, fan, inward_circular, radial, equal_angle, ape layout tree will use rectangular layer,

 unrooted and daylight layout tree use will use encircle layer. You can specify this parameter to

 \code{rect} (rectangular layer) or \code{encircle} (encircle layer), 'gradient' (gradient color),

@@ -27,12 +27,12 @@ unrooted and daylight layout tree use will use encircle layer. You can specify t

 \item \code{align} control the align direction of the edge of high light rectangular.

 Options is 'none' (default), 'left', 'right', 'both'. This argument only work when the

 'geom_hilight' is plotting using geom_hilight(mapping=aes(...)).

-\item \code{gradient.direction} character, the direction of gradient color, default is 'rt'

+\item \code{gradient.direction} character, the direction of gradient color, defaults to 'rt'

 meaning the locations of gradient color is from root to tip, options are 'rt' and 'tr'.

 \item \code{gradient.length.out} integer, desired length of the sequence of gradient color,

-default is 2.

+defaults to 2.

 \item \code{roundrect.r} numeric, the radius of the rounded corners, when \code{roundrect=TRUE},

-default is 0.05.

+defaults to 0.05.

 }}

 }

 \value{

@@ -51,27 +51,27 @@ you can see the Aesthetics section to set parameters.

 aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

-\item \code{colour} the colour of margin, default is NA.

-\item \code{fill} the colour of fill, default is 'steelblue'.

-\item \code{alpha} the transparency of fill, default is 0.5.

-\item \code{extend} extend xmax of the rectangle, default is 0.

-\item \code{extendto} specify a value, meaning the rectangle extend to, default is NULL.

-\item \code{linetype} the line type of margin, default is 1.

-\item \code{size} the width of line of margin, default is 0.5.

+\item \code{colour} the colour of margin, defaults to NA.

+\item \code{fill} the colour of fill, defaults to 'steelblue'.

+\item \code{alpha} the transparency of fill, defaults to 0.5.

+\item \code{extend} extend xmax of the rectangle, defaults to 0.

+\item \code{extendto} specify a value, meaning the rectangle extend to, defaults to NULL.

+\item \code{linetype} the line type of margin, defaults to 1.

+\item \code{size} the width of line of margin, defaults to 0.5.

 }

 \code{geom_hilight()} understands the following aesthethics for encircle layer (required

 aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

-\item \code{colour} the colour of margin, default is 'black'.

-\item \code{fill} the colour of fill, default is 'steelblue'.

-\item \code{alpha} the transparency of fill, default is 0.5.

-\item \code{expand} expands the xspline clade region, default is 0.

+\item \code{colour} the colour of margin, defaults to 'black'.

+\item \code{fill} the colour of fill, defaults to 'steelblue'.

+\item \code{alpha} the transparency of fill, defaults to 0.5.

+\item \code{expand} expands the xspline clade region, defaults to 0.

 \item \code{spread} control the size, when only one point.

-\item \code{size} the width of line of margin, default is 0.5.

-\item \code{linetype} the line type of margin, default is 1.

-\item \code{s_shape} the shape of the spline relative to the control points, default is 0.5.

-\item \code{s_open}  whether the spline is a line or a closed shape, default is FALSE.

+\item \code{size} the width of line of margin, defaults to 0.5.

+\item \code{linetype} the line type of margin, defaults to 1.

+\item \code{s_shape} the shape of the spline relative to the control points, defaults to 0.5.

+\item \code{s_open}  whether the spline is a line or a closed shape, defaults to FALSE.

 }

 }

@@ -95,6 +95,11 @@ p7 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), type = "gradie

 p8 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type), type = "roundrect", alpha=0.68)

 p2/ p3/ p4/ p5 / p6/ p7/ p8

 }

+\references{

+For more detailed demonstration, please refer to chapter 5.2.2 of

+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}

+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.

+}

 \author{

 Guangchuang Yu and Shuangbin Xu

 }

@@ -9,9 +9,9 @@ geom_aline(mapping = NULL, linetype = "dotted", size = 1, ...)

 \arguments{

 \item{mapping}{aes mapping}

-\item{linetype}{line type}

+\item{linetype}{set line type of the line, defaults to "dotted"}

-\item{size}{line size}

+\item{size}{set line size of the line, defaults to 1}

 \item{...}{additional parameter}

 }

@@ -19,7 +19,11 @@ geom_aline(mapping = NULL, linetype = "dotted", size = 1, ...)

 aline layer

 }

 \description{

-add horizontal align lines

+add horizontal align lines layer to a tree

+}

+\details{

+'geom_aline'align all tips to the longest one by adding

+padding characters to the right side of the tip.

 }

 \author{

 Yu Guangchuang

@@ -14,17 +14,17 @@ geom_balance(

 )

 }

 \arguments{

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

+\item{node}{selected node (balance) to highlight its two direct descendant}

-\item{fill}{color fill}

+\item{fill}{color to fill in the highlight rectangle, default to "steelblue"}

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

+\item{color}{color to outline highlight rectangle and divide balance, defaults to "white"}

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

+\item{alpha}{alpha (transparency) for the highlight rectangle, defaults to 0.5}

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

+\item{extend}{extend xmax of the highlight rectangle by the value of extend}

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

+\item{extendto}{extend xmax of the highlight rectangle to the value of extendto}

 }

 \value{

 ggplot2

@@ -35,10 +35,22 @@ 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.

+}

+\examples{

+library(ggtree)

+set.seed(123)

+tr<- rtree(15)

+x <- ggtree(tr)

+x + geom_balance(17)

+

 }

 \references{

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

 analysis of compositional microbiota data}. (in preparation)

+

+For more detailed demonstration, please refer to chapter 5.2.2 of

+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}

+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.

 }

 \author{

 Justin Silverman and modified by Guangchuang Yu

@@ -19,34 +19,34 @@ geom_cladelab(

 \item{label}{character, character to be showed, when data and mapping is NULL, it is required.}

-\item{data}{data.frame, the data to be displayed in the annotation, default is NULL.}

+\item{data}{data.frame, the data to be displayed in the annotation, defaults to NULL.}

-\item{mapping}{Set of aesthetic mappings, default is NULL. The detail see the following explanation.}

+\item{mapping}{Set of aesthetic mappings, defaults to NULL. The detail see the following explanation.}

 \item{geom}{character, one of 'text', 'label', 'shadowtext', 'image' and 'phylopic',

-default is 'text', and the parameter see the Aesthetics For Specified Geom.}

+defaults to 'text', and the parameter see the Aesthetics For Specified Geom.}

-\item{parse}{logical, whether parse label to emoji font, default is FALSE.}

+\item{parse}{logical, whether parse label to emoji font, defaults to FALSE.}

 \item{...}{additional parameters, see also following section.

 additional parameters can refer the following parameters.

 \itemize{

 \item \code{offset} distance bar and tree, offset of bar and text from

-the clade, default is 0.

+the clade, defaults to 0.

 \item \code{offset.text} distance bar and text, offset of text from bar,

-default is 0.

-\item \code{align} logical, whether align clade lab, default is FALSE.

-\item \code{extend} numeric, extend the length of bar, default is 0.

+defaults to 0.

+\item \code{align} logical, whether align clade lab, defaults to FALSE.

+\item \code{extend} numeric, extend the length of bar, defaults to 0.

 \item \code{angle} numeric or 'auto', if angle is auto, the angle of text will

-be calculated automatically, which is useful for the circular etc layout, default is 0.

-\item \code{horizontal} logical, whether set label to horizontal, default is TRUE.

-\item \code{barsize} the width of line, default is 0.5.

-\item \code{barcolour} the colour of line, default is 'black'.

-\item \code{fontsize} the size of text, default is 3.88.

-\item \code{textcolour} the colour of text, default is 'black'.

-\item \code{imagesize} the size of image, default is 0.05.

-\item \code{imagecolor} the colour of image, default is NULL, when

+be calculated automatically, which is useful for the circular etc layout, defaults to 0.

+\item \code{horizontal} logical, whether set label to horizontal, defaults to TRUE.

+\item \code{barsize} the width of line, defaults to 0.5.

+\item \code{barcolour} the colour of line, defaults to 'black'.

+\item \code{fontsize} the size of text, defaults to 3.88.

+\item \code{textcolour} the colour of text, defaults to 'black'.

+\item \code{imagesize} the size of image, defaults to 0.05.

+\item \code{imagecolor} the colour of image, defaults to NULL, when

 geom="phylopic", it should be required.

 }

 The parameters also can be set in mapping, when data is provided. Note: the barsize, barcolour,

@@ -64,16 +64,16 @@ aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

 \item \strong{\code{label}} labels showed, it is required.

-\item \code{colour} the colour of text, default is "black".

-\item \code{size} the size of text, default is 3.88.

-\item \code{angle} the angle of text, default is 0.

-\item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

-\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

-\item \code{alpha} the transparency of text, default is NA.

-\item \code{family} the family of text, default is 'sans'.

-\item \code{fontface} the font face of text, default is 1 (plain), others are

+\item \code{colour} the colour of text, defaults to "black".

+\item \code{size} the size of text, defaults to 3.88.

+\item \code{angle} the angle of text, defaults to 0.

+\item \code{hjust} A numeric vector specifying horizontal justification, defaults to 0.

+\item \code{vjust} A numeric vector specifying vertical justification, defaults to 0.5.

+\item \code{alpha} the transparency of text, defaults to NA.

+\item \code{family} the family of text, defaults to 'sans'.

+\item \code{fontface} the font face of text, defaults to 1 (plain), others are

 2 (bold), 3 (italic), 4 (bold.italic).

-\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+\item \code{lineheight} The height of a line as a multiple of the size of text, defaults to 1.2 .

 }

 when the colour, size are not be set in mapping, and user want to modify the colour of text,

 they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

@@ -83,17 +83,17 @@ aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

 \item \strong{\code{label}} labels to be showed, it is required.

-\item \code{colour} the colour of text, default is "black".

-\item \code{fill} the background colour of the label, default is "white".

-\item \code{size} the size of text, default is 3.88.

-\item \code{angle} the angle of text, default is 0.

-\item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

-\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

-\item \code{alpha} the transparency of text, default is NA.

-\item \code{family} the family of text, default is 'sans'.

-\item \code{fontface} the font face of text, default is 1 (plain), others are

+\item \code{colour} the colour of text, defaults to "black".

+\item \code{fill} the background colour of the label, defaults to "white".

+\item \code{size} the size of text, defaults to 3.88.

+\item \code{angle} the angle of text, defaults to 0.

+\item \code{hjust} A numeric vector specifying horizontal justification, defaults to 0.

+\item \code{vjust} A numeric vector specifying vertical justification, defaults to 0.5.

+\item \code{alpha} the transparency of text, defaults to NA.

+\item \code{family} the family of text, defaults to 'sans'.

+\item \code{fontface} the font face of text, defaults to 1 (plain), others are

 2 (bold), 3 (italic), 4 (bold.italic).

-\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+\item \code{lineheight} The height of a line as a multiple of the size of text, defaults to 1.2 .

 }

 when the colour, size are not be set in mapping, and user want to modify the colour of text,

 they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

@@ -103,18 +103,18 @@ aesthetics are in bold):

 \itemize{

 \item \strong{\code{node}} selected node to hight light, it is required.

 \item \strong{\code{label}} labels to be showed, it is required.

-\item \code{colour} the colour of text, default is "black".

-\item \code{bg.colour} the background colour of text, default is 'black'.

-\item \code{bg.r} the width of background text, default is 0.1.

-\item \code{size} the size of text, default is 3.88.

-\item \code{angle} the angle of text, default is 0.

-\item \code{hjust} A numeric vector specifying horizontal justification, default is 0.

-\item \code{vjust} A numeric vector specifying vertical justification, default is 0.5.

-\item \code{alpha} the transparency of text, default is NA.

-\item \code{family} the family of text, default is 'sans'.

-\item \code{fontface} the font face of text, default is 1 (plain), others are

+\item \code{colour} the colour of text, defaults to "black".

+\item \code{bg.colour} the background colour of text, defaults to 'black'.

+\item \code{bg.r} the width of background text, defaults to 0.1.

+\item \code{size} the size of text, defaults to 3.88.

+\item \code{angle} the angle of text, defaults to 0.

+\item \code{hjust} A numeric vector specifying horizontal justification, defaults to 0.

+\item \code{vjust} A numeric vector specifying vertical justification, defaults to 0.5.

+\item \code{alpha} the transparency of text, defaults to NA.

+\item \code{family} the family of text, defaults to 'sans'.

+\item \code{fontface} the font face of text, defaults to 1 (plain), others are

 2 (bold), 3 (italic), 4 (bold.italic).

-\item \code{lineheight} The height of a line as a multiple of the size of text, default is 1.2 .

+\item \code{lineheight} The height of a line as a multiple of the size of text, defaults to 1.2 .

 }

 when the colour, size are not be set in mapping, and user want to modify the colour of text,

 they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

@@ -126,9 +126,9 @@ aesthetics are in bold):

 \item \strong{\code{label}} labels to be showed, it is required.

 \item \strong{\code{image}} the image to be annotated, when geom="phylopic",

 the uid of phylopic databases, it is required.

-\item \code{colour} the color of image, default is NULL.

-\item \code{size} the size of image, default is 0.05.

-\item \code{alpha} the alpha of image, default is 0.8.

+\item \code{colour} the color of image, defaults to NULL.

+\item \code{size} the size of image, defaults to 0.05.

+\item \code{alpha} the alpha of image, defaults to 0.8.

 }

 when the colour, size are not be set in mapping, and user want to modify the colour of image,

 they should use imagecolour, imagesize to avoid the confusion with bar layer annotation.

@@ -56,7 +56,7 @@ geom_cladelabel(

 \item{parse}{logical, whether parse label}

 \item{horizontal}{logical, whether set label to horizontal,

-default is TRUE.}

+defaults to TRUE.}

 \item{...}{additional parameter}

 }

@@ -50,7 +50,7 @@ geom_cladelabel2(

 \item{parse}{logical, whether parse label}

 \item{horizontal}{logical, whether set label to horizontal,

-default is TRUE.}

+defaults to TRUE.}

 \item{...}{additional parameter}

 }

@@ -23,36 +23,36 @@ geom_label2(

 )

 }

 \arguments{

-\item{mapping}{the aesthetic mapping}

+\item{mapping}{Set of aesthetic mappings, defaults to NULL.}

 \item{data}{A layer specific dataset -

 only needed if you want to override the plot defaults.}

-\item{...}{other arguments passed on to 'layer'}

+\item{...}{other arguments passed on to 'layer'.}

-\item{stat}{Name of stat to modify data}

+\item{stat}{Name of the stat to modify data.}

-\item{position}{The position adjustment to use for overlapping points on this layer}

+\item{position}{The position adjustment to use for overlapping points on this layer.}

-\item{family}{sans by default, can be any supported font}

+\item{family}{"sans" by default, can be any supported font.}

-\item{parse}{if TRUE, the labels will be parsed as expressions}

+\item{parse}{if 'TRUE', the labels will be parsed as expressions, defaults to 'FALSE'.}

-\item{nudge_x}{horizontal adjustment}

+\item{nudge_x}{adjust the horizontal position of the labels.}

-\item{nudge_y}{vertical adjustment}

+\item{nudge_y}{adjust the vertical position of the labels.}

-\item{label.padding}{Amount of padding around label.}

+\item{label.padding}{Amount of padding around label, defaults to 'unit(0.25, "lines")'.}

-\item{label.r}{Radius of rounded corners.}

+\item{label.r}{Use to set the radius of rounded corners of the label, defaults to 'unit(0.15, "lines")'.}

-\item{label.size}{Size of label border, in mm}

+\item{label.size}{Size of label border, in mm, defaults to 0.25.}

-\item{na.rm}{logical}

+\item{na.rm}{If "FALSE" (default), missing values are removed with a warning. If "TRUE", missing values are silently removed, logical.}

-\item{show.legend}{logical}

+\item{show.legend}{Whether to show legend, logical, defaults to "NA".}

-\item{inherit.aes}{logical}

+\item{inherit.aes}{Whether to inherit aesthetic mappings, logical, defaults to "TRUE".}

 }

 \value{

 label layer

@@ -60,6 +60,21 @@ label layer

 \description{

 geom_label2 support aes(subset) via setup_data

 }

+\details{

+'geom_label2' is a modified version of geom_label, with subset aesthetic supported

+}

+\examples{

+library(ggtree)

+set.seed(123)

+tr<- rtree(15)

+x <- ggtree(tr)

+x + geom_label2(aes(label = node, subset = isTip == FALSE))

+}

+\references{

+For more detailed demonstration of this function, please refer to chapter A.4.5 of

+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}

+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.

+}

 \seealso{

 \link[ggplot2:geom_text]{geom_label}

 }

@@ -15,15 +15,15 @@ geom_nodelab(

 )

 }

 \arguments{

-\item{mapping}{aes mapping}

+\item{mapping}{aesthetic mappings, defaults to NULL}

-\item{nudge_x}{horizontal adjustment to nudge label}

+\item{nudge_x}{horizontal adjustment to nudge labels, defaults to 0}

-\item{nudge_y}{vertical adjustment to nudge label}

+\item{nudge_y}{vertical adjustment to nudge labels, defaults to 0}

 \item{geom}{one of 'text', "shadowtext", 'label', 'image' and 'phylopic'}

-\item{hjust}{horizontal alignment, one of 0, 0.5 or 1}

+\item{hjust}{horizontal alignment, defaults to 0.5}

 \item{node}{a character indicating which node labels will be displayed,

 it should be one of 'internal', 'external' and 'all'. If it is set to 'internal'

@@ -37,7 +37,12 @@ the additional parameters of \code{\link[=geom_tiplab]{geom_tiplab()}}.}

 geom layer

 }

 \description{

-add node label layer

+add node label layer for a tree

+}

+\references{

+For demonstration of this function, please refer to chapter A.4.5 of

+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}

+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.

 }

 \seealso{

 \code{\link[=geom_tiplab]{geom_tiplab()}}

@@ -14,15 +14,15 @@ geom_nodelab2(

 )

 }

 \arguments{

-\item{mapping}{aes mapping}

+\item{mapping}{aesthetic mappings, defaults to NULL}

-\item{nudge_x}{horizontal adjustment to nudge label}

+\item{nudge_x}{horizontal adjustment to nudge labels, defaults to 0}

-\item{nudge_y}{vertical adjustment to nudge label}

+\item{nudge_y}{vertical adjustment to nudge labels, defaults to 0}

 \item{geom}{one of 'text', "shadowtext", 'label', 'image' and 'phylopic'}

-\item{hjust}{horizontal alignment, one of 0, 0.5 or 1}

+\item{hjust}{horizontal alignment, defaults to 0.5}

 \item{...}{additional parameters, see also

 the additional parameters of \code{\link[=geom_tiplab]{geom_tiplab()}}.}

@@ -20,16 +20,16 @@ If \code{inherit.aes = TRUE}, the mapping can be inherited from the plot mapping

 specified in the call to \code{ggplot()}.}

 \item{data}{The data to be displayed in this layer. If 'NULL' (the default),

-the data is inherited from the plot data as specified in the call to 'ggplot()',}

+the data is inherited from the plot data as specified in the call to \code{ggplot()}.}

 \item{position}{Position adjustment.}

-\item{na.rm}{logical. If 'FALSE' (the default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}

+\item{na.rm}{logical. If 'FALSE' (default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}

 \item{show.legend}{logical. Should this layer be included in the legends?

 'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.}

-\item{inherit.aes}{logical (default is 'TRUE'). If 'FALSE', overrides the default aesthetics,

+\item{inherit.aes}{logical (defaults to 'TRUE'). If 'FALSE', overrides the default aesthetics,

 rather then combining with them.}

 \item{...}{addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like \code{colour = "red"} or \code{size = 3}.}

@@ -38,8 +38,17 @@ rather then combining with them.}

 node point layer

 }

 \description{

-add node point

+add node point layer to a tree

+}

+\references{

+For more detailed demonstration, please refer to chapter 4.3.2 of

+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}

+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.

 }

 \author{

 Guangchuang Yu

+library(ggtree)

+tr<- rtree(15)

+x <- ggtree(tr)

+x + geom_nodepoint()

 }

@@ -21,18 +21,18 @@ If \code{inherit.aes = TRUE}, the mapping can be inherited from the plot mapping

 specified in the call to \code{ggplot()}.}

 \item{data}{The data to be displayed in this layer. If 'NULL' (the default),

-the data is inherited from the plot data as specified in the call to 'ggplot()',}

+the data is inherited from the plot data as specified in the call to \code{ggplot()}.}

 \item{stat}{Name of the statistical transformation to be used on the data for this layer.}

 \item{position}{Position adjustment.}

-\item{na.rm}{logical. If 'FALSE' (the default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}

+\item{na.rm}{logical. If 'FALSE' (default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}

 \item{show.legend}{logical. Should this layer be included in the legends?

 'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.}

-\item{inherit.aes}{logical (default is 'TRUE'). If 'FALSE', overrides the default aesthetics,

+\item{inherit.aes}{logical (defaults to 'TRUE'). If 'FALSE', overrides the default aesthetics,

 rather then combining with them.}

 \item{...}{addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like \code{colour = "red"} or \code{size = 3}.}

@@ -51,12 +51,12 @@ geom_point2 is a modified version of geom_point that supports aes(subset)

 \code{geom_point2()} understands the following aesthetics

 \itemize{

 \item \code{subset} logical expression indicating elements or rows to keep: missing values are taken as false; should be in aes().

-\item \code{colour} the colour of point, default is black.

-\item \code{fill} the colour of fill, default is black.

-\item \code{alpha} the transparency of fill, default is 1.

-\item \code{size} the size of point, default is 1.5.

-\item \code{shape} specify a shape, default is 19.

-\item \code{stroke} control point border thickness of point, default is 0.5.

+\item \code{colour} the colour of point, defaults to "black".

+\item \code{fill} the colour of fill, defaults to "black".

+\item \code{alpha} the transparency of fill, defaults to 1.

+\item \code{size} the size of point, defaults to 1.5.

+\item \code{shape} specify a shape, defaults to 19.

+\item \code{stroke} control point border thickness of point, defaults to 0.5.

 }

 }

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

 geom_range(range, center = "auto", ...)

 }

 \arguments{

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

+\item{range}{range(interval) to be displayed, e.g. "height_0.95_HPD"}

 \item{center}{center of the range, mean, median or auto (default, the center of the range)}

@@ -17,7 +17,12 @@ geom_range(range, center = "auto", ...)

 ggplot layer

 }

 \description{

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

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

+}

+\references{