@@ -1,6 +1,7 @@

 # ggtree 1.11.4

++ update treeVisualization vignette, with more layout examples added (2017-12-22, Fri)

 + update vignette (2017-12-21, Thu)

     - remove ggtreeUtilities.Rmd

     - merge treeAnnotation and advanceTreeAnnotation

-    

\ No newline at end of file

+

@@ -1469,7 +1469,7 @@ add_angle_slanted <- function(res) {

 calculate_branch_mid <- function(res) {

     res$branch <- with(res, (x[match(parent, node)] + x)/2)

-    if (!is.null(res$branch.length)) {

+    if (!is.null(res[['branch.length']])) {

         res$branch.length[is.na(res$branch.length)] <- 0

     }

     res$branch[is.na(res$branch)] <- 0

@@ -6,7 +6,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.4-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-22621/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--12--21-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--12--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

@@ -46,8 +46,7 @@ Biocpkg <- function (pkg) {

 To view a phylogenetic tree, we first need to parse the tree file into *R*. The

-`r Biocpkg('ggtree')` package supports many file formats via the `r

-Biocpkg('treeio')` package, including output files of commonly used software

+`r Biocpkg('ggtree')` [@yu_ggtree:_2017] package supports many file formats via the `r Biocpkg('treeio')` package, including output files of commonly used software

 packages in evolutionary biology. For more details, plase refer to

 the [treeio vignette](https://bioconductor.org/packages/devel/bioc/vignettes/treeio/inst/doc/Importer.html).

@@ -61,7 +60,7 @@ tree <- read.tree(nwk)

 # Viewing a phylogenetic tree with *ggtree*

-The `r Biocpkg('ggtree')` package extends `r CRANpkg('ggplot2')` package to support viewing phylogenetic tree.

+The `r Biocpkg('ggtree')` package extends `r CRANpkg('ggplot2')` [@wickham_ggplot2_2009] package to support viewing phylogenetic tree.

 It implements `geom_tree` layer for displaying phylogenetic tree, as shown below:

@@ -102,6 +101,10 @@ for *phylogram* (by default) and *cladogram* if user explicitly setting

 *branch.length='none'*. Unrooted (equal angle and daylight methods), time-scaled

 and 2-dimensional layouts are also supported.

+

+## Phylogram and Cladogram

+

+

 ```{r eval=F}

 library(ggtree)

 set.seed(2017-02-16)

@@ -120,37 +123,68 @@ ggtree(tr, layout="daylight", branch.length = 'none')

 ```{r echo=F,  fig.width=8, fig.height=8, message=FALSE}

 library(ggtree)

 set.seed(2017-02-16)

-x <- rtree(50)

+tr <- rtree(50)

 library(cowplot)

 theme_layout <- theme(plot.title = element_text(hjust = 0.5))

 plot_grid(

-    ggtree(x) + ggtitle("rectangular (phylogram)")+ theme_layout,

-    ggtree(x, layout="slanted") + ggtitle("slanted (phylogram)")+theme_layout,

-    ggtree(x, layout="circular") + ggtitle("circular (phylogram)")+theme_layout,

-    ggtree(x, layout="fan", open.angle=120) + ggtitle("fan (phylogram)")+theme_layout,

-    ggtree(x, layout="equal_angle")+ ggtitle("equal angle (unrooted)")+theme_layout,

-    ggtree(x, layout="daylight")+ ggtitle("daylight (unrooted)")+theme_layout,

-    ggtree(x, branch.length='none')+ ggtitle("rectangular (cladogram)")+theme_layout,

-    ggtree(x, branch.length='none', layout='circular')+ ggtitle("circular (cladogram)")+theme_layout,

-    ggtree(x, layout="daylight", branch.length = 'none')+ ggtitle("daylight (cladogram)")+theme_layout,

+    ggtree(tr) + ggtitle("rectangular (phylogram)")+ theme_layout,

+    ggtree(tr, layout="slanted") + ggtitle("slanted (phylogram)")+theme_layout,

+    ggtree(tr, layout="circular") + ggtitle("circular (phylogram)")+theme_layout,

+    ggtree(tr, layout="fan", open.angle=120) + ggtitle("fan (phylogram)")+theme_layout,

+    ggtree(tr, layout="equal_angle")+ ggtitle("equal angle (unrooted)")+theme_layout,

+    ggtree(tr, layout="daylight")+ ggtitle("daylight (unrooted)")+theme_layout,

+    ggtree(tr, branch.length='none')+ ggtitle("rectangular (cladogram)")+theme_layout,

+    ggtree(tr, branch.length='none', layout='circular')+ ggtitle("circular (cladogram)")+theme_layout,

+    ggtree(tr, layout="daylight", branch.length = 'none')+ ggtitle("daylight (cladogram)")+theme_layout,

     ncol=3)

 ```

+There are also other possible layouts that can be drawed by modifying

+scales/coordination, for examples, reverse label of time

+scale^[https://github.com/GuangchuangYu/ggtree/issues/87], repropotion

+circular/fan tree

+^[https://groups.google.com/d/msgid/bioc-ggtree/6db25ec7-ffb1-4776-bfe4-4a1ba239c8e8%40googlegroups.com], *etc.*.

+

+```{r eval=FALSE}

+ggtree(tr) + scale_x_reverse()

+ggtree(tr) + coord_flip()

+ggtree(tr) + scale_x_reverse() + coord_flip()

+ggtree(tr, layout='slanted') + coord_flip()

+ggtree(tr, layout='slanted', branch.length='none') +

+    coord_flip() + scale_y_reverse() +scale_x_reverse()

+ggtree(tr, layout='circular') + xlim(-10, NA)

+ggtree(tr) + scale_x_reverse() + coord_polar(theta='y')

+ggtree(tr) + scale_x_reverse(limits=c(10, 0)) + coord_polar(theta='y')

+```

+

+```{r fig.width=8, fig.height = 4, echo=FALSE}

+plot_grid(

+    ggtree(tr) + scale_x_reverse(),

+    ggtree(tr) + coord_flip(),

+    ggtree(tr) + scale_x_reverse() + coord_flip(),

+    ggtree(tr, layout='slanted') + coord_flip(),

+    ggtree(tr, layout='slanted', branch.length='none') + coord_flip() + scale_y_reverse() +scale_x_reverse(),

+    ggtree(tr, layout='circular') + xlim(-10, NA),

+    ggtree(tr) + scale_x_reverse() + coord_polar(theta='y'),

+    ggtree(tr) + scale_x_reverse(limits=c(15, 0)) + coord_polar(theta='y'),

+    ncol = 4, labels = LETTERS[1:6])

+```

+

 ## Time-scaled tree

-A phylogenetic tree can be scaled by time (time-scaled tree) by specifying the parameter, `mrsd` (most recent sampling date).

+A phylogenetic tree can be scaled by time (time-scaled tree) by specifying the parameter, *mrsd* (most recent sampling date).

-```{r fig.width=9, fig.height=9, fig.align="center"}

+```{r fig.width=8, fig.height=4, fig.align="center"}

 tree2d <- read.beast(system.file("extdata", "twoD.tree", package="treeio"))

 ggtree(tree2d, mrsd = "2014-05-01") + theme_tree2()

 ```

 ## Two dimensional tree

-`ggtree` implemented two dimensional tree. It accepts parameter _`yscale`_ to scale the y-axis based on the selected tree attribute. The attribute should be numerical variable. If it is *character*/*category* variable, user should provides a name vector of mapping the variable to numeric by passing it to parameter _`yscale_mapping`_.

+`r Biocpkg('ggtree')` implemented two dimensional tree. It accepts parameter *yscale* to scale the y-axis based on the selected tree attribute. The attribute should be numerical variable. If it is *character*/*category* variable, user should provides a name vector of mapping the variable to numeric by passing it to parameter *yscale_mapping*.

 ```{r fig.width=9, fig.height=4, fig.align="center"}

@@ -175,35 +209,42 @@ ggtree(tree) + geom_treescale()

 `geom_treescale()` supports the following parameters:

-+ `x` and `y` for tree scale position

-+ `width` for the length of the tree scale

-+ `fontsize` for the size of the text

-+ `linesize` for the size of the line

-+ `offset` for relative position of the line and the text

-+ `color` for color of the tree scale

++ *x* and *y* for tree scale position

++ *width* for the length of the tree scale

++ *fontsize* for the size of the text

++ *linesize* for the size of the line

++ *offset* for relative position of the line and the text

++ *color* for color of the tree scale

-```{r fig.width=4, fig.height=4, fig.align="center"}

-ggtree(tree)+geom_treescale(x=0, y=12, width=6, color='red')

+```{r eval=F}

+ggtree(tree) + geom_treescale(x=0, y=12, width=6, color='red')

+ggtree(tree) + geom_treescale(fontsize=8, linesize=2, offset=-1)

 ```

-```{r fig.width=4, fig.height=4, fig.align="center"}

-ggtree(tree)+geom_treescale(fontsize=8, linesize=2, offset=-1)

+```{r fig.width=8, fig.height=4, fig.align="center", echo=F}

+plot_grid(

+    ggtree(tree)+geom_treescale(x=0, y=12, width=6, color='red'),

+    ggtree(tree)+geom_treescale(fontsize=8, linesize=2, offset=-1),

+    ncol = 2, labels = LETTERS[1:2])

 ```

-We can also use `theme_tree2()` to display the tree scale by adding `x axis`.

+We can also use `theme_tree2()` to display the tree scale by adding *x axis*.

+

 ```{r fig.width=3, fig.height=3, fig.align="center"}

 ggtree(tree) + theme_tree2()

 ```

-Tree scale is not restricted to evolution distance, `ggtree` can re-scale the tree with other numerical variable. More details can be found in the [Tree Annotation](treeAnnotation.html) vignette.

+

+Tree scale is not restricted to evolution distance, `r Biocpkg('ggtree')` can re-scale the tree with other numerical variable. More details can be found in the [Tree Annotation](treeAnnotation.html) vignette.

 # Displaying nodes/tips

-Showing all the internal nodes and tips in the tree can be done by adding a layer of points using _`geom_nodepoint`_,  _`geom_tippoint`_ or _`geom_point`_.

+Showing all the internal nodes and tips in the tree can be done by adding a layer of points using `geom_nodepoint`,  `geom_tippoint` or `geom_point`.

+

 ```{r fig.width=3, fig.height=3, fig.align="center"}

 ggtree(tree)+geom_point(aes(shape=isTip, color=isTip), size=3)

@@ -216,19 +257,32 @@ p + geom_tippoint(color="#FDAC4F", shape=8, size=3)

 ## Displaying labels

-Users can use _`geom_text`_ to display the node (if available) and tip labels simultaneously or `geom_tiplab` to only display tip labels:

+Users can use `geom_text` or `geom_label` to display the node (if available) and tip labels simultaneously or `geom_tiplab` to only display tip labels:

+

 ```{r fig.width=3, fig.height=3, warning=FALSE, fig.align="center"}

 p + geom_tiplab(size=3, color="purple")

 ```

-For _`circular`_ and _`unrooted`_ layout, `ggtree` supports rotating node labels according to the angles of the branches.

+`geom_tiplab` not only supports using *text* or *label* geom to display labels,

+it also supports *image* geom to label tip with image files. A corresponding

+geom, `geom_nodelab` is also provided for displaying node labels. For details of

+label nodes with images, please refer to

+the vignette,

+[Annotating phylogenetic tree with images](https://cran.r-project.org/web/packages/ggimage/vignettes/ggtree.html).

+

+

+

+For *circular* and *unrooted* layout, `r Biocpkg('ggtree')` supports rotating node labels according to the angles of the branches.

+

 ```{r fig.width=6, fig.height=6, warning=FALSE, fig.align="center"}

 ggtree(tree, layout="circular") + geom_tiplab(aes(angle=angle), color='blue')

 ```

-To make it more readable for human eye, `ggtree` provides a `geom_tiplab2` for `circular` layout (see post [1](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/o35PV3iHO-0) and [2](https://groups.google.com/forum/#!topic/bioc-ggtree/p42R5l8J-14)).

+

+To make it more readable for human eye, `r Biocpkg('ggtree')` provides a `geom_tiplab2` for `circular` layout (see post [1](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/o35PV3iHO-0) and [2](https://groups.google.com/forum/#!topic/bioc-ggtree/p42R5l8J-14)).

+

 ```{r fig.width=6, fig.height=6, warning=FALSE, fig.align="center"}

 ggtree(tree, layout="circular") + geom_tiplab2(color='blue')

@@ -236,12 +290,15 @@ ggtree(tree, layout="circular") + geom_tiplab2(color='blue')

 By default, the positions are based on the node positions, we can change them to based on the middle of the branch/edge.

+

 ```{r fig.width=4, fig.height=3, warning=FALSE, fig.align="center"}

 p + geom_tiplab(aes(x=branch), size=3, color="purple", vjust=-0.3)

 ```

+

 Based on the middle of branch is very useful when annotating transition from parent node to child node.

+

 # update tree view with a new tree

 In previous example, we have a _`p`_ object that stored the tree viewing of 13 tips and internal nodes highlighted with specific colored big dots. If users want to apply this pattern (we can imaging a more complex one) to a new tree, you don't need to build the tree step by step. `ggtree` provides an operator, _`%<%`_, for applying the visualization pattern to a new tree.

@@ -251,19 +308,28 @@ For example, the pattern in the _`p`_ object will be applied to a new tree with

 p %<% rtree(50)

 ```

-Another example can be found in the [Tree Data Import](treeImport.html#rst-file) vignette.

-

 # theme

-`theme_tree()` defined a totally blank canvas, while _`theme_tree2()`_ adds phylogenetic distance (via x-axis). These two themes all accept a parameter of _`bgcolor`_ that defined the background color.

+`theme_tree()` defined a totally blank canvas, while _`theme_tree2()`_ adds

+phylogenetic distance (via x-axis). These two themes all accept a parameter of

+_`bgcolor`_ that defined the background color. Users can pass

+any [theme components](http://ggplot2.tidyverse.org/reference/theme.html) to the

+`theme_tree()` function to modify them.

+

-```{r fig.width=6, fig.height=3, fig.align="center"}

+```{r eval=F}

+ggtree(rtree(30), color="red") + theme_tree("steelblue")

+ggtree(rtree(20), color="white") + theme_tree("black")

+```

+

+```{r fig.width=8, fig.height=3, fig.align="center", echo=F}

 cowplot::plot_grid(

     ggtree(rtree(30), color="red") + theme_tree("steelblue"),

-    ggtree(rtree(20), color="white") + theme_tree("black"),

+    ggtree(rtree(20), color="purple") + theme_tree("black"),

     ncol=2)

 ```

+

 # Visualize a list of trees

 `ggtree` supports `multiPhylo` object and a list of trees can be viewed simultaneously.