@@ -38,7 +38,7 @@ Biocpkg <- function (pkg) {

 # Vignette

-Please go to <https://yulab-smu.github.io/treedata-book/> for the full vignette.

+Please go to <https://yulab-smu.top/treedata-book/> for the full vignette.

 # Citation

@@ -45,10 +45,10 @@ Please go to <https://yulab-smu.github.io/treedata-book/> for the full vignette.

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-

-1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.

+1. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).

+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.

 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

-2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

 visualization and annotation of phylogenetic trees with their covariates and

 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

@@ -1,5 +1,5 @@

 ---

-title: "ggtree: phylogenetic tree visualization and annotation"

+title: "ggtree: tree visualization and annotation"

 author: "Guangchuang Yu\\

         School of Basic Medical Sciences, Southern Medical University"

@@ -45,12 +45,34 @@ Please go to <https://yulab-smu.github.io/treedata-book/> for the full vignette.

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+

+1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.

+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

+2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

 visualization and annotation of phylogenetic trees with their covariates and

 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

-2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.

-doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

+

+

+

+

+# Need helps?

+

+

+If you have questions/issues, please visit

+[ggtree homepage](https://guangchuangyu.github.io/software/ggtree/) first.

+Your problems are mostly documented. 

+

+

+If you think you found a bug, please follow

+[the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) and

+provide a reproducible example to be posted

+on

+[github issue tracker](https://github.com/GuangchuangYu/ggtree/issues).

+For questions, please post

+to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree). Users

+are highly recommended to subscribe to the [mailing list](https://groups.google.com/forum/#!forum/bioc-ggtree).

+

@@ -232,21 +254,3 @@ published images and links to related resources).

 -->

-# Need helps?

-

-

-If you have questions/issues, please visit

-[ggtree homepage](https://guangchuangyu.github.io/software/ggtree/) first.

-Your problems are mostly documented. 

-

-

-If you think you found a bug, please follow

-[the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) and

-provide a reproducible example to be posted

-on

-[github issue tracker](https://github.com/GuangchuangYu/ggtree/issues).

-For questions, please post

-to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree). Users

-are highly recommended to subscribe to the [mailing list](https://groups.google.com/forum/#!forum/bioc-ggtree).

-

-

@@ -49,7 +49,7 @@ If you use `r Biocpkg('ggtree')` in published research, please cite the most app

 visualization and annotation of phylogenetic trees with their covariates and

 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

-2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted.

+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.

 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

@@ -1,12 +1,14 @@

 ---

-title: "ggtree: a phylogenetic tree viewer for different types of tree annotations"

+title: "ggtree: phylogenetic tree visualization and annotation"

 author: "Guangchuang Yu\\

         School of Basic Medical Sciences, Southern Medical University"

 date: "`r Sys.Date()`"

 output:

-  html_document:

-    toc: true

+  prettydoc::html_pretty:

+    toc: false

+    theme: cayman

+    highlight: github

   pdf_document:

     toc: true

 vignette: >

@@ -4,20 +4,15 @@ author: "Guangchuang Yu\\

         School of Basic Medical Sciences, Southern Medical University"

 date: "`r Sys.Date()`"

-bibliography: ggtree.bib

-biblio-style: apalike

 output:

-  prettydoc::html_pretty:

+  html_document:

     toc: true

-    theme: cayman

-    highlight: github

   pdf_document:

     toc: true

 vignette: >

-  %\VignetteIndexEntry{01 ggtree Introduction}

+  %\VignetteIndexEntry{ggtree}

   %\VignetteEngine{knitr::rmarkdown}

   %\usepackage[utf8]{inputenc}

-  %\VignetteEncoding{UTF-8}

 ---

 ```{r style, echo=FALSE, results="asis", message=FALSE}

@@ -39,11 +34,9 @@ Biocpkg <- function (pkg) {

 ```

-> You can't even begin to understand biology, you can't understand life, unless

-> you understand what it's all there for, how it arose - and that means

-> evolution.

->

-> --- Richard Dawkins

+# Vignette

+

+Please go to <https://yulab-smu.github.io/treedata-book/> for the full vignette.

 # Citation

@@ -59,6 +52,8 @@ doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

+<!--

+

 # Introduction

 This project arose from our needs to annotate nucleotide substitutions in the

@@ -232,13 +227,18 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 information about the package, more documentation, a gallery of beautiful

 published images and links to related resources).

+-->

+

 # Need helps?

 If you have questions/issues, please visit

 [ggtree homepage](https://guangchuangyu.github.io/software/ggtree/) first.

-Your problems are mostly documented. If you think you found a bug, please follow

+Your problems are mostly documented. 

+

+

+If you think you found a bug, please follow

 [the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) and

 provide a reproducible example to be posted

 on

@@ -248,14 +248,3 @@ to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree). Users

 are highly recommended to subscribe to the [mailing list](https://groups.google.com/forum/#!forum/bioc-ggtree).

-

-# Session info

-

-Here is the output of `sessionInfo()` on the system on which this document was compiled:

-

-```{r echo=FALSE}

-sessionInfo()

-```

-

-

-# References

@@ -48,12 +48,15 @@ Biocpkg <- function (pkg) {

 # Citation

-If you use `r Biocpkg('ggtree')` in published research, please cite:

+If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

 visualization and annotation of phylogenetic trees with their covariates and

 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted.

+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

+

 # Introduction

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

 ---

 title: "ggtree: a phylogenetic tree viewer for different types of tree annotations"

-author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

+author: "Guangchuang Yu\\

-        School of Public Health, The University of Hong Kong"

+        School of Basic Medical Sciences, Southern Medical University"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

 biblio-style: apalike

@@ -245,8 +245,6 @@ to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree). Users

 are highly recommended to subscribe to the [mailing list](https://groups.google.com/forum/#!forum/bioc-ggtree).

-For Chinese user, you can follow me on [WeChat (微信)](https://guangchuangyu.github.io/blog_images/biobabble.jpg).

-

 # Session info

@@ -192,12 +192,8 @@ knitr::kable(geoms, caption = "Geom layers defined in ggtree.", booktabs = T)

 ```

 `r Biocpkg('ggtree')` supports creating phylomoji using Emoji fonts, please

-refer to `r CRANpkg("emojifont")` package vignette for details. The vignette can

-be opened via the following command:

-

-```r

-vignette("phylomoji", package="emojifont")

-```

+refer to the

+[Phylomoji](https://guangchuangyu.github.io/software/ggtree/vignettes/phylomoji.html) vignette.

 `r Biocpkg('ggtree')` integrates [phylopic](http://phylopic.org/) database and silhouette images of organisms can

@@ -224,7 +220,7 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 + [Tree Visualization](treeVisualization.html)

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

-+ [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

++ [Phylomoji](https://guangchuangyu.github.io/software/ggtree/vignettes/phylomoji.html)

 + [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-ggimage.html)

 + [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-inset.html)

@@ -17,6 +17,7 @@ vignette: >

   %\VignetteIndexEntry{01 ggtree Introduction}

   %\VignetteEngine{knitr::rmarkdown}

   %\usepackage[utf8]{inputenc}

+  %\VignetteEncoding{UTF-8}

 ---

 ```{r style, echo=FALSE, results="asis", message=FALSE}

@@ -232,10 +233,23 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 information about the package, more documentation, a gallery of beautiful

 published images and links to related resources).

-# Feedback

- - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

- - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree).

+# Need helps?

+

+

+If you have questions/issues, please visit

+[ggtree homepage](https://guangchuangyu.github.io/software/ggtree/) first.

+Your problems are mostly documented. If you think you found a bug, please follow

+[the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) and

+provide a reproducible example to be posted

+on

+[github issue tracker](https://github.com/GuangchuangYu/ggtree/issues).

+For questions, please post

+to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree). Users

+are highly recommended to subscribe to the [mailing list](https://groups.google.com/forum/#!forum/bioc-ggtree).

+

+

+For Chinese user, you can follow me on [WeChat (微信)](https://guangchuangyu.github.io/blog_images/biobabble.jpg).

 # Session info

@@ -228,7 +228,7 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 + [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-inset.html)

-**ggtree homepage**: <https://guangchuangyu.github.io/ggtree> (contains more

+**ggtree homepage**: <https://guangchuangyu.github.io/software/ggtree> (contains more

 information about the package, more documentation, a gallery of beautiful

 published images and links to related resources).

@@ -224,8 +224,8 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

-+ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html)

-+ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-inset.html)

++ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-ggimage.html)

++ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-inset.html)

 **ggtree homepage**: <https://guangchuangyu.github.io/ggtree> (contains more

@@ -225,6 +225,7 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 + [Tree Annotation](treeAnnotation.html)

 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

 + [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html)

++ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-inset.html)

 **ggtree homepage**: <https://guangchuangyu.github.io/ggtree> (contains more

@@ -224,12 +224,14 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

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

++ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html)

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

+**ggtree homepage**: <https://guangchuangyu.github.io/ggtree> (contains more

+information about the package, more documentation, a gallery of beautiful

+published images and links to related resources).

-# Feedback #

+# Feedback

  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

  - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree).

@@ -14,7 +14,7 @@ output:

   pdf_document:

     toc: true

 vignette: >

-  %\VignetteIndexEntry{00 ggtree introduction}

+  %\VignetteIndexEntry{01 ggtree Introduction}

   %\VignetteEngine{knitr::rmarkdown}

   %\usepackage[utf8]{inputenc}

 ---

@@ -124,14 +124,29 @@ and *daylight* for *unrooted* layout, time-scaled and two dimentional

 phylogenies. [Tree Visualization](treeVisualization.html) vignette describes

 these feature in details.

-We implement several functions to manipulate a phylogenetic tree.

+We implement several functions to manipulate a phylogenetic tree visually,

+including viewing selected clade to explore large tree, taxa clustering,

+rotating clade or tree, zoom out or collapsing clades *etc.*.

-+ taxa can be clustered together using `groupClade` or `groupOTU` functions

-+ clades can be collapsed via `collapse` function

-+ collapsed clade can be expanded by using `expand` function

-+ clade can be re-scale to zoom in or zoom out by `scaleClade` function

-+ selected clade can be rotated by 180 degree using `rotate` function

-+ position of two selected clades (should share a same parent) can be exchanged by `flip` function

+

+

+```{r treeman, echo=FALSE, out.extra='', message=FALSE}

+treeman <- matrix(c(

+  "collapse", "collapse a selecting clade",

+  "expand", "expand collapsed clade",

+  "flip", "exchange position of 2 clades that share a parent node",

+  "groupClade", "grouping clades",

+  "groupOTU", "grouping OTUs by tracing back to most recent common ancestor",

+  "identify", "interactive tree manipulation",

+  "rotate", "rotating a selected clade by 180 degree",

+  "rotate_tree", "rotating circular layout tree by specific angle",

+  "scaleClade", "zoom in or zoom out selecting clade",

+  "open_tree", "convert a tree to fan layout by specific open angle"

+), ncol=2, byrow=TRUE)

+treeman <- as.data.frame(treeman)

+colnames(treeman) <- c("Function", "Descriptiotn")

+knitr::kable(treeman, caption = "Tree manipulation functions.", booktabs = T)

+```

 Details and examples can be found in [Tree Manipulation](treeManipulation.html) vignette.

@@ -38,7 +38,10 @@ Biocpkg <- function (pkg) {

 ```

-> You can't even begin to understand biology, you can't understand life, unless you understand what it's all there for, how it arose - and that means evolution.

+> You can't even begin to understand biology, you can't understand life, unless

+> you understand what it's all there for, how it arose - and that means

+> evolution.

+>

 > --- Richard Dawkins

@@ -114,7 +117,12 @@ visualize or annotate phylogenetic tree in `r Biocpkg('ggtree')` [@yu_ggtree:_20

 # Tree Visualization and Annotation

-Tree Visualization in `ggtree` is easy, with one line of command `ggtree(tree_object)`. It supports several layouts, including `rectangular`, `slanted` and `circular` for `Phylogram` and `Cladogram`, `unrooted` layout, time-scaled and two dimentional phylogenies. [Tree Visualization](treeVisualization.html) vignette describes these feature in details.

+Tree Visualization in `r Biocpkg('ggtree')` is easy, with one line of command

+`ggtree(tree_object)`. It supports several layouts, including *rectangular*,

+*slanted*, *circular* and *fan* for *phylogram* and *cladogram*, *equal_angle*

+and *daylight* for *unrooted* layout, time-scaled and two dimentional

+phylogenies. [Tree Visualization](treeVisualization.html) vignette describes

+these feature in details.

 We implement several functions to manipulate a phylogenetic tree.

@@ -125,27 +133,73 @@ We implement several functions to manipulate a phylogenetic tree.

 + selected clade can be rotated by 180 degree using `rotate` function

 + position of two selected clades (should share a same parent) can be exchanged by `flip` function

+

 Details and examples can be found in [Tree Manipulation](treeManipulation.html) vignette.

-Most of the phylogenetic trees are scaled by evolutionary distance (substitution/site), in `ggtree` a phylogenetic tree can be re-scaled by any numerical variable inferred by evolutionary analysis (e.g. species divergence time, *dN/dS*, _etc_). Numerical and category variable can be used to color a phylogenetic tree.

+Most of the phylogenetic trees are scaled by evolutionary distance

+(substitution/site), in `r Biocpkg('ggtree')` a phylogenetic tree can be

+re-scaled by any numerical variable inferred by evolutionary analysis (e.g.

+species divergence time, *d~N~/d~S~*, _etc_). Numerical and category variable can be

+used to color a phylogenetic tree.

+

+The `r Biocpkg('ggtree')` package provides several layers to annotate a

+phylogenetic tree. These layers are building blocks that can be freely combined

+together to create complex tree visualization.

+

+```{r geoms, echo=FALSE, message=FALSE}

+geoms <- matrix(c(

+  "geom_balance", "highlights the two direct descendant clades of an internal node",

+  "geom_cladelabel", "annotate a clade with bar and text label",

+  "geom_cladelabel2", "annotate a clade with bar and text label for unrooted layout",

+  "geom_hilight", "highlight a clade with rectangle",

+  "geom_hilight_encircle", "highlight a clade with xspline for unrooted layout",

+  "geom_label2", "modified version of geom_label, with subsetting supported",

+  "geom_nodelab", "layer for node labels, which can be text or image",

+  "geom_nodepoint", "annotate internal nodes with symbolic points",

+  "geom_point2", "modified version of geom_point, with subsetting supported",

+  "geom_range", "bar layer to present uncertainty of evolutionary inference",

+  "geom_rootpoint", "annotate root node with symbolic point",

+  "geom_segment2", "modified version of geom_segment, with subsetting supported",

+  "geom_strip", "annotate associated taxa with bar and (optional) text label",

+  "geom_taxalink", "associate two related taxa by linking them with a curve",

+  "geom_text2", "modified version of geom_text, with subsetting supported",

+  "geom_tiplab", "layer of tip labels, which can be text or image",

+  "geom_tiplab2", "layer of tip labels for circular layout",

+  "geom_tippoint", "annotate external nodes with symbolic points",

+  "geom_tree", "tree structure layer, with multiple layout supported",

+  "geom_treescale", "tree branch scale legend"

+), ncol=2, byrow=TRUE)

+geoms <- as.data.frame(geoms)

+colnames(geoms) <- c("Layer", "Description")

+knitr::kable(geoms, caption = "Geom layers defined in ggtree.", booktabs = T)

+```

+

+`r Biocpkg('ggtree')` supports creating phylomoji using Emoji fonts, please

+refer to `r CRANpkg("emojifont")` package vignette for details. The vignette can

+be opened via the following command:

+

+```r

+vignette("phylomoji", package="emojifont")

+```

-The `ggtree` package provides several layers to annotate a phylogenetic tree, including:

-+ `geom_cladelabel` for labelling selected clades

-+ `geom_hilight` for highlighting selected clades

-+ `geom_range` to indicate uncertainty of branch lengths

-+ `geom_strip` for adding strip/bar to label associated taxa (with optional label)

-+ `geom_taxalink` for connecting related taxa

-+ `geom_tiplab` for adding tip labels

-+ `geom_treescale` for adding a legend of tree scale

+`r Biocpkg('ggtree')` integrates [phylopic](http://phylopic.org/) database and silhouette images of organisms can

+be downloaded and used to annotate phylogenetic directly. `r Biocpkg('ggtree')` also supports

+using local or remote images to annotate a phylogenetic tree. For details,

+please refer to the `r CRANpkg('ggimage')` package vignette, which can be opened

+via the following command:

-It supports annotating phylogenetic trees with analyses obtained from R packages and other commonly used evolutionary software. User's specific annotation (e.g. experimental data) can be integrated to annotate phylogenetic trees. `ggtree` provides `write.jplace` function to combine Newick tree file and user's own data to a single `jplace` file that can be parsed and the data can be used to annotate the tree directly in `ggtree`.

+```r

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

+```

-`ggtree` integrates `phylopic` database and silhouette images of organisms can be downloaded and used to annotate phylogenetic directly. `ggtree` also supports using local images to annotate a phylogenetic tree.

-Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype table), multiple sequence alignment and subplots are also supported in `ggtree`. Examples of annotating phylogenetic trees can be found in the [Tree Annotation](treeAnnotation.html) and [Advance Tree Annotation](advanceTreeAnnotation.html) vignettes.

+Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

+table), multiple sequence alignment and subplots are also supported in `ggtree`.

+Examples of annotating phylogenetic trees can be found in

+the [Tree Annotation](treeAnnotation.html) vignette.

 # Vignette Entry

@@ -154,14 +208,13 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

 + [Tree Visualization](treeVisualization.html)

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

-+ [Advance Tree Annotation](advanceTreeAnnotation.html)

 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

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

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

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

-## Feedback ##

+# Feedback #

  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

  - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree).

@@ -5,7 +5,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

-csl: nature.csl

+biblio-style: apalike

 output:

   prettydoc::html_pretty:

     toc: true

@@ -25,14 +25,18 @@ knitr::opts_chunk$set(tidy = FALSE,

 ```

-```{r echo=FALSE, results="hide", message=FALSE}

-library("colorspace")

-library("ape")

-library("ggplot2")

-library("ggtree")

-```

+```{r echo=FALSE}

+CRANpkg <- function (pkg) {

+    cran <- "https://CRAN.R-project.org/package"

+    fmt <- "[%s](%s=%s)"

+    sprintf(fmt, pkg, cran, pkg)

+}

+Biocpkg <- function (pkg) {

+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)

+}

+```

 > You can't even begin to understand biology, you can't understand life, unless you understand what it's all there for, how it arose - and that means evolution.

 > --- Richard Dawkins

@@ -40,27 +44,73 @@ library("ggtree")

 # Citation

-If you use `ggtree` in published research, please cite:

+If you use `r Biocpkg('ggtree')` in published research, please cite:

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628).

+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+visualization and annotation of phylogenetic trees with their covariates and

+other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

+doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

 # Introduction

-This project arose from our needs to annotate nucleotide substitutions in the phylogenetic tree, and we found that there is no tree visualization software can do this easily. Existing tree viewers are designed for displaying phylogenetic tree, but not annotating it. Although some tree viewers can displaying bootstrap values in the tree, it is hard/impossible to display other information in the tree. Our first solution for displaying nucleotide substituitions in the tree is to add this information in the node/tip names and use traditional tree viewer to show it. We displayed the information in the tree successfully, but we believe this indirect approach is inefficient.

-

-Previously, phylogenetic trees were much smaller. Annotation of phylogenetic trees was not as necessary as nowadays much more data is becomming available. We want to associate our experimental data, for instance antigenic change, with the evolution relationship. Visualizing these associations in a phylogenetic tree can help us to identify evolution patterns. We believe we need a next generation tree viewer that should be programmable and extensible. It can view a phylogenetic tree easily as we did with classical software and support adding annotation data in a layer above the tree. This is the objective of developing the `ggtree`. Common tasks of annotating a phylogenetic tree should be easy and complicated tasks can be possible to achieve by adding multiple layers of annotation.

-

-The `ggtree` is designed by extending the `ggplot2`[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and takes all the good parts of `ggplot2`. There are other R packages that implement tree viewer using `ggplot2`, including `OutbreakTools`, `phyloseq`[@mcmurdie_phyloseq_2013] and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex tree view functions for their specific needs. Internally, these packages interpret a phylogenetic as a collection of `lines`, which makes it hard to annotate diverse user input that are related to node (taxa). The `ggtree` is different to them by interpreting a tree as a collection of `taxa` and allowing general flexibilities of annotating phylogenetic tree with diverse types of user inputs.

-

-

-# Getting data into `R`

-

-Most of the tree viewer software (including `R` packages) focus on `Newick` and `Nexus` file format, while there are file formats from different evolution analysis software that contain supporting evidences within the file that are ready for annotating a phylogenetic tree. In addition to `Newick` and `Nexus`, ggtree supports `NHX`, `jplace` and `Phylip` file formats. `ggtree` also supports software outputs from [BEAST](http://beast2.org/)[@bouckaert_beast_2014], [EPA](http://sco.h-its.org/exelixis/web/software/epa/index.html)[@berger_EPA_2011], [HYPHY](http://hyphy.org/w/index.php/Main_Page)[@pond_hyphy_2005], [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], [PHYLDOG](http://pbil.univ-lyon1.fr/software/phyldog/)[@boussau_genome-scale_2013], [pplacer](http://matsen.fhcrc.org/pplacer/)[@matsen_pplacer_2010], [r8s](http://loco.biosci.arizona.edu/r8s/)[@marazzi_locating_2012], [RAxML](http://sco.h-its.org/exelixis/web/software/raxml/)[@stamatakis_raxml_2014] and [RevBayes](http://revbayes.github.io/intro.html)[@hohna_probabilistic_2014].

+This project arose from our needs to annotate nucleotide substitutions in the

+phylogenetic tree, and we found that there is no tree visualization software can

+do this easily. Existing tree viewers are designed for displaying phylogenetic

+tree, but not annotating it. Although some tree viewers can displaying bootstrap

+values in the tree, it is hard/impossible to display other information in the

+tree. Our first solution for displaying nucleotide substituitions in the tree is

+to add this information in the node/tip names and use traditional tree viewer to

+show it. We displayed the information in the tree successfully, but we believe

+this indirect approach is inefficient.

+

+Previously, phylogenetic trees were much smaller. Annotation of phylogenetic

+trees was not as necessary as nowadays much more data is becomming available. We

+want to associate our experimental data, for instance antigenic change, with the

+evolution relationship. Visualizing these associations in a phylogenetic tree

+can help us to identify evolution patterns. We believe we need a next generation

+tree viewer that should be programmable and extensible. It can view a

+phylogenetic tree easily as we did with classical software and support adding

+annotation data in a layer above the tree. This is the objective of developing

+the `r Biocpkg('ggtree')` [@yu_ggtree:_2017]. Common tasks of annotating a phylogenetic tree should

+be easy and complicated tasks can be possible to achieve by adding multiple

+layers of annotation.

+

+The `r Biocpkg('ggtree')` is designed by extending the `r CRANpkg('ggplot2')`

+[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and

+takes all the good parts of `r CRANpkg('ggplot2')`. There are other R packages that implement

+tree viewer using `r CRANpkg('ggplot2')`, including `r CRANpkg('OutbreakTools')`,

+`r Biocpkg('phyloseq')` [@mcmurdie_phyloseq_2013]

+and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex

+tree view functions for their specific needs. Internally, these packages

+interpret a phylogenetic as a collection of lines, which makes it hard to

+annotate diverse user input that are related to node (taxa). The `r Biocpkg('ggtree')` is

+different to them by interpreting a tree as a collection of taxa and allowing

+general flexibilities of annotating phylogenetic tree with diverse types of user

+inputs.

+

+

+# Getting data into *R*

+

+Most of the tree viewer software (including *R* packages) focus on *Newick* and

+*Nexus* file format, while there are file formats from different evolution

+analysis software that contain supporting evidences within the file that are

+ready for annotating a phylogenetic tree. The `r Biocpkg('treeio')` package

+supports several file formats and software outputs. It brings analysis findings

+to *R* users for further analysis (*e.g.* summarization, visualization,

+comparison and test, *etc.*). It also allows external data to be mapped on the

+phylogeny. Please refer to the `r Biocpkg('treeio')` vignette

+for more details.

+

+Users can use the following command to open the vignette:

+

+```r

+vignette("Importer", package="treeio")

+```

-Parsing data from a number of molecular evolution software is not only for visualization in `ggtree`, but also bring these data to `R` users for further analysis (e.g. summarization, visualization, comparision, test, _etc_).

+All the data parsed/integrated by `r Biocpkg('treeio')` package can be used to

+visualize or annotate phylogenetic tree in `r Biocpkg('ggtree')` [@yu_ggtree:_2017].

-For more details, please refer to [Tree Data Import](treeImport.html) vignette.

 # Tree Visualization and Annotation

@@ -100,25 +150,27 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

 # Vignette Entry

-+ [Tree Data Import](https://bioconductor.org/packages/release/bioc/vignettes/treeio/inst/doc/treeio.html)

++ [Tree Data Import](https://bioconductor.org/packages/devel/bioc/vignettes/treeio/inst/doc/Importer.html)

 + [Tree Visualization](treeVisualization.html)

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

 + [Advance Tree Annotation](advanceTreeAnnotation.html)

-+ [ggtree utilities](ggtreeUtilities.html)

 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

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

+

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

 ## Feedback ##

  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

- - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree) or post to [Bioconductor support site](https://support.bioconductor.org/) or [Biostars](https://www.biostars.org/). We are following every post tagged with **ggtree**.

+ - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree).

 # Session info

 Here is the output of `sessionInfo()` on the system on which this document was compiled:

+

 ```{r echo=FALSE}

 sessionInfo()

 ```

@@ -27,7 +27,6 @@ knitr::opts_chunk$set(tidy = FALSE,

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("colorspace")

-library("Biostrings")

 library("ape")

 library("ggplot2")

 library("ggtree")

@@ -101,7 +101,7 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

 # Vignette Entry

-+ [Tree Data Import](treeImport.html)

++ [Tree Data Import](https://bioconductor.org/packages/release/bioc/vignettes/treeio/inst/doc/treeio.html)

 + [Tree Visualization](treeVisualization.html)

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

@@ -43,7 +43,7 @@ library("ggtree")

 If you use `ggtree` in published research, please cite:

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)

+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628).

 # Introduction

@@ -6,7 +6,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

 csl: nature.csl

-output: 

+output:

   prettydoc::html_pretty:

     toc: true

     theme: cayman

@@ -52,7 +52,7 @@ This project arose from our needs to annotate nucleotide substitutions in the ph

 Previously, phylogenetic trees were much smaller. Annotation of phylogenetic trees was not as necessary as nowadays much more data is becomming available. We want to associate our experimental data, for instance antigenic change, with the evolution relationship. Visualizing these associations in a phylogenetic tree can help us to identify evolution patterns. We believe we need a next generation tree viewer that should be programmable and extensible. It can view a phylogenetic tree easily as we did with classical software and support adding annotation data in a layer above the tree. This is the objective of developing the `ggtree`. Common tasks of annotating a phylogenetic tree should be easy and complicated tasks can be possible to achieve by adding multiple layers of annotation.

-The `ggtree` is designed by extending the `ggplot2`[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and takes all the good parts of `ggplot2`. There are other R packages that implement tree viewer using `ggplot2`, including `OutbreakTools`, `phyloseq`[@mcmurdie_phyloseq_2013] and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex tree view functions for their specific needs. Internally, these packages interpret a phylogenetic as a collection of `lines`, which makes it hard to annotate diverse user input that are related to node (taxa). The `ggtree` is different to them by interpreting a tree as a collection of `taxa` and allowing general flexibilities of annotating phylogenetic tree with diverse types of user inputs. 

+The `ggtree` is designed by extending the `ggplot2`[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and takes all the good parts of `ggplot2`. There are other R packages that implement tree viewer using `ggplot2`, including `OutbreakTools`, `phyloseq`[@mcmurdie_phyloseq_2013] and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex tree view functions for their specific needs. Internally, these packages interpret a phylogenetic as a collection of `lines`, which makes it hard to annotate diverse user input that are related to node (taxa). The `ggtree` is different to them by interpreting a tree as a collection of `taxa` and allowing general flexibilities of annotating phylogenetic tree with diverse types of user inputs.

 # Getting data into `R`

@@ -84,7 +84,7 @@ Most of the phylogenetic trees are scaled by evolutionary distance (substitution

 The `ggtree` package provides several layers to annotate a phylogenetic tree, including:

 + `geom_cladelabel` for labelling selected clades

-+ `geom_hilight` for highlighting selected clades 

++ `geom_hilight` for highlighting selected clades

 + `geom_range` to indicate uncertainty of branch lengths

 + `geom_strip` for adding strip/bar to label associated taxa (with optional label)

 + `geom_taxalink` for connecting related taxa

@@ -107,7 +107,7 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

 + [Tree Annotation](treeAnnotation.html)

 + [Advance Tree Annotation](advanceTreeAnnotation.html)

 + [ggtree utilities](ggtreeUtilities.html)

-

++ [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

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

@@ -115,7 +115,7 @@ More documents can be found in <https://guangchuangyu.github.io/ggtree>.

  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

  - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree) or post to [Bioconductor support site](https://support.bioconductor.org/) or [Biostars](https://www.biostars.org/). We are following every post tagged with **ggtree**.

-  

+

 # Session info

@@ -40,9 +40,10 @@ library("ggtree")

 # Citation

+

 If you use `ggtree` in published research, please cite:

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)

+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)

 # Introduction

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

 ---

 title: "ggtree: a phylogenetic tree viewer for different types of tree annotations"

-author: "\\

-

-	Guangchuang Yu (<guangchuangyu@gmail.com>) and Tommy Tsan-Yuk Lam (<ttylam@hku.hk>)\\

+author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

 csl: nature.csl

 output: 

-  html_document:

+  prettydoc::html_pretty:

     toc: true

+    theme: cayman

+    highlight: github

   pdf_document:

     toc: true

 vignette: >

@@ -42,7 +42,7 @@ library("ggtree")

 # Citation

 If you use `ggtree` in published research, please cite:

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_

+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)

 # Introduction

@@ -42,11 +42,8 @@ library("ggtree")

 # Citation

 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 trees with their covariates and other associated data.

-Methods in Ecology and Evolution, revised.

-```

+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_

+

 # Introduction

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

 library("ape")

 library("ggplot2")

 library("ggtree")

-library("phangorn")

 ```

@@ -112,11 +112,13 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

 + [ggtree utilities](ggtreeUtilities.html)

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

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

-# Bugs/Feature requests

+## Feedback ##

-If you have any, [let me know](https://github.com/GuangchuangYu/ggtree/issues). Thx!

+ - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

+ - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree) or post to [Bioconductor support site](https://support.bioconductor.org/) or [Biostars](https://www.biostars.org/). We are following every post tagged with **ggtree**.

+  

 # Session info

@@ -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.