similarity index 100%

rename from vignettes/ggtreeUtilities.Rmd

rename to inst/ggtreeUtilities.Rmd

@@ -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).