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update ggtree vignette

guangchuang yu authored on 21/12/2017 07:45:38
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rename from vignettes/ggtreeUtilities.Rmd
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rename to inst/ggtreeUtilities.Rmd
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@@ -38,7 +38,10 @@ Biocpkg <- function (pkg) {
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 ```
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-> 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.
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+> You can't even begin to understand biology, you can't understand life, unless
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+> you understand what it's all there for, how it arose - and that means
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+> evolution.
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+>
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 > --- Richard Dawkins
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@@ -114,7 +117,12 @@ visualize or annotate phylogenetic tree in `r Biocpkg('ggtree')` [@yu_ggtree:_20
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 # Tree Visualization and Annotation
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-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.
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+Tree Visualization in `r Biocpkg('ggtree')` is easy, with one line of command
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+`ggtree(tree_object)`. It supports several layouts, including *rectangular*,
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+*slanted*, *circular* and *fan* for *phylogram* and *cladogram*, *equal_angle*
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+and *daylight* for *unrooted* layout, time-scaled and two dimentional
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+phylogenies. [Tree Visualization](treeVisualization.html) vignette describes
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+these feature in details.
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 We implement several functions to manipulate a phylogenetic tree.
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@@ -125,27 +133,73 @@ We implement several functions to manipulate a phylogenetic tree.
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 + selected clade can be rotated by 180 degree using `rotate` function
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 + position of two selected clades (should share a same parent) can be exchanged by `flip` function
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+
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 Details and examples can be found in [Tree Manipulation](treeManipulation.html) vignette.
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-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.
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+Most of the phylogenetic trees are scaled by evolutionary distance
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+(substitution/site), in `r Biocpkg('ggtree')` a phylogenetic tree can be
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+re-scaled by any numerical variable inferred by evolutionary analysis (e.g.
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+species divergence time, *d~N~/d~S~*, _etc_). Numerical and category variable can be
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+used to color a phylogenetic tree.
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+
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+The `r Biocpkg('ggtree')` package provides several layers to annotate a
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+phylogenetic tree. These layers are building blocks that can be freely combined
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+together to create complex tree visualization.
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+
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+```{r geoms, echo=FALSE, message=FALSE}
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+geoms <- matrix(c(
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+  "geom_balance", "highlights the two direct descendant clades of an internal node",
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+  "geom_cladelabel", "annotate a clade with bar and text label",
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+  "geom_cladelabel2", "annotate a clade with bar and text label for unrooted layout",
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+  "geom_hilight", "highlight a clade with rectangle",
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+  "geom_hilight_encircle", "highlight a clade with xspline for unrooted layout",
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+  "geom_label2", "modified version of geom_label, with subsetting supported",
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+  "geom_nodelab", "layer for node labels, which can be text or image",
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+  "geom_nodepoint", "annotate internal nodes with symbolic points",
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+  "geom_point2", "modified version of geom_point, with subsetting supported",
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+  "geom_range", "bar layer to present uncertainty of evolutionary inference",
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+  "geom_rootpoint", "annotate root node with symbolic point",
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+  "geom_segment2", "modified version of geom_segment, with subsetting supported",
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+  "geom_strip", "annotate associated taxa with bar and (optional) text label",
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+  "geom_taxalink", "associate two related taxa by linking them with a curve",
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+  "geom_text2", "modified version of geom_text, with subsetting supported",
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+  "geom_tiplab", "layer of tip labels, which can be text or image",
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+  "geom_tiplab2", "layer of tip labels for circular layout",
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+  "geom_tippoint", "annotate external nodes with symbolic points",
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+  "geom_tree", "tree structure layer, with multiple layout supported",
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+  "geom_treescale", "tree branch scale legend"
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+), ncol=2, byrow=TRUE)
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+geoms <- as.data.frame(geoms)
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+colnames(geoms) <- c("Layer", "Description")
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+knitr::kable(geoms, caption = "Geom layers defined in ggtree.", booktabs = T)
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+```
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+
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+`r Biocpkg('ggtree')` supports creating phylomoji using Emoji fonts, please
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+refer to `r CRANpkg("emojifont")` package vignette for details. The vignette can
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+be opened via the following command:
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+
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+```r
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+vignette("phylomoji", package="emojifont")
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+```
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-The `ggtree` package provides several layers to annotate a phylogenetic tree, including:
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-+ `geom_cladelabel` for labelling selected clades
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-+ `geom_hilight` for highlighting selected clades
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-+ `geom_range` to indicate uncertainty of branch lengths
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-+ `geom_strip` for adding strip/bar to label associated taxa (with optional label)
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-+ `geom_taxalink` for connecting related taxa
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-+ `geom_tiplab` for adding tip labels
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-+ `geom_treescale` for adding a legend of tree scale
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+`r Biocpkg('ggtree')` integrates [phylopic](http://phylopic.org/) database and silhouette images of organisms can
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+be downloaded and used to annotate phylogenetic directly. `r Biocpkg('ggtree')` also supports
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+using local or remote images to annotate a phylogenetic tree. For details,
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+please refer to the `r CRANpkg('ggimage')` package vignette, which can be opened
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+via the following command:
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-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`.
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+```r
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+vignette("ggtree", package="ggimage")
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+```
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-`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.
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-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.
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+Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype
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+table), multiple sequence alignment and subplots are also supported in `ggtree`.
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+Examples of annotating phylogenetic trees can be found in
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+the [Tree Annotation](treeAnnotation.html) vignette.
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 # Vignette Entry
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@@ -154,14 +208,13 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype
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 + [Tree Visualization](treeVisualization.html)
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 + [Tree Manipulation](treeManipulation.html)
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 + [Tree Annotation](treeAnnotation.html)
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-+ [Advance Tree Annotation](advanceTreeAnnotation.html)
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 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)
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-+ [Annotating phylogenetic tree with images using ggtree and ggimage](https://cran.r-project.org/web/packages/ggimage/vignettes/ggtree.html)
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++ [Annotating phylogenetic tree with images](https://cran.r-project.org/web/packages/ggimage/vignettes/ggtree.html)
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 More documents can be found in <https://guangchuangyu.github.io/ggtree>.
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-## Feedback ##
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+# Feedback #
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  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).
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  - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree).