---
 title: "ggtree utilities"

 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:

   prettydoc::html_pretty:

     toc: true

     theme: cayman
     highlight: github

   pdf_document:
     toc: true
 vignette: >

   %\VignetteIndexEntry{06 ggtree utilities}

   %\VignetteEngine{knitr::rmarkdown}
   %\usepackage[utf8]{inputenc}
 ---
 
 ```{r style, echo=FALSE, results="asis", message=FALSE}
 knitr::opts_chunk$set(tidy = FALSE,
 		   message = FALSE)
 ```
 
 
 ```{r echo=FALSE, results="hide", message=FALSE}
 library("ape")
 library("ggplot2")
 library("ggtree")
 ```
 
 # Layers that allows subsetting
 

 `Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s).

 
 In `ggtree`, we provides modified version of layers defined in `ggplot2` to support `subsetting`, including:
 
 + geom_segment2
 + geom_point2
 + geom_text2
 + geom_label2
 
 ```{r fig.width=5, fig.height=5}

 file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio")

 beast <- read.beast(file)
 ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')
 ```
 

 # Multiple graphs on one page
 
 To support viewing multiple plots, ggtree provides `multiplot` function that similar to `gridExtra::grid.arrange` with extra feature of labeling the plots.
 
 

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

 multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))
 ```
 

 <!--

 # subplots in ggplot object
 

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object.

 #``` {r fig.width=8, fig.height=8, warning=F}

 set.seed(2016-01-04)
 tr <- rtree(30)
 tr <- groupClade(tr, node=45)
 p <- ggtree(tr, aes(color=group)) + geom_tippoint()
 p1 <- p + geom_hilight(node=45)
 p2 <- viewClade(p, node=45) + geom_tiplab()
 subview(p2, p1+theme_transparent(), x=2.3, y=28.5)

 #```

 
 This is the backend of the [inset](advanceTreeAnnotation.html) function.
 
 This `subview` function works with any `ggplot` objects and it had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).
 

 #``` {r eval=FALSE}

 library(ggtree)
 dd <- data.frame(x=LETTERS[1:3], y=1:3)
 pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()
 x <- sample(2:9)
 y <- sample(2:9)
 width <- sample(seq(0.05, 0.15, length.out=length(x)))
 height <- width
 p <- ggplot(data=data.frame(x=c(0, 10), y=c(0, 10)), aes(x, y))+geom_blank()
 for (i in seq_along(x)) {
     p <- subview(p, pie, x[i], y[i], width[i], height[i])
     print(p)
 }

 #```

 ![](figures/subview_animation.gif)

 -->