deleted file mode 100644

@@ -1,97 +0,0 @@

-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)

-

-

deleted file mode 100644

@@ -1,60 +0,0 @@

-

-# Tree annotation with analysis of R packages

-

-## annotating tree with ape bootstraping analysis

-

-```{r results='hide', message=FALSE}

-library(ape)

-data(woodmouse)

-d <- dist.dna(woodmouse)

-tr <- nj(d)

-bp <- boot.phylo(tr, woodmouse, function(xx) nj(dist.dna(xx)))

-```

-

-

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

-library(treeio)

-tree <- as.treedata(tr, boot = bp)

-ggtree(tree) + geom_label(aes(label=bootstrap)) + geom_tiplab()

-```

-

-## annotating tree with phangorn output

-

-```{r results='hide', message=FALSE, fig.width=12, fig.height=10, width=60, warning=FALSE, fig.align="center", eval=FALSE}

-library(phangorn)

-treefile <- system.file("extdata", "pa.nwk", package="treeio")

-tre <- read.tree(treefile)

-tipseqfile <- system.file("extdata", "pa.fas", package="treeio")

-tipseq <- read.phyDat(tipseqfile,format="fasta")

-fit <- pml(tre, tipseq, k=4)

-fit <- optim.pml(fit, optNni=FALSE, optBf=T, optQ=T,

-                 optInv=T, optGamma=T, optEdge=TRUE,

-                 optRooted=FALSE, model = "GTR")

-

-phangorn <- phyPML(fit, type="ml")

-ggtree(phangorn) + geom_text(aes(x=branch, label=AA_subs, vjust=-.5))

-```

-

-![](figures/phangorn_example.png)

-

-

-## phylo4d

-

-`phylo4d` was defined in the `phylobase` package, which can be employed to integrate user's data with phylogenetic tree. `phylo4d` was supported in `ggtree` and the data stored in the object can be used directly to annotate the tree.

-

-```{r fig.width=6, fig.height=5, warning=FALSE, fig.align="center", eval=FALSE}

-dd2 <- dd[, -1]

-rownames(dd2) <- dd[,1]

-require(phylobase)

-tr2 <- phylo4d(tree, dd2)

-ggtree(tr2) + geom_tiplab(aes(color=place)) +

-    geom_tippoint(aes(size=value, shape=place, color=place), alpha=0.25)

-```

-

-

-![](figures/phylobase_example.png)

-

-## jplace file format

-

-`ggtree` provides `write.jplace()` function to store user's own data and associated newick tree to a single `jplace` file, which can be parsed directly in `ggtree` and user's data can be used to annotate the tree directly. For more detail, please refer to the [Tree Data Import](treeImport.html#jplace-file-format) vignette.

-

@@ -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).

-

-