@@ -33,6 +33,7 @@ Suggests:

     EBImage,

     emojifont,

     knitr,

+    prettydoc,

     rmarkdown,

     scales,

     testthat

@@ -2,6 +2,7 @@

 S3method(as.binary,phylo)

 S3method(as.data.frame,phylo)

+S3method(as.data.frame,treedata)

 S3method(fortify,apeBootstrap)

 S3method(fortify,beast)

 S3method(fortify,codeml)

@@ -20,6 +21,7 @@ S3method(fortify,phylo4d)

 S3method(fortify,phyloseq)

 S3method(fortify,r8s)

 S3method(fortify,raxml)

+S3method(fortify,treedata)

 S3method(identify,gg)

 S3method(print,beastList)

 export("%+>%")

@@ -1,3 +1,90 @@

+##' @importFrom ggplot2 fortify

+##' @method fortify treedata

+##' @export

+fortify.treedata <- function(model, data, layout="rectangular", branch.length ="branch.length",

+                             ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {

+    model <- set_branch_length(model, branch.length)

+    x <- reorder.phylo(get.tree(model), "postorder")

+    if (is.null(x$edge.length) || branch.length == "none") {

+        xpos <- getXcoord_no_length(x)

+    } else {

+        xpos <- getXcoord(x)

+    }

+    ypos <- getYcoord(x)

+    N <- Nnode(x, internal.only=FALSE)

+    xypos <- data.frame(node=1:N, x=xpos, y=ypos)

+

+    df <- as.data.frame(model, branch.length="branch.length") # already set by set_branch_length

+    idx <- is.na(df$parent)

+    df$parent[idx] <- df$node[idx]

+    rownames(df) <- df$node

+

+    res <- merge(df, xypos, by='node', all.y=TRUE)

+

+    ## add branch mid position

+    res <- calculate_branch_mid(res)

+

+    ## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle

+    res <- calculate_angle(res)

+    res

+}

+

+##' @method as.data.frame treedata

+##' @export

+## @importFrom treeio Nnode

+## @importFrom treeio Ntip

+as.data.frame.treedata <- function(x, row.names, optional, branch.length = "branch.length", ...) {

+    tree <- set_branch_length(x, branch.length)

+

+    ## res <- as.data.frame(tree@phylo)

+    res <- as.data.frame_(tree@phylo)

+    tree_anno <- get_tree_data(x)

+    if (nrow(tree_anno) > 0) {

+        res <- merge(res, tree_anno, by="node", all.x=TRUE)

+    }

+    return(res)

+}

+

+##@method as.data.frame phylo

+##@export

+as.data.frame_ <- function(x, row.names, optional, branch.length = "branch.length", ...) {

+    phylo <- x

+    ntip <- Ntip(phylo)

+    N <- Nnode(phylo, internal.only=FALSE)

+

+    tip.label <- phylo[["tip.label"]]

+    res <- as.data.frame(phylo[["edge"]])

+    colnames(res) <- c("parent", "node")

+    if (!is.null(phylo$edge.length))

+        res$branch.length <- phylo$edge.length

+

+    label <- rep(NA, N)

+    label[1:ntip] <- tip.label

+    if ( !is.null(phylo$node.label) ) {

+        label[(ntip+1):N] <- phylo$node.label

+    }

+    label.df <- data.frame(node=1:N, label=label)

+    res <- merge(res, label.df, by='node', all.y=TRUE)

+    isTip <- rep(FALSE, N)

+    isTip[1:ntip] <- TRUE

+    res$isTip <- isTip

+

+    return(res)

+}

+

+get_tree_data <- function(tree_object) {

+    tree_anno <- tree_object@data

+    if (has.extraInfo(tree_object)) {

+        if (nrow(tree_anno) > 0) {

+            tree_anno <- merge(tree_anno, tree_object@extraInfo, by="node")

+        } else {

+            return(tree_object@extraInfo)

+        }

+    }

+    return(tree_anno)

+}

+

+

 ##' convert tip or node label(s) to internal node number

 ##'

 ##'

@@ -8,9 +8,11 @@ author: "\\

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

 bibliography: ggtree.bib

 csl: nature.csl

-output: 

-  html_document:

+output:

+  prettydoc::html_pretty:

     toc: true

+    theme: cayman

+    highlight: github

   pdf_document:

     toc: true

 vignette: >

@@ -44,38 +46,43 @@ The `gheatmap` function is designed to visualize phylogenetic tree with heatmap

 In the following example, we visualized a tree of H3 influenza viruses with their associated genotype.

-```{r fig.width=20, fig.height=16, fig.align="center"}

+```{r fig.width=8, fig.height=6, fig.align="center", warning=FALSE, message=FALSE}

 beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree")

 beast_tree <- read.beast(beast_file)

 genotype_file <- system.file("examples/Genotype.txt", package="ggtree")

 genotype <- read.table(genotype_file, sep="\t", stringsAsFactor=F)

-p <- ggtree(beast_tree, mrsd="2013-01-01") + geom_treescale(x=2008, y=1)

-p <- p + geom_tiplab(size=3)

-gheatmap(p, genotype, offset = 2, width=0.5)

+colnames(genotype) <- sub("\\.$", "", colnames(genotype))

+p <- ggtree(beast_tree, mrsd="2013-01-01") + geom_treescale(x=2008, y=1, offset=2)

+p <- p + geom_tiplab(size=2)

+gheatmap(p, genotype, offset = 5, width=0.5, font.size=3, colnames_angle=-45, hjust=0) +

+    scale_fill_manual(breaks=c("HuH3N2", "pdm", "trig"), values=c("steelblue", "firebrick", "darkgreen"))

 ```

 The _width_ parameter is to control the width of the heatmap. It supports another parameter _offset_ for controlling the distance between the tree and the heatmap, for instance to allocate space for tip labels.

-For time-scaled tree, as in this example, it's more often to use x axis by using `theme_tree2`. But with this solution, the heatmap is just another layer and will change the `x` axis. To overcome this issue, we implemented `scale_x_ggtree` to set the x axis more reasonable. 

+For time-scaled tree, as in this example, it's more often to use x axis by using `theme_tree2`. But with this solution, the heatmap is just another layer and will change the `x` axis. To overcome this issue, we implemented `scale_x_ggtree` to set the x axis more reasonable.

 <!-- User can also use `gplot` and tweak the positions of two plot to align properly. -->

-```{r fig.width=20, fig.height=16, fig.align="center", warning=FALSE}

-p <- ggtree(beast_tree, mrsd="2013-01-01") + geom_tiplab(size=3, align=TRUE) + theme_tree2()

+

+

+```{r fig.width=8, fig.height=6, fig.align="center", warning=FALSE}

+p <- ggtree(beast_tree, mrsd="2013-01-01") + geom_tiplab(size=2, align=TRUE, linesize=.5) + theme_tree2()

 pp <- (p + scale_y_continuous(expand=c(0, 0.3))) %>%

-    gheatmap(genotype, offset=4, width=0.5, colnames=FALSE) %>%

+    gheatmap(genotype, offset=8, width=0.6, colnames=FALSE) %>%

         scale_x_ggtree()

 pp + theme(legend.position="right")

 ```

+

 # Visualize tree with multiple sequence alignment

 With `msaplot` function, user can visualize multiple sequence alignment with phylogenetic tree, as demonstrated below:

 ```{r fig.width=8, fig.height=12, fig.align='center'}

 fasta <- system.file("examples/FluA_H3_AA.fas", package="ggtree")

-msaplot(ggtree(beast_tree), fasta) 

+msaplot(ggtree(beast_tree), fasta)

 ```

 A specific slice of the alignment can also be displayed by specific _window_ parameter.