@@ -10,6 +10,7 @@ S3method(fortify,hyphy)

 S3method(fortify,jplace)

 S3method(fortify,multiPhylo)

 S3method(fortify,nhx)

+S3method(fortify,obkData)

 S3method(fortify,paml_rst)

 S3method(fortify,phangorn)

 S3method(fortify,phylo)

@@ -98,6 +99,7 @@ export(theme_inset)

 export(theme_transparent)

 export(theme_tree)

 export(theme_tree2)

+export(viewClade)

 export(write.jplace)

 exportClasses(apeBootstrap)

 exportClasses(beast)

@@ -1,5 +1,7 @@

 CHANGES IN VERSION 1.3.8

 ------------------------

+ o add viewClade function <2016-01-12, Tue>

+ o support obkData object defined by OutbreakTools <2016-01-12, Tue>

  o update vignettes <2016-01-07, Thu>

  o 05 advance tree annotation vignette <2016-01-04, Mon>

  o export theme_inset <2016-01-04, Mon>

@@ -611,7 +611,7 @@ fortify.multiPhylo <-  function(model, data, layout="rectangular",

     df$.id <- factor(df$.id, levels=names(df.list))

     nNode <- sapply(df.list, nrow)

-    nNode2 <- cumsum(nNode) - nNode[1]

+    nNode2 <- cumsum(c(0, nNode[-length(nNode)])) 

     df$parent <- df$parent + rep(nNode2, times=nNode)

     return(df)

 }

@@ -626,3 +626,38 @@ fortify.r8s <- function(model, data, layout="rectangular",

     phylo <- trees[[branch.length]]

     fortify(phylo, layout=layout, ladderize = ladderize, right=right, mrsd=mrsd, ...)

 }

+

+##' @method fortify obkData

+##' @export

+fortify.obkData <- function(model, data, layout="rectangular",

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

+

+    df <- fortify(model@trees[[1]], layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

+

+    meta.df <- model@dna@meta

+    meta.df <- data.frame(taxa=rownames(meta.df), meta.df)

+    loc <- model@individuals

+    loc <- data.frame(individualID=rownames(loc), loc)

+    meta_loc <- merge(meta.df, loc, by="individualID")

+    meta_loc <- meta_loc[,-1]

+

+    df <- merge(df, meta_loc, by.x="label", by.y="taxa", all.x=TRUE)

+    df <- df[order(df$node, decreasing = FALSE),]

+    return(df)

+}

+                            

+                         

+## fortify.cophylo <- function(model, data, layout="rectangular",

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

+##     trees <- model$trees

+##     df.list <- lapply(trees, function(x) fortify(x, layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...))

+##     df1 <- df.list[[1]]

+##     df2 <- df.list[[2]]

+

+##     df2$x <- max(df2$x) + df2$x * -1 + max(df1$x) * 1.1

+##     df2$parent <- df2$parent+nrow(df1)

+##     df <- rbind(df1, df2)

+

+##     ggplot(df) + geom_tree()

+

+## }

new file mode 100644

@@ -0,0 +1,13 @@

+##' view a clade of tree

+##'

+##' 

+##' @title viewClade

+##' @param tree_view full tree view 

+##' @param node internal node number

+##' @return clade plot

+##' @export

+##' @author Guangchuang Yu

+viewClade <- function(tree_view, node) {

+    cpos <- get_clade_position(tree_view, node=node)

+    with(cpos, p+xlim(xmin, xmax*1.01)+ylim(ymin, ymax))

+}

new file mode 100644

@@ -0,0 +1,23 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/viewClade.R

+\name{viewClade}

+\alias{viewClade}

+\title{viewClade}

+\usage{

+viewClade(tree_view, node)

+}

+\arguments{

+\item{tree_view}{full tree view}

+

+\item{node}{internal node number}

+}

+\value{

+clade plot

+}

+\description{

+view a clade of tree

+}

+\author{

+Guangchuang Yu

+}

+

@@ -83,7 +83,7 @@ A specific slice of the alignment can also be displayed by specific _window_ par

 msaplot(ggtree(beast_tree), fasta, window=c(150, 200)) 

 ```

-# Annotate a phylogenetic with insets

+# Annotate a phylogenetic tree with insets

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object. It had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).

@@ -92,10 +92,9 @@ set.seed(2016-01-04)

 tr <- rtree(30)

 tr <- groupClade(tr, node=45)

 p <- ggtree(tr, aes(color=group)) + geom_tippoint()

-cpos <- get_clade_position(p, node=45)

 p1 <- p + geom_hilight(node=45)

-p2 <- with(cpos, p+xlim(xmin, xmax*1.01)+ylim(ymin, ymax))

-with(cpos, subview(p2+geom_tiplab(), p1+theme_transparent(), x=xmin+(xmax-xmin)*.15, y=ymin+(ymax-ymin)*.85))

+p2 <- viewClade(p, node=45) + geom_tiplab()

+subview(p2, p1+theme_transparent(), x=2.3, y=28.5)

 ```

 To make it more easy to use subview function for annotating taxa with subplots, *ggtree* provides a function, `inset`, for adding subplots to a phylogenetic tree. The input is a tree graphic object and a named list of ggplot graphic objects (can be any kind of charts), these objects should named by node numbers. To facilitate adding bar and pie charts (e.g. summarized stats of results from ancestral reconstruction) to phylogenetic tree, *ggtree* provides `nodepie` and `nodebar` functions to create a list of pie or bar charts.

@@ -38,7 +38,7 @@ The `ggtree` package should not be viewed solely as a standalone software. While

 # Supported File Formats

 Most of the tree viewer software (including `R` packages) focus on `Newick` and `Nexus` file format, while there are file formats from different evolution analysis software that contain supporting evidences within the file that are ready for annotating a phylogenetic tree.

-The `ggtree` package define several parser functions and `S4` classes to store statistical evidences inferred by commonly used software packages. It supports several file format, including:

+The `ggtree` package define several parser functions and `S4` classes to store statistical evidences inferred by commonly used software packages. It supports several file formats, including:

 + Newick (via `ape`)

 + Nexus (via `ape`)