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

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.5.0

+Version: 1.5.1

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -44,6 +44,7 @@ export(geom_point2)

 export(geom_range)

 export(geom_rootpoint)

 export(geom_segment2)

+export(geom_strip)

 export(geom_taxalink)

 export(geom_text2)

 export(geom_tiplab)

@@ -1,3 +1,19 @@

+CHANGES IN VERSION 1.5.1

+------------------------

+ o update vignettes <2016-05-10, Tue>

+   + add geom_range example in treeImport

+   + add geom_strip and geom_taxalink example in treeAnnotation

+   + add ggtreeUtilities vignette

+ o gheatmap now works with data.frame of only one column <2016-05-09, Mon>

+   + contributed by Justin Silverman <jsilve24@gmail.com>

+   + https://github.com/GuangchuangYu/ggtree/pull/57

+ o geom_strip for associated taxa <2016-05-09, Mon>

+   + https://github.com/GuangchuangYu/ggtree/issues/52

+ 

+CHANGES IN VERSION 1.4.0

+------------------------

+ o BioC 3.3 released <2016-05-05, Thu>

+ 

 CHANGES IN VERSION 1.3.16

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

  o geom_treescale() supports family argument <2016-04-27, Wed>

new file mode 100644

@@ -0,0 +1,177 @@

+##' annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label

+##'

+##' 

+##' @title geom_strip

+##' @param taxa1 taxa1

+##' @param taxa2 taxa2

+##' @param label optional label

+##' @param offset offset of bar and text from the clade

+##' @param offset.text offset of text from bar

+##' @param align logical

+##' @param barsize size of bar

+##' @param barextend extend bar vertically

+##' @param fontsize size of text

+##' @param angle angle of text

+##' @param geom one of 'text' or 'label'

+##' @param hjust hjust

+##' @param fill fill label background, only work with geom='label'

+##' @param family sans by default, can be any supported font

+##' @param ... additional parameter

+##' @return ggplot layers

+##' @export

+##' @author Guangchuang Yu

+geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

+                       align=TRUE, barsize=0.5, barextend=0, fontsize=3.88,

+                       angle=0, geom="text", hjust=0, fill=NA, family="sans", ...) {

+    mapping <- NULL

+    data <- NULL

+    position <- "identity"

+    show.legend <- NA

+    na.rm <- TRUE

+    inherit.aes <- FALSE

+

+    layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, offset=offset, align=align,

+                               size=barsize, barextend=barextend,

+                               mapping=mapping, data=data, 

+                               position=position, show.legend = show.legend,

+                               inherit.aes = inherit.aes, na.rm=na.rm, ...)

+

+    if (is.na(label) || is.null(label)) {

+        return(layer_bar)

+    }

+    

+    if (geom == "text") {

+        ## no fill parameter

+        layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

+                                    align=align, size=fontsize, angle=angle, family=family,

+                                    mapping=mapping, data=data, geom=geom, hjust=hjust,

+                                    position=position, show.legend = show.legend,

+                                    inherit.aes = inherit.aes, na.rm=na.rm, ...)

+        

+    } else {

+        layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

+                                    align=align, size=fontsize, angle=angle, fill=fill,family=family,

+                                    mapping=mapping, data=data, geom=geom, hjust=hjust,

+                                    position=position, show.legend = show.legend,

+                                    inherit.aes = inherit.aes, na.rm=na.rm, ...)

+    }

+    

+    list(

+        layer_bar,

+        layer_text

+    )

+}

+

+

+stat_stripText <- function(mapping=NULL, data=NULL,

+                           geom="text", position="identity",

+                           taxa1, taxa2, label, offset, align, ...,

+                           show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

+    default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent,label=~label)

+    if (is.null(mapping)) {

+        mapping <- default_aes

+    } else {

+        mapping <- modifyList(mapping, default_aes)

+    }

+    

+    layer(stat=StatStripText,

+          data=data,

+          mapping=mapping,

+          geom=geom,

+          position=position,

+          show.legend = show.legend,

+          inherit.aes = inherit.aes,

+          params=list(taxa1=taxa1,

+                      taxa2=taxa2,

+                      label=label,

+                      offset=offset,

+                      align=align,

+                      na.rm=na.rm,

+                      ...)

+          )

+    

+}

+

+stat_stripBar <- function(mapping=NULL, data=NULL,

+                          geom="segment", position="identity",

+                          taxa1, taxa2, offset, align, barextend, ...,

+                          show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

+    default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, label=~label)

+    if (is.null(mapping)) {

+        mapping <- default_aes

+    } else {

+        mapping <- modifyList(mapping, default_aes)

+    }

+    

+    layer(stat=StatStripBar,

+          data=data,

+          mapping=mapping,

+          geom=geom,

+          position=position,

+          show.legend = show.legend,

+          inherit.aes = inherit.aes,

+          params=list(taxa1=taxa1,

+                      taxa2=taxa2,

+                      offset=offset,

+                      align=align,

+                      barextend=barextend,

+                      na.rm=na.rm,

+                      ...)

+          )

+

+}

+

+StatStripText <- ggproto("StatStripText", Stat,

+                         compute_group = function(self, data, scales, params, taxa1, taxa2,

+                                                  label, offset, align) {

+                             df <- get_striplabel_position(data, taxa1, taxa2, offset, align, adjustRatio = 1.03)

+                             df$y <- mean(c(df$y, df$yend))

+                             df$label <- label

+                             return(df)

+                         },

+                         required_aes = c("x", "y", "label")

+                         )

+

+                         

+                          

+StatStripBar <- ggproto("StatStripBar", Stat,

+                        compute_group = function(self, data, scales, params,

+                                                 taxa1, taxa2, offset, align, barextend) {

+                            get_striplabel_position(data, taxa1, taxa2, offset, align, barextend, adjustRatio=1.02)

+                        },

+                        required_aes = c("x", "y", "xend", "yend")

+                        )

+

+

+get_striplabel_position <- function(data, taxa1, taxa2, offset, align, barextend, adjustRatio) {

+    df <- get_striplabel_position_(data, taxa1, taxa2, barextend)

+    if (align) {

+        mx <- max(data$x, na.rm=TRUE)

+    } else {

+        mx <- df$x

+    }

+    mx <- mx * adjustRatio + offset

+    data.frame(x=mx, xend=mx, y=df$y, yend=df$yend)

+}

+

+

+get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {

+    node1 <- taxa2node(data, taxa1)

+    node2 <- taxa2node(data, taxa2)

+

+    xx <- with(data, c(x[node == node1], x[node == node2]))

+    yy <- with(data, c(y[node == node1], y[node == node2]))

+

+    data.frame(x=max(xx), y=min(yy)-barextend, yend=max(yy)+barextend)

+}

+

+## used in geom_strip, geom_taxalink

+taxa2node <- function(data, taxa) {

+    idx <- with(data, which(taxa == label | taxa == node))

+

+    if (length(idx) == 0) {

+        stop("input taxa is not valid...")

+    }

+    

+    return(data$node[idx])

+}

@@ -37,10 +37,8 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {

 StatTaxalink <- ggproto("StatTaxalink", Stat,

                         compute_group = function(self, data, scales, params, taxa1, taxa2) {

-                            node <- data$node

-                            label <- data$label

-                            node1 <- which(taxa1 == label | taxa1 == node)

-                            node2 <- which(taxa2 == label | taxa2 == node)

+                            node1 <- taxa2node(data, taxa1)

+                            node2 <- taxa2node(data, taxa2)

                             x <- data$x

                             y <- data$y

@@ -26,27 +26,28 @@

 ##' @author Guangchuang Yu

 gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color="white",

                      colnames=TRUE, colnames_position="bottom", colnames_level=NULL, font.size=4) {

-

+    

     colnames_position %<>% match.arg(c("bottom", "top"))

     variable <- value <- lab <- y <- NULL

     ## if (is.null(width)) {

     ##     width <- (p$data$x %>% range %>% diff)/30

     ## }

-

+    

     ## convert width to width of each cell

     width <- width * (p$data$x %>% range %>% diff) / ncol(data)

     isTip <- x <- y <- variable <- value <- from <- to <- NULL

- 

+    

     df <- p$data

     df <- df[df$isTip,]

     start <- max(df$x) + offset

-

-    dd <- data[df$label[order(df$y)],]

-    dd$y <- sort(df$y)

-

+    

+    dd <- data

     dd$lab <- rownames(dd)

+    dd <- dd[df$label[order(df$y)],]

+    dd$y <- sort(df$y)

+    

     ## dd <- melt(dd, id=c("lab", "y"))

     dd <- gather(dd, variable, value, -c(lab, y))

@@ -61,13 +62,14 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     V2 <- start + as.numeric(dd$variable) * width

     mapping <- data.frame(from=dd$variable, to=V2)

     mapping <- unique(mapping)

-

+    

     dd$x <- V2

-

+    dd$width <- width

+    

     if (is.null(color)) {

-        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), inherit.aes=FALSE)

+        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value, width=width), inherit.aes=FALSE)

     } else {

-        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), color=color, inherit.aes=FALSE)

+        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value, width=width), color=color, inherit.aes=FALSE)

     }

     if (is(dd$value,"numeric")) {

         p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")

@@ -83,7 +85,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

         }

         p2 <- p2 + geom_text(data=mapping, aes(x=to, label=from), y=y, size=font.size, inherit.aes = FALSE)

     }

-

+    

     p2 <- p2 + theme(legend.position="right", legend.title=element_blank())

     p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

new file mode 100644

@@ -0,0 +1,52 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/geom_strip.R

+\name{geom_strip}

+\alias{geom_strip}

+\title{geom_strip}

+\usage{

+geom_strip(taxa1, taxa2, label = NA, offset = 0, offset.text = 0,

+  align = TRUE, barsize = 0.5, barextend = 0, fontsize = 3.88,

+  angle = 0, geom = "text", hjust = 0, fill = NA, family = "sans",

+  ...)

+}

+\arguments{

+\item{taxa1}{taxa1}

+

+\item{taxa2}{taxa2}

+

+\item{label}{optional label}

+

+\item{offset}{offset of bar and text from the clade}

+

+\item{offset.text}{offset of text from bar}

+

+\item{align}{logical}

+

+\item{barsize}{size of bar}

+

+\item{barextend}{extend bar vertically}

+

+\item{fontsize}{size of text}

+

+\item{angle}{angle of text}

+

+\item{geom}{one of 'text' or 'label'}

+

+\item{hjust}{hjust}

+

+\item{fill}{fill label background, only work with geom='label'}

+

+\item{family}{sans by default, can be any supported font}

+

+\item{...}{additional parameter}

+}

+\value{

+ggplot layers

+}

+\description{

+annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label

+}

+\author{

+Guangchuang Yu

+}

+

@@ -84,19 +84,7 @@ msaplot(ggtree(beast_tree), fasta, window=c(150, 200)) + coord_polar(theta='y')

 # 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).

-

-```{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)

-```

-

-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.

+`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.

 ## Annotate with bar charts

@@ -84,7 +84,16 @@ Details and examples can be found in [Tree Manipulation](treeManipulation.html)

 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.

-The `ggtree` package provides several layers to annotate a phylogenetic tree, including `geom_tiplab` for adding tip labels, `geom_treescale` for adding a legend of tree scale, `geom_hilight` for highlighting selected clades and `geom_cladelabel` for labelling selected clades. 

+The `ggtree` package provides several layers to annotate a phylogenetic tree, including:

+

++ `geom_cladelabel` for labelling selected clades

++ `geom_hilight` for highlighting selected clades 

++ `geom_range` to indicate uncertainty of branch lengths

++ `geom_strip` for adding strip/bar to label associated taxa (with optional label)

++ `geom_taxalink` for connecting related taxa

++ `geom_tiplab` for adding tip labels

++ `geom_treescale` for adding a legend of tree scale

+

 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`.

@@ -100,8 +109,10 @@ Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

 + [Advance Tree Annotation](advanceTreeAnnotation.html)

++ [ggtree utilities](ggtreeUtilities.html)

+

-More documents can be found in <http://guangchuangyu.github.io/tags/ggtree>.

+More documents can be found in <http://guangchuangyu.github.io/ggtree>.

 # Bugs/Feature requests

new file mode 100644

@@ -0,0 +1,85 @@

+---

+title: "ggtree utilities"

+author: "\\

+

+	Guangchuang Yu (<guangchuangyu@gmail.com>) and Tommy Tsan-Yuk Lam (<ttylam@hku.hk>)\\

+

+        School of Public Health, The University of Hong Kong"

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

+bibliography: ggtree.bib

+csl: nature.csl

+output: 

+  html_document:

+    toc: true

+  pdf_document:

+    toc: true

+vignette: >

+  %\VignetteIndexEntry{00 ggtree introduction}

+  %\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="ggtree")

+beast <- read.beast(file)

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

+```

+

+# 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 fig.show='animate', interval=.1}

+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)

+}

+```

+

+

@@ -99,7 +99,7 @@ ggtree(beast_tree, aes(color=rate)) +

 User can use any feature (if available), including clade posterior and *dN/dS* _etc._, to scale the color of the tree.

-## Annotate clades

+# Annotate clades

 `ggtree` implements _`geom_cladelabel`_ layer to annotate a selected clade with a bar indicating the clade with a corresponding label.

@@ -169,6 +169,23 @@ ggtree(tree, layout="circular") + geom_hilight(node=21, fill="steelblue", alpha=

 Another way to highlight selected clades is setting the clades with different colors and/or line types as demonstrated in [Tree Manipulation](treeManipulation.html#groupclade) vignette.

+# labelling associated taxa (Monophyletic, Polyphyletic or Paraphyletic)

+

+`geom_cladelabel` is designed to labelling Monophyletic (Clade) while there are related taxa that are not form a clade. `ggtree` provides `geom_strip` to add a strip/bar to indicate the association with optional label (see [the issue](https://github.com/GuangchuangYu/ggtree/issues/52)).

+

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

+ggtree(tree) + geom_tiplab() + geom_strip('E', 'G', barsize=2, color='red') + geom_strip('F', 'L', barsize=2, color='blue')

+```

+

+# taxa connection

+

+Some evolutionary events (e.g. reassortment, horizontal gene transfer) can be modeled by a simple tree. `ggtree` provides `geom_taxalink` layer that allows drawing straight or curved lines between any of two nodes in the tree, allow it to represent evolutionary events by connecting taxa.

+

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

+ggtree(tree) + geom_tiplab() + geom_taxalink('A', 'E') + geom_taxalink('F', 'K', color='red', arrow=grid::arrow(length = grid::unit(0.02, "npc")))

+```

+

+

 # Tree annotation with analysis of R packages

 ## annotating tree with ape bootstraping analysis

@@ -136,6 +136,18 @@ Users can use `ggtree(beast)` to visualize the tree and add layer to annotate it

 ggtree(beast, ndigits=2, branch.length = 'none') + geom_text(aes(x=branch, label=length_0.95_HPD), vjust=-.5, color='firebrick')

 ```

+`ggtree` provides `geom_range` layer to display uncertainty of branch length.

+

+```{r warning=FALSE, fig.width=10, fig.height=10}

+ggtree(beast) + geom_range(range='height_0.95_HPD', color='red', alpha=.6, size=2)

+```

+

+In `FigTree`, only `heigh_0.95_HPD` is meaningful since the branch is scaled by `height`. In `ggtree` we can display HPD of `rate`, `height` or other variable if available since `ggtree` can rescale a tree using `rescale_tree` function or by specifing `branch.length` in `ggtree` function.

+

+```{r warning=FALSE, fig.width=10, fig.height=10}

+ggtree(beast, branch.length = 'rate') + geom_range(range='rate_0.95_HPD', color='red', alpha=.6, size=2)

+```

+

 With `ggtree`, evolutionary evidences inferred by commonly used software packages (`BEAST` in this example) can be easily transformed to a tidy `data.frame` by `fortify` method.

 ```{r}

@@ -217,6 +217,12 @@ For _`circular`_ and _`unrooted`_ layout, `ggtree` supports rotating node labels

 ggtree(tree, layout="circular") + geom_tiplab(aes(angle=angle), color='blue')

 ```

+To make it more readable for human eye, `ggtree` provides a `geom_tiplab2` for `circular` layout (see post [1](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/o35PV3iHO-0) and [2](https://groups.google.com/forum/#!topic/bioc-ggtree/p42R5l8J-14)).

+

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

+ggtree(tree, layout="circular") + geom_tiplab2(color='blue')

+```

+

 By default, the positions are based on the node positions, we can change them to based on the middle of the branch/edge.

 ```{r fig.width=4, fig.height=3, warning=FALSE, fig.align="center"}