@@ -3,3 +3,4 @@ TODO.md

 appveyor.yml

 .gitignore

 .svnignore

+Makefile

@@ -11,7 +11,6 @@ Depends:

     ggplot2 (>= 2.0.0)

 Imports:

     ape,

-    Biostrings,

     grDevices,

     grid,

     jsonlite,

@@ -21,19 +20,17 @@ Imports:

     tidyr,

     utils

 Suggests:

+    Biostrings,

     colorspace,

     EBImage,

     knitr,

-    phylobase,

-    phytools,

-    phangorn,

     rmarkdown,

     scales,

     testthat

 VignetteBuilder: knitr

 ByteCompile: true

 License: Artistic-2.0

-URL: http://guangchuangyu.github.io/ggtree

+URL: https://guangchuangyu.github.io/ggtree

 BugReports: https://github.com/GuangchuangYu/ggtree/issues

 Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Alignment, Annotation, Clustering, DataImport,

@@ -147,11 +147,6 @@ exportMethods(plot)

 exportMethods(reroot)

 exportMethods(scale_color)

 exportMethods(show)

-importFrom(Biostrings,BStringSet)

-importFrom(Biostrings,DNAStringSet)

-importFrom(Biostrings,GENETIC_CODE)

-importFrom(Biostrings,readBStringSet)

-importFrom(Biostrings,toString)

 importFrom(ape,Nnode)

 importFrom(ape,Ntip)

 importFrom(ape,drop.tip)

@@ -232,9 +227,14 @@ importFrom(magrittr,"%<>%")

 importFrom(magrittr,"%>%")

 importFrom(magrittr,add)

 importFrom(magrittr,equals)

+importFrom(methods,"slot<-")

+importFrom(methods,.hasSlot)

+importFrom(methods,is)

+importFrom(methods,missingArg)

+importFrom(methods,new)

 importFrom(methods,show)

+importFrom(methods,slot)

 importFrom(stats4,plot)

 importFrom(tidyr,gather)

 importFrom(utils,download.file)

 importFrom(utils,modifyList)

-importMethodsFrom(Biostrings,width)

@@ -1,5 +1,11 @@

 CHANGES IN VERSION 1.5.6

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

+ o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>

+   + still needed for building vignette and for processing FASTA file

+ o remove dependency of EBImage for building & installing ggtree <2016-07-21, Thu>

+   + the package is still needed if user want to annotate tree with image file

+ o `%<+%` now works with tbl_df <2016-07-21, Thu>

+   + https://github.com/GuangchuangYu/ggtree/issues/66

  o identify method for ggtree <2016-06-28, Tue>

    + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree

  o geom_balance contributed by Justin Silverman <2016-06-22, Wed>

@@ -309,6 +309,7 @@ setClass("phangorn",

          )

+

 ##' Class "phylip"

 ##' This class stores phylip tree(s)

 ##'

@@ -330,7 +331,7 @@ setClass("phylip",

              fields = "character",

              phylo = "phyloOrmultiPhylo",

              ntree = "numeric",

-             sequence = "BStringSet",

+             sequence = "character",

              extraInfo = "data.frame")

          )

@@ -15,6 +15,7 @@ geom_range <- function(range="height_0.95_HPD", ...) {

     inherit.aes = FALSE    

     default_aes <- aes_(x=~x, y=~y)

+    

     mapping <- modifyList(default_aes, aes_string(branch.length="branch.length", label=range))

     layer(

@@ -7,8 +7,8 @@

 ##'               one of hyphy output

 ##' @param tip.fasfile tip sequence file

 ##' @return A hyphy object

-##' @importFrom Biostrings readBStringSet

-##' @importFrom Biostrings toString

+## @importFrom Biostrings readBStringSet

+## @importFrom Biostrings toString

 ##' @export

 ##' @author Guangchuang Yu \url{http://ygc.name}

 ##' @examples

@@ -86,6 +86,9 @@ read.hyphy <- function(nwk, ancseq, tip.fasfile=NULL) {

                )

     if ( !is.null(tip.fasfile) ) {

+        readBStringSet <- get_fun_from_pkg("Biostrings", "readBStringSet")

+        toString <- get_fun_from_pkg("Biostrings", "toString")

+        

         tip_seq <- readBStringSet(tip.fasfile)

         nn <- names(tip_seq)

         tip_seq <- sapply(seq_along(tip_seq), function(i) {

@@ -107,7 +107,7 @@ setMethod("show", signature(object = "phylip"),

               cat("...@ tree: ")

               print.phylo(get.tree(object))                  

               msg <- paste0("\nwith sequence alignment available (", length(object@sequence),

-                            " sequences of length ", width(object@sequence)[1], ")\n")

+                            " sequences of length ", nchar(object@sequence)[1], ")\n")

               cat(msg)

           })

@@ -10,8 +10,8 @@

 ##' @param window specific a slice to display

 ##' @return tree view

 ##' @export

-##' @importFrom Biostrings readBStringSet

-##' @importMethodsFrom Biostrings width

+## @importFrom Biostrings readBStringSet

+## @importMethodsFrom Biostrings width

 ## @importFrom colorspace rainbow_hcl

 ##' @importFrom ggplot2 geom_segment

 ##' @importFrom ggplot2 geom_rect

@@ -23,22 +23,26 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

     } else if (is(fasta, "BStringSet")) {

         aln <- fasta

     } else if (is(fasta, "character")) {

+        readBStringSet <- get_fun_from_pkg("Biostrings", "readBStringSet")

         aln <- readBStringSet(fasta)

     } else {

         aln <- NULL

     }

     if (is(p, "phylip")) {

-        aln <- p@sequence

+        BStringSet <- get_fun_from_pkg("Biostrings", "BStringSet")

+        aln <- BStringSet(p@sequence)

         p <- ggtree(p) + geom_tiplab()

     }

     if (is.null(aln)) {

         stop("multiple sequence alignment is not available...\n-> check the parameter 'fasta'...")

     }

+

+    width_fun <- get_fun_from_pkg("Biostrings", "width")

     if (is.null(window)) {

-        window <- c(1, width(aln)[1])

+        window <- c(1, width_fun(aln)[1])

     }

     slice <- seq(window[1], window[2], by=1)

@@ -81,7 +81,7 @@

         d2 <- d2[, ii]

         dd <- merge(d1, d2, by.x="node", by.y="node", all.x=TRUE)

     } else {

-        d2[,1] <- as.character(d2[,1])

+        d2[,1] <- as.character(unlist(d2[,1])) ## `unlist` to work with tbl_df

         dd <- merge(d1, d2, by.x="label", by.y=1, all.x=TRUE)

     }

     dd <- dd[match(d1$node, dd$node),]

@@ -20,8 +20,8 @@ read.baseml <- function(rstfile, mlbfile) {

 ##' read rst file from paml output

 ##'

 ##' 

-##' @importFrom Biostrings readBStringSet

-##' @importFrom Biostrings toString

+## @importFrom Biostrings readBStringSet

+## @importFrom Biostrings toString

 ##' @title read.paml_rst

 ##' @param rstfile rst file

 ##' @return A \code{paml_rst} object

@@ -119,10 +119,11 @@ setMethod("get.fields", signature(object="phangorn"),

 ##' @param pml pml object

 ##' @param includeAncestor logical 

 ##' @return XStringSet

-##' @importFrom Biostrings DNAStringSet

+## @importFrom Biostrings DNAStringSet

 ##' @export

 ##' @author ygc

 pmlToSeq <- function(pml, includeAncestor=TRUE) {

+    DNAStringSet <- get_fun_from_pkg("Biostrings", "DNAStringSet")

     pmlToSeqString(pml, includeAncestor) %>%

         DNAStringSet

 }

@@ -132,10 +133,7 @@ pmlToSeqString <- function(pml, type, includeAncestor=TRUE) {

     if (includeAncestor == FALSE) {

         phyDat <- pml$data

     } else {

-        pkg <- "phangorn"

-        require(pkg, character.only = TRUE)

-        ## requireNamespace("phangorn")

-        ancestral.pml <- eval(parse(text="phangorn::ancestral.pml"))

+        ancestral.pml <- get_fun_from_pkg("phangorn", "ancestral.pml")

         phyDat <- ancestral.pml(pml, type)

     }

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

 ##' @param file phylip file

 ##' @return an instance of 'phylip'

 ##' @export

-##' @importFrom Biostrings BStringSet

+## @importFrom Biostrings BStringSet

 ##' @author Guangchuang Yu

 read.phylip <- function(file) {

     phylip <- readLines(file)

@@ -27,17 +27,16 @@ read.phylip <- function(file) {

     seq_with_name <- lapply(seqlines, function(x) unlist(strsplit(x, "\\s+")))

     seqs <- sapply(seq_with_name, function(x) x[2])

     names(seqs) <- sapply(seq_with_name, function(x) x[1])

-    seq_obj <- BStringSet(seqs)

-    if (any(width(seq_obj) != seqLen)) {

-        stop(paste("sequence length not consistent...\n->", paste0(width(seq_obj), collapse=" ")))

+    if (any(nchar(seqs) != seqLen)) {

+        stop(paste("sequence length not consistent...\n->", paste0(nchar(seqs), collapse=" ")))

     }

     new("phylip",

         file = filename(file),

         phylo = trees,

         ntree = ntree,

-        sequence = seq_obj

+        sequence = seqs

         )

 }

@@ -32,8 +32,9 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     imgfile <- tempfile(fileext = ".png")

     download.phylopic_internal(id, size, imgfile)

-    requireNamespace("EBImage")

-    channel <- eval(parse(text=paste0("EBImage::", "channel")))

+    channel <- get_fun_from_pkg("EBImage", "channel")

+    readImage <- get_fun_from_pkg("EBImage", "readImage")

+    

     img <- readImage(imgfile)

     color <- col2rgb(color) / 255

@@ -135,6 +136,7 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

     x <- df[idx, "x"]

     y <- df[idx, "y"]

+    readImage <- get_fun_from_pkg("EBImage", "readImage")

     images <- lapply(img_info[,2], readImage)

     ARs <- sapply(images, getAR)

@@ -30,6 +30,7 @@ subview <- function(mainview, subview, x, y, width=.1, height=.1) {

     } else if (is(subview, "grob")) {

         sv <- subview

     } else if (file.exists(subview)) {

+        readImage <- get_fun_from_pkg("EBImage", "readImage")

         sv <- rasterGrob(readImage(subview))

     } else {

         stop("subview should be a ggplot or grob object, or an image file...")

@@ -19,6 +19,7 @@ get_tree_view <- function(tree_view) {

 }

+##' @importFrom methods .hasSlot is missingArg new slot slot<-

 has.slot <- function(object, slotName) {

     if (!isS4(object)) {

         return(FALSE)

@@ -251,8 +252,10 @@ seq2codon <- function(x) {

     substring(x, first=seq(1, nchar(x)-2, 3), last=seq(3, nchar(x), 3))

 }

-##' @importFrom Biostrings GENETIC_CODE

+## @importFrom Biostrings GENETIC_CODE

 codon2AA <- function(codon) {

+    ## a genetic code name vector

+    GENETIC_CODE <- get_fun_from_pkg("Biostrings", "GENETIC_CODE") 

     aa <- GENETIC_CODE[codon]

     aa[is.na(aa)] <- "X"

     return(aa)

@@ -493,13 +496,15 @@ getCols <- function (n) {

 get_fun_from_pkg <- function(pkg, fun) {

-    requireNamespace(pkg)

-    eval(parse(text=paste0(pkg, "::", fun)))

+    ## requireNamespace(pkg)

+    ## eval(parse(text=paste0(pkg, "::", fun)))

+    require(pkg, character.only = TRUE)

+    eval(parse(text = fun))

 }

 hist <- get_fun_from_pkg("graphics", "hist")

-readImage <- get_fun_from_pkg("EBImage", "readImage")

+

@@ -16,6 +16,7 @@ output:

 vignette: >

   %\VignetteIndexEntry{05 Advance Tree Annotation}

   %\VignetteEngine{knitr::rmarkdown}

+  %\VignetteDepends{Biostrings}

   %\usepackage[utf8]{inputenc}

 ---

@@ -27,6 +28,7 @@ knitr::opts_chunk$set(tidy = FALSE,

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("ape")

+library("Biostrings")

 library("ggplot2")

 library("ggtree")

 ```

@@ -31,7 +31,6 @@ library("Biostrings")

 library("ape")

 library("ggplot2")

 library("ggtree")

-library("phangorn")

 ```

@@ -16,8 +16,6 @@ output:

 vignette: >

   %\VignetteIndexEntry{04 Tree Annotation}

   %\VignetteEngine{knitr::rmarkdown}

-  %\VignetteDepends{phangorn}

-  %\VignetteDepends{phylobase}

   %\usepackage[utf8]{inputenc}

 ---

@@ -215,7 +213,7 @@ ggtree(tree) + geom_label(aes(label=bootstrap)) + geom_tiplab()

 ## annotating tree with phangorn output

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

+```{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="ggtree")

 tre <- read.tree(treefile)

@@ -225,13 +223,13 @@ 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")

-```

-```{r fig.width=12, fig.height=10, width=60, warning=FALSE, fig.align="center"}

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

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

 ```

+![](figures/phangorn_example.png)

+

 # Tree annotation with output from evolution software

 In `ggtree`, we implemented several parser functions to parse output from commonly used software package in evolutionary biology, including:

@@ -300,7 +298,7 @@ p + geom_text(aes(color=place, label=place), hjust=1, vjust=-0.4, size=3) +

 `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"}

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

 dd2 <- dd[, -1]

 rownames(dd2) <- dd[,1]

 require(phylobase)

@@ -309,7 +307,9 @@ 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.

@@ -17,6 +17,7 @@ vignette: >

   %\VignetteIndexEntry{01 Tree Data Import}

   %\VignetteEngine{knitr::rmarkdown}

   %\VignetteDepends{scales}

+  %\VignetteDepends{Biostrings)

   %\usepackage[utf8]{inputenc}

 ---

@@ -28,6 +29,7 @@ knitr::opts_chunk$set(tidy = FALSE,

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("ape")

+library("Biostrings")

 library("ggplot2")

 library("ggtree")

 ```

@@ -139,7 +141,7 @@ ggtree(beast, ndigits=2, branch.length = 'none') + geom_text(aes(x=branch, label

 `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)

+ggtree(beast) + geom_range(range='length_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.