@@ -13,4 +13,6 @@ __init__.pyc

 .web_cache

 ggtree.Rproj

 .Rproj.user

-ggtree*.html

+ggtree

+*.html

+

@@ -30,7 +30,6 @@ Imports:

     treeio (>= 1.3.3),

     utils

 Suggests:

-    Biostrings,

     colorspace,

     cowplot,

     emojifont,

@@ -200,6 +200,7 @@ importFrom(treeio,Nnode)

 importFrom(treeio,Ntip)

 importFrom(treeio,as.phylo)

 importFrom(treeio,as.treedata)

+importFrom(treeio,read.fasta)

 importFrom(utils,modifyList)

 importFrom(utils,packageDescription)

 importFrom(utils,packageVersion)

@@ -1,5 +1,6 @@

 CHANGES IN VERSION 1.11.3

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

+ o update msaplot to use DNAbin/AAbin internally and also compatible with treedata object <2017-12-14, Thu>

  o clean up code <2017-12-13, Thu>

  o remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3) <2017-12-07, Thu>

@@ -12,52 +12,51 @@

 ##' @param height height ratio of sequence

 ##' @return tree view

 ##' @export

-## @importFrom Biostrings readBStringSet

-## @importMethodsFrom Biostrings width

 ## @importFrom colorspace rainbow_hcl

+##' @importFrom treeio read.fasta

 ##' @importFrom ggplot2 geom_segment

 ##' @importFrom ggplot2 geom_rect

 ##' @importFrom ggplot2 scale_fill_manual

 ##' @author Guangchuang Yu

 msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_line = TRUE, height = 0.8){

     if (missingArg(fasta)) {

-        aln <- NULL

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

-        aln <- fasta

+        x <- NULL

+    } else if (is(fasta, "DNAbin")) {

+        x <- fasta

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

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

-        aln <- readBStringSet(fasta)

+        x <- read.fasta(fasta)

     } else {

-        aln <- NULL

+        x <- NULL

     }

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

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

-        aln <- BStringSet(p@sequence)

+

+    if (is.null(x) && is(p, "treedata") && length(p@tip_seq)) {

+        x <- p@tip_seq

         p <- ggtree(p) + geom_tiplab()

     }

-    if (is.null(aln)) {

+    if (is.null(x)) {

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

     }

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

+    x <- as.matrix(x)

     if (is.null(window)) {

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

+        window <- c(1, ncol(x))

     }

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

-    seqs <- lapply(1:length(aln), function(i) {

-        x <- toString(aln[i])

-        seq <- substring(x, slice, slice)

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

+    x <- x[, slice]

+    seqs <- lapply(1:nrow(x), function(i) {

+        seq <- as.vector(as.character(x[i,]))

         seq[seq == '?'] <- '-'

         seq[seq == '*'] <- '-'

         seq[seq == ' '] <- '-'

         return(seq)

     })

-    names(seqs) <- names(aln)

+

+    names(seqs) <- labels(x)

     if(is.null(color)) {

         alphabet <- unlist(seqs) %>% unique

@@ -108,9 +107,10 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_lin

     msa.df <- do.call("rbind", msa)

-    p <- p + geom_rect(data=msa.df, aes(x=xmin, y=ymin,

-                           xmin=xmin, xmax=xmax,

-                           ymin=ymin, ymax=ymax, fill=seq)) +

+    p <- p + geom_rect(aes(xmin=xmin, xmax=xmax,

+                           ymin=ymin, ymax=ymax,

+                           fill=seq),

+                       data=msa.df, inherit.aes = FALSE) +

                                scale_fill_manual(values=color)

     breaks <- hist(seq_along(slice), breaks=10, plot=FALSE)$breaks

@@ -120,4 +120,3 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_lin

     return(p)

 }

-

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

 vignette: >

   %\VignetteIndexEntry{05 Advance Tree Annotation}

   %\VignetteEngine{knitr::rmarkdown}

-  %\VignetteDepends{Biostrings}

   %\usepackage[utf8]{inputenc}

 ---

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

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

 library("ape")

-library("Biostrings")

 library("treeio")

 library("ggplot2")

 library("ggtree")

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

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

 library("colorspace")

-library("Biostrings")

 library("ape")

 library("ggplot2")

 library("ggtree")