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

 Package: ggtree

 Type: Package

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

-Version: 1.1.6

+Version: 1.1.7

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -48,6 +48,7 @@ export(groupOTU)

 export(gzoom)

 export(hilight)

 export(merge_tree)

+export(msaplot)

 export(phylopic)

 export(plot)

 export(read.baseml)

@@ -114,6 +115,7 @@ importFrom(ggplot2,element_rect)

 importFrom(ggplot2,element_text)

 importFrom(ggplot2,fortify)

 importFrom(ggplot2,geom_point)

+importFrom(ggplot2,geom_rect)

 importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

 importFrom(ggplot2,geom_tile)

@@ -124,6 +126,7 @@ importFrom(ggplot2,labs)

 importFrom(ggplot2,scale_color_manual)

 importFrom(ggplot2,scale_fill_discrete)

 importFrom(ggplot2,scale_fill_gradient)

+importFrom(ggplot2,scale_fill_manual)

 importFrom(ggplot2,scale_x_continuous)

 importFrom(ggplot2,scale_x_reverse)

 importFrom(ggplot2,scale_y_continuous)

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.1.7

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

+ o msaplot for adding multiple sequence alignment <2015-05-22, Fri>

+ 

 CHANGES IN VERSION 1.1.6

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

  o add vertical_only parameter to scaleClade and set to TRUE by default.

@@ -61,6 +61,92 @@ gheatmap <- function(p, data, offset=0, width=NULL, low="green", high="red",

     return(p2)

 }

+##' multiple sequence alignment with phylogenetic tree

+##'

+##' 

+##' @title msaplot

+##' @param p tree view

+##' @param fasta fasta file, multiple sequence alignment

+##' @param offset offset of MSA to tree

+##' @param width width of each character

+##' @param color color 

+##' @param window specific a slice to display

+##' @return tree view

+##' @export

+##' @importFrom Biostrings readBStringSet

+##' @importFrom colorspace rainbow_hcl

+##' @importFrom ggplot2 geom_segment

+##' @importFrom ggplot2 geom_rect

+##' @importFrom ggplot2 scale_fill_manual

+##' @author Guangchuang Yu

+msaplot <- function(p, fasta, offset=0, width=NULL, color=NULL, window=NULL){

+    aln <- readBStringSet(fasta)

+    if (is.null(window)) {

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

+    }

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

+    

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

+        x <- toString(aln[i])

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

+

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

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

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

+        return(seq)

+    })

+    names(seqs) <- names(aln)

+    

+    if(is.null(color)) {

+        alphabet <- unlist(seqs) %>% unique

+        alphabet <- alphabet[alphabet != '-']

+        color <- rainbow_hcl(length(alphabet))

+        names(color) <- alphabet

+        color <- c(color, '-'=NA)

+    }

+

+    df <- p$data

+    if (is.null(width)) {

+        width <- (df$x %>% range %>% diff)/500

+    }

+

+    df=df[df$isTip,]

+    start <- max(df$x) * 1.02 + offset

+

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

+    ## seqs.df <- do.call("rbind", seqs)

+

+    h <- ceiling(diff(range(df$y))/length(df$y))

+    xmax <- start + seq_along(slice) * width

+    xmin <- xmax -width

+    y <- sort(df$y)

+    ymin <- y - 0.4 *h

+    ymax <- y + 0.4 *h

+

+    from <- to <- NULL

+    

+    lines.df <- data.frame(from=min(xmin), to=max(xmax), y = y)

+

+    p <- p + geom_segment(data=lines.df, aes(x=from, xend=to, y=y, yend=y))

+    msa <- lapply(1:length(y), function(i) {

+        data.frame(name=names(seqs)[i],

+                   xmin=xmin,

+                   xmax=xmax,

+                   ymin=ymin[i],

+                   ymax=ymax[i],

+                   seq=seqs[[i]])

+    })

+

+    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)) +

+                               scale_fill_manual(values=color)

+

+    return(p)

+}

+

 ##' scale x for tree with heatmap

 ##'

 ##' 

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

   and compare the feature from parent to children and add store the info in tree object.

   So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,

   not only substitution supported internally.

-+ support more features that can be plotted at the right hand side of the tree,

-  not only matrix but also for example sequence alignment or specific window of alignment.

++ support more features that can be plotted at the right hand side of the tree.

+  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_

@@ -13,9 +13,7 @@ install:

 build_script:

   - travis-tool.sh install_deps

-  - travis-tool.sh install_bioc EBImage

-  - travis-tool.sh install_bioc BiocStyle

-  - travis-tool.sh install_bioc Biostrings

+  - travis-tool.sh install_bioc BiocStyle Biostrings EBImage

 ##  - travis-tool.sh install_bioc_deps

 test_script:

new file mode 100644

@@ -0,0 +1,31 @@

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/gplot.R

+\name{msaplot}

+\alias{msaplot}

+\title{msaplot}

+\usage{

+msaplot(p, fasta, offset = 0, width = NULL, color = NULL, window = NULL)

+}

+\arguments{

+\item{p}{tree view}

+

+\item{fasta}{fasta file, multiple sequence alignment}

+

+\item{offset}{offset of MSA to tree}

+

+\item{width}{width of each character}

+

+\item{color}{color}

+

+\item{window}{specific a slice to display}

+}

+\value{

+tree view

+}

+\description{

+multiple sequence alignment with phylogenetic tree

+}

+\author{

+Guangchuang Yu

+}

+