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

 CHANGES IN VERSION 1.9.2

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

+ o add bg_line and height parameter in msaplot <2017-07-26, Wed>

+   + use can set bg_line = FALSE and height = 1 to plot more beautiful alignment

  o extend parameter in geom_cladebar <2017-07-26, Wed>

    + https://github.com/GuangchuangYu/ggtree/issues/142#issuecomment-317817995

  o scaleClade works after calling viewClade <2017-07-20, Thu>

@@ -1,13 +1,15 @@

 ##' 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 total width of alignment, compare to width of tree

-##' @param color color 

+##' @param color color

 ##' @param window specific a slice to display

+##' @param bg_line whether add background line in alignment

+##' @param height height ratio of sequence

 ##' @return tree view

 ##' @export

 ## @importFrom Biostrings readBStringSet

@@ -17,7 +19,7 @@

 ##' @importFrom ggplot2 geom_rect

 ##' @importFrom ggplot2 scale_fill_manual

 ##' @author Guangchuang Yu

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

+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")) {

@@ -28,7 +30,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

     } else {

         aln <- NULL

     }

-        

+

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

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

         aln <- BStringSet(p@sequence)

@@ -40,12 +42,12 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

     }

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

-    

+

     if (is.null(window)) {

         window <- c(1, width_fun(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)

@@ -56,7 +58,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

         return(seq)

     })

     names(seqs) <- names(aln)

-    

+

     if(is.null(color)) {

         alphabet <- unlist(seqs) %>% unique

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

@@ -73,7 +75,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

     ## convert width to width of each cell

     width <- width * (df$x %>% range %>% diff) / diff(window)

-    

+

     df=df[df$isTip,]

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

@@ -84,14 +86,17 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

     xmax <- start + seq_along(slice) * width

     xmin <- xmax - width

     y <- sort(df$y)

-    ymin <- y - 0.4 *h

-    ymax <- y + 0.4 *h

+    ymin <- y - height/2 *h

+    ymax <- y + height/2 *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))

+    if (bg_line) {

+        p <- p + geom_segment(data=lines.df, aes(x=from, xend=to, y=y, yend=y), size=h*.2)

+    }

+

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

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

                    xmin=xmin,

@@ -103,7 +108,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

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

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

+    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)

@@ -112,7 +117,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

     pos <- start + breaks * width

     mapping <- data.frame(from=breaks+1, to=pos)

     attr(p, "mapping") <- mapping

-    

+

     return(p)

 }

@@ -27,7 +27,7 @@ Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.

-[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-351-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-29-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-350-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-29-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

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

@@ -4,7 +4,8 @@

 \alias{msaplot}

 \title{msaplot}

 \usage{

-msaplot(p, fasta, offset = 0, width = 1, color = NULL, window = NULL)

+msaplot(p, fasta, offset = 0, width = 1, color = NULL, window = NULL,

+  bg_line = TRUE, height = 0.8)

 }

 \arguments{

 \item{p}{tree view}

@@ -18,6 +19,10 @@ msaplot(p, fasta, offset = 0, width = 1, color = NULL, window = NULL)

 \item{color}{color}

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

+

+\item{bg_line}{whether add background line in alignment}

+

+\item{height}{height ratio of sequence}

 }

 \value{

 tree view