Browse code

update msaplot to use DNAbin/AAbin

guangchuang yu authored on 14/12/2017 10:29:44
Showing7 changed files

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@@ -13,4 +13,6 @@ __init__.pyc
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 .web_cache
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 ggtree.Rproj
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 .Rproj.user
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-ggtree*.html
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+ggtree
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+*.html
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+
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@@ -30,7 +30,6 @@ Imports:
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     treeio (>= 1.3.3),
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     utils
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 Suggests:
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-    Biostrings,
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     colorspace,
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     cowplot,
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     emojifont,
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@@ -200,6 +200,7 @@ importFrom(treeio,Nnode)
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 importFrom(treeio,Ntip)
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 importFrom(treeio,as.phylo)
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 importFrom(treeio,as.treedata)
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+importFrom(treeio,read.fasta)
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 importFrom(utils,modifyList)
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 importFrom(utils,packageDescription)
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 importFrom(utils,packageVersion)
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@@ -1,5 +1,6 @@
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 CHANGES IN VERSION 1.11.3
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 ------------------------
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+ o update msaplot to use DNAbin/AAbin internally and also compatible with treedata object <2017-12-14, Thu>
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  o clean up code <2017-12-13, Thu>
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  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>
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@@ -12,52 +12,51 @@
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 ##' @param height height ratio of sequence
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 ##' @return tree view
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 ##' @export
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-## @importFrom Biostrings readBStringSet
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-## @importMethodsFrom Biostrings width
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 ## @importFrom colorspace rainbow_hcl
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+##' @importFrom treeio read.fasta
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 ##' @importFrom ggplot2 geom_segment
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 ##' @importFrom ggplot2 geom_rect
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 ##' @importFrom ggplot2 scale_fill_manual
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 ##' @author Guangchuang Yu
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 msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_line = TRUE, height = 0.8){
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     if (missingArg(fasta)) {
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-        aln <- NULL
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-    } else if (is(fasta, "BStringSet")) {
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-        aln <- fasta
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+        x <- NULL
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+    } else if (is(fasta, "DNAbin")) {
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+        x <- fasta
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     } else if (is(fasta, "character")) {
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-        readBStringSet <- get_fun_from_pkg("Biostrings", "readBStringSet")
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-        aln <- readBStringSet(fasta)
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+        x <- read.fasta(fasta)
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     } else {
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-        aln <- NULL
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+        x <- NULL
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     }
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-    if (is(p, "phylip")) {
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-        BStringSet <- get_fun_from_pkg("Biostrings", "BStringSet")
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-        aln <- BStringSet(p@sequence)
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+
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+    if (is.null(x) && is(p, "treedata") && length(p@tip_seq)) {
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+        x <- p@tip_seq
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         p <- ggtree(p) + geom_tiplab()
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     }
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-    if (is.null(aln)) {
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+    if (is.null(x)) {
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         stop("multiple sequence alignment is not available...\n-> check the parameter 'fasta'...")
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     }
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-    width_fun <- get_fun_from_pkg("Biostrings", "width")
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+    x <- as.matrix(x)
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     if (is.null(window)) {
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-        window <- c(1, width_fun(aln)[1])
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+        window <- c(1, ncol(x))
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     }
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-    slice <- seq(window[1], window[2], by=1)
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-    seqs <- lapply(1:length(aln), function(i) {
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-        x <- toString(aln[i])
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-        seq <- substring(x, slice, slice)
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+    slice <- seq(window[1], window[2], by=1)
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+    x <- x[, slice]
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+    seqs <- lapply(1:nrow(x), function(i) {
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+        seq <- as.vector(as.character(x[i,]))
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         seq[seq == '?'] <- '-'
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         seq[seq == '*'] <- '-'
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         seq[seq == ' '] <- '-'
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         return(seq)
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     })
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-    names(seqs) <- names(aln)
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+
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+    names(seqs) <- labels(x)
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     if(is.null(color)) {
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         alphabet <- unlist(seqs) %>% unique
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@@ -108,9 +107,10 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_lin
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     msa.df <- do.call("rbind", msa)
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-    p <- p + geom_rect(data=msa.df, aes(x=xmin, y=ymin,
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-                           xmin=xmin, xmax=xmax,
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-                           ymin=ymin, ymax=ymax, fill=seq)) +
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+    p <- p + geom_rect(aes(xmin=xmin, xmax=xmax,
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+                           ymin=ymin, ymax=ymax,
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+                           fill=seq),
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+                       data=msa.df, inherit.aes = FALSE) +
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                                scale_fill_manual(values=color)
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     breaks <- hist(seq_along(slice), breaks=10, plot=FALSE)$breaks
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@@ -120,4 +120,3 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL, bg_lin
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     return(p)
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 }
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-
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@@ -16,7 +16,6 @@ output:
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 vignette: >
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   %\VignetteIndexEntry{05 Advance Tree Annotation}
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   %\VignetteEngine{knitr::rmarkdown}
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-  %\VignetteDepends{Biostrings}
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   %\usepackage[utf8]{inputenc}
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 ---
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@@ -28,7 +27,6 @@ knitr::opts_chunk$set(tidy = FALSE,
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 ```{r echo=FALSE, results="hide", message=FALSE}
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 library("ape")
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-library("Biostrings")
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 library("treeio")
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 library("ggplot2")
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 library("ggtree")
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@@ -27,7 +27,6 @@ knitr::opts_chunk$set(tidy = FALSE,
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 ```{r echo=FALSE, results="hide", message=FALSE}
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 library("colorspace")
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-library("Biostrings")
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 library("ape")
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 library("ggplot2")
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 library("ggtree")