ggmsa.R

##' Plot multiple sequence alignment using ggplot2 with multiple color schemes 
##' supported.
##'
##'
##' @title ggmsa
##' @param msa Multiple aligned sequence files or objects representing either 
##' nucleotide sequences or AA sequences.
##' @param start a numeric vector. Start position to plot.
##' @param end a numeric vector. End position to plot.
##' @param font font families, possible values are 'helvetical', 'mono', and 
##' 'DroidSansMono', 'TimesNewRoman'.  Defaults is 'helvetical'. 
##' If font = NULL, only plot the background tile.
##' @param color a Color scheme. One of 'Clustal', 'Chemistry_AA', 
##' 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER', 'CN6', 'Chemistry_NT', 
##' 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Chemistry_AA'.
##' @param custom_color A data frame with two column called "names" and 
##' "color".Customize the color scheme.
##' @param char_width a numeric vector. Specifying the character width in 
##' the range of 0 to 1. Defaults is 0.9.
##' @param by_conservation a logical value. The most conserved regions have 
##' the brightest colors.
##' @param none_bg a logical value indicating whether background should be
##'  displayed. Defaults is FALSE.
##' @param position_highlight A numeric vector of the position that need to be
##'  highlighted.
##' @param seq_name a logical value indicating whether sequence names 
##' should be displayed. Defaults is 'NULL' which indicates that the 
##' sequence name is displayed when 'font = null', but 'font = char' 
##' will not be displayed. If 'seq_name = TRUE' the sequence name will 
##' be displayed in any case. If 'seq_name = FALSE' the sequence name 
##' will not be displayed under any circumstances.
##' @param border a character string. The border color.
##' @param consensus_views a logical value that opening consensus views.
##' @param use_dot a logical value. Displays characters as dots instead 
##' of fading their color in the consensus view.
##' @param disagreement a logical value. Displays characters that 
##' disagreememt to consensus(excludes ambiguous disagreements).
##' @param ignore_gaps a logical value. When selected TRUE, gaps in column 
##' are treated as if that row didn't exist.
##' @param ref a character string. Specifying the reference sequence which 
##' should be one of input sequences when 'consensus_views' is TRUE.
##' @param show.legend logical. Should this layer be included in the legends?
##' @return ggplot object
##' @importFrom tidyr gather
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes_
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 theme_minimal
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 geom_polygon
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 coord_fixed
##' @importFrom ggplot2 geom_point
##' @importFrom ggplot2 element_blank
##' @importFrom magrittr %>%
##' @importFrom stats setNames
##' @importFrom grid unit
##' @examples
##' #plot multiple sequences by loading fasta format
##' fasta <- system.file("extdata", "sample.fasta", package = "ggmsa")
##' ggmsa(fasta, 164, 213, color="Chemistry_AA")
##'
##'\dontrun{
##' #XMultipleAlignment objects can be used as input in the 'ggmsa'
##' AAMultipleAlignment <- Biostrings::readAAMultipleAlignment(fasta)
##' ggmsa(AAMultipleAlignment, 164, 213, color="Chemistry_AA")
##'
##' #XStringSet objects can be used as input in the 'ggmsa'
##' AAStringSet <- Biostrings::readAAStringSet(fasta)
##' ggmsa(AAStringSet, 164, 213, color="Chemistry_AA")
##'
##' #Xbin objects from 'seqmagick' can be used as input in the 'ggmsa'
##' AAbin <- seqmagick::fa_read(fasta)
##' ggmsa(AAbin, 164, 213, color="Chemistry_AA")
##' }
##' @export
##' @author Guangchuang Yu
ggmsa <- function(msa,
                  start = NULL,
                  end = NULL,
                  font = "helvetical",
                  color = "Chemistry_AA",
                  custom_color = NULL,
                  char_width = 0.9,
                  none_bg = FALSE,
                  by_conservation = FALSE,
                  position_highlight = NULL,
                  seq_name = NULL,
                  border = NULL,
                  consensus_views = FALSE,
                  use_dot = FALSE,
                  disagreement = TRUE,
                  ignore_gaps = FALSE,
                  ref = NULL,
                  show.legend = FALSE,
                  msa.type=NULL) {

    data <- tidy_msa(msa, start = start, end = end, msa.type = msa.type)

    ggplot() + geom_msa(data, font = font,
                        color = color,
                        custom_color = custom_color,
                        char_width = char_width,
                        none_bg = none_bg,
                        by_conservation = by_conservation,
                        position_highlight = position_highlight,
                        seq_name = seq_name,
                        border = border,
                        consensus_views = consensus_views,
                        use_dot = use_dot,
                        disagreement = disagreement,
                        ignore_gaps = ignore_gaps,
                        ref = ref,
                        show.legend = show.legend) +
               theme_msa()

}