ggmsa {ggmsa} | R Documentation

## ggmsa

### Description

Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.

### Usage

    ggmsa(
      msa,
      start = NULL,
      end = NULL,
      font = "helvetical",
      color = "Chemistry_AA",
      custom_color = NULL,
      char_width = 0.9,
      none_bg = FALSE,
      by_conservation = FALSE,
      posHighligthed = NULL,
      seq_name = NULL,
      border = NULL,
      consensus_views = FALSE,
      use_dot = FALSE,
      disagreement = TRUE,
      ignore_gaps = FALSE,
      ref = NULL,
      show.legend = FALSE
    )

### Arguments

`msa` | Multiple aligned sequence files or objects representing either nucleotide sequences or AA sequences.
`start` | a numeric vector. Start position to plot.
`end` | a numeric vector. End position to plot.
`font` | font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'. If font = NULL, only plot the background tile.
`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'.
`custom_color` | A data frame with two column called "names" and "color".Customize the color scheme.
`char_width` | a numeric vector. Specifying the character width in the range of 0 to 1. Defaults is 0.9.
`none_bg` | a logical value indicating whether background should be displayed. Defaults is FALSE.
`by_conservation` | a logical value. The most conserved regions have the brightest colors.
`posHighligthed` | A numeric vector of the position that need to be highlighted.
`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.
`border` | a character string. The border color.
`consensus_views` | a logical value that opening consensus views.
`use_dot` | a logical value. Displays characters as dots instead of fading their color in the consensus view.
`disagreement` | a logical value. Displays characters that disagreememt to consensus(excludes ambiguous disagreements).
`ignore_gaps` | a logical value. When selected TRUE, gaps in column are treated as if that row didn't exist.
`ref` | a character string. Specifying the reference sequence which should be one of input sequences when 'consensus_views' is TRUE.
`show.legend` | logical. Should this layer be included in the legends?

### Value

ggplot object

### Author(s)

Guangchuang Yu

### Examples

    #plot multiple sequences by loading fasta format
    fasta <- system.file("extdata", "sample.fasta", package = "ggmsa")
    ggmsa(fasta, 164, 213, color="Chemistry_AA")

    #XMultipleAlignment objects can be used as input in the 'ggmsa'
    #AAMultipleAlignment <- readAAMultipleAlignment(fasta)
    #ggmsa(AAMultipleAlignment, 164, 213, color="Chemistry_AA")

    #XStringSet objects can be used as input in the 'ggmsa'
    #AAStringSet <- readAAStringSet(fasta)
    #ggmsa(AAStringSet, 164, 213, color="Chemistry_AA")

    #Xbin objects from 'seqmagick' can be used as input in the 'ggmsa'
    #AAbin <- fa_read(fasta)
    #ggmsa(AAbin, 164, 213, color="Chemistry_AA")

[Package ggmsa version 1.0.0 Index]