ggmsa (version 1.0.2)

ggmsa: 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 cloumn 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 disaplayed. 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 seqence 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 opeaning 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

Examples

# NOT RUN {
#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 <- 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")
# }