geom_msa: geom_msa

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

geom_msa

Description

Multiple sequence alignment layer for ggplot2. It creates background tiles with/without sequence characters.

Usage

geom_msa(
  data,
  font = "helvetical",
  mapping = NULL,
  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,
  position = "identity",
  show.legend = FALSE,
  dms = FALSE,
  position_color = FALSE,
  ...
)

Arguments

data	sequence alignment with data frame, generated by tidy_msa().
font	font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'.
mapping	aes mapping 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.
position_highlight	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 disagreement 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.
position	Position adjustment, either as a string, or the result of a call to a position adjustment function, default is 'identity' meaning 'position_identity()'.
show.legend	logical. Should this layer be included in the legends?
dms	logical.
position_color	logical.
...	additional parameter

Value

A list

Author(s)

Guangchuang Yu, Lang Zhou seq_name' work position_highlight' work border' work none_bg' work

Examples

library(ggplot2)
aln <- system.file("extdata", "sample.fasta", package = "ggmsa")
tidy_aln <- tidy_msa(aln, start = 150, end = 170)
ggplot() + geom_msa(data = tidy_aln, font = NULL) + coord_fixed()

YuLab-SMU/ggmsa documentation built on Dec. 18, 2024, 11:53 p.m.