geom_msa: geom_msa

Description Usage Arguments Value Author(s)

View source: R/geom_msa.R

Description

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

Usage

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geom_msa(
  data,
  font = "helvetical",
  mapping = NULL,
  color = "Chemistry_AA",
  custom_color = NULL,
  order = 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,
  position = "identity",
  ...
)

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 cloumn called "names" and "color".Customize the color scheme.

order

vectors.Specified sequences order.

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.

position

Position adjustment, either as a string, or the result of a call to a position adjustment function, default is 'identity' meaning 'position_identity()'.

...

additional parameter

Value

A list

Author(s)

Guangchuang Yu


ggmsa documentation built on Feb. 2, 2021, 5:14 p.m.