geom_msa: geom_msa
In ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

Description Usage Arguments Value Author(s)

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

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

`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.
`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()'.
`show.legend`	logical. Should this layer be included in the legends?
`...`	additional parameter