geom_msa {ggmsa} | R Documentation

## 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,
      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,
      ...
    )

### 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.
`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 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?
`...` | additional parameter

### Value

A list

### Author(s)

Guangchuang Yu, Lang Zhou seq_name' work posHighligthed' 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()

[Package ggmsa version 1.0.0 Index]