geom_seqlogo {ggmsa} | R Documentation

## geom_seqlogo

### Description

Multiple sequence alignment layer for ggplot2. It plot sequence motifs.

### Usage

    geom_seqlogo(
      font = "DroidSansMono",
      color = "Chemistry_AA",
      adaptive = TRUE,
      top = TRUE,
      custom_color = NULL,
      show.legend = FALSE,
      ...
    )

### Arguments

`font` | font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'DroidSansMono'.
`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'.
`adaptive` | A logical value indicating whether the overall height of seqlogo corresponds to the number of sequences.If is FALSE, seqlogo overall height = 4,fixedly.
`top` | A logical value. If TRUE, seqlogo is aligned to the top of MSA.
`custom_color` | A data frame with two cloumn called "names" and "color".Customize the color scheme.
`show.legend` | logical. Should this layer be included in the legends?
`...` | additional parameter

### Value

A list

### Author(s)

Lang Zhou

### Examples

    #plot multiple sequence alignment and sequence motifs
    f <- system.file("extdata/LeaderRepeat_All.fa", package="ggmsa")
    ggmsa(f,font = NULL,color = "Chemistry_NT") + geom_seqlogo()

[Package ggmsa version 1.0.0 Index]