seqlogo {ggmsa} | R Documentation

## seqlogo

### Description

plot sequence logo for MSA based 'ggolot2'

### Usage

    seqlogo(
      msa,
      start = NULL,
      end = NULL,
      font = "DroidSansMono",
      color = "Chemistry_AA",
      adaptive = FALSE,
      top = FALSE,
      custom_color = NULL
    )

### Arguments

`msa` | Multiple sequence alignment file or object for representing either nucleotide sequences or peptide sequences.
`start` | Start position to plot.
`end` | End position to plot.
`font` | font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'DroidSansMono'. If font=NULL, only the background tiles is drawn.
`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 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.

### Value

ggplot object

### Author(s)

Lang Zhou

### Examples

    #plot sequence motif independently
    nt_sequence <- system.file("extdata", "LeaderRepeat_All.fa",
                               package = "ggmsa")
    seqlogo(nt_sequence, color = "Chemistry_NT")

[Package ggmsa version 1.0.0 Index]