geom_seqlogo: geom_seqlogo

Description Usage Arguments Value Author(s) Examples

View source: R/seqlogo.R

Description

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

Usage

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(
  font = "DroidSansMono",
  color = "Chemistry_NT",
  adaptive = TRUE,
  top = TRUE,
  custom_color = NULL,
  ...
)

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.

...

additional parameter

Value

A list

Author(s)

Lang Zhou

Examples

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

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