ggmsa (version 1.0.2)

geom_seqlogo: 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

Examples

# NOT RUN {
#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()
# }