geom_seqlogo — geom_seqlogo • ggmsa

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

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

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()