seqlogo: seqlogo

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

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")

YuLab-SMU/ggmsa documentation built on Dec. 18, 2024, 11:53 p.m.