ggmsa (version 0.0.1)

ggmsa: ggmsa

Description

Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.

Usage

ggmsa(fasta, start = NULL, end = NULL, font = "helvetica_regular",
  color = "Clustal")

Arguments

fasta

Aligned FASTA format file for representing either nucleotide sequences or peptide sequences.

start

Start position to plot, If font=NULL, only the background frame is drawn, and no character.

end

End position to plot,If font=NULL, only the background frame is drawn, and no character.

font

Character font, Defaults is 'helvetica_regular'.

color

A Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Clustal'.

Value

ggplot object

Examples

# NOT RUN {
#plot multiple sequence alignment
f <- system.file("extdata/sample.fasta", package="ggmsa")
ggmsa(f, 164, 213, color="Chemistry_AA")
# }