plot_alignment: Plot a multiple sequence alignment

In alignfigR: Visualizing Multiple Sequence Alignments with 'ggplot2'

Description

This function uses ggplot (in particular, w/ geom_rect) to plot a sequence alignment

Usage

plot_alignment(seq_list, palette = NA, taxa = c(), columns = c(),
  exclude_taxa = FALSE, exclude_columns = FALSE,
  legend_title = "Character")

Arguments

seq_list	Sequence list parsed using the function 'read_alignment'
palette	Named-array mapping sequence to color or a pre-defined color scheme (random, rainbow, etc.)
taxa	Array of taxa (the actual labels, not order) intended to restrict figure to or to exclude from figure.
columns	Array of columns (indexed from 1) intended to restrict figure to or to exclude from figure.
exclude_taxa	Boolean argument indicating that taxa should be excluded from plot. Default: False
exclude_columns	Boolean argument indicating that columns should be excluded from plot. Default: False
legend_title	String determining title of legend. Default: "Character"

Value

ggplot object which may be saved or edited as desired

Examples

fasta_file <- system.file("extdata", "example.fasta", package = "alignfigR")
plot_frame <- read_alignment(file = fasta_file)
align_plot <- plot_alignment(plot_frame, "DNA")
align_plot <- plot_alignment(plot_frame, "protein")
align_plot <- plot_alignment(plot_frame, taxa = c("Cow", "Whale"), columns = c(1:25))
align_plot <- plot_alignment(plot_frame, taxa = c("Whale"), exclude_taxa = TRUE)
align_plot <- plot_alignment(plot_frame, legend_title = "") ## Remove the title

Example output

Welcome to alignfigR!

alignfigR documentation built on May 1, 2019, 9:11 p.m.