extract_subalign: Extract subset of sequence alignment

In sjspielman/alignfigR: Visualizing Multiple Sequence Alignments with 'ggplot2'

Description

This function builds a data frame to plot an alignment from a specified subset of the full alignment.

Usage

extract_subalign(seqs, plot_step = 1, tlist = c(), clist = c(),
  texcl = FALSE, cexcl = FALSE, cincl = FALSE)

Arguments

seqs	Sequence list, as parsed by the function 'read_alignment'
plot_step	Step size for alignment block. Default, 1.
tlist	Array of taxa intended to restrict figure to or to exclude from figure.
clist	Array of columns intended to restrict figure to or to exclude from figure.
texcl	Boolean indicating if taxa in tlist should be excluded. Default, False
cexcl	Boolean indicating if columns in clist should be excluded. Default, False
cincl	Boolean indicating if columns in clist should be included. Default, False

Value

plot_frame, a data frame to be plotted

Examples

fasta_file <- system.file("extdata", "example.fasta", package = "alignfigR")
plot_frame <- read_alignment(file = fasta_file)
subset_seq_list <- extract_subalign(plot_frame, tlist = c("Cow", "Human", "Whale"), texcl = TRUE)
subset_seq_list <- extract_subalign(plot_frame, clist = 1:25)

sjspielman/alignfigR documentation built on Oct. 20, 2021, 4:19 p.m.