align_plot_dna: Plot DNA alignments

In j-a-thia/genomalicious: A smorgasbord of R functions for population genomic analyses

Plot DNA alignments

Description

This function takes in an alignment of DNA sequences in a matrix format and returns a plot of that alignment.

Usage

align_plot_dna(
  alignMat,
  nuc_colours = NULL,
  other_colours = NULL,
  gap_colour = NA,
  border_colour = NA,
  pos_vec = NULL,
  show_bases = TRUE,
  base_size = 3,
  show_legend = FALSE
)

Arguments

alignMat	Matrix: the DNA alignments. Rows are the taxa, columns are the base positions, and cells contain the values. Values should be one of 'A', 'T', 'G', 'C', '?', 'N', '-'.
nuc_colours	Character: named vector of colour values for nucleotides. For example, c('A'='blue', 'T'='yellow', 'G'='green', 'C'='red'). Default is NA, which will produce automated colours.
other_colours	Character: named vector colour values for '?' or 'N' values. For example, c('?'='black', 'N'='black'). Default is NA, which will produce automated colours.
gap_colour	Chracter: named vector colour for gaps. For examples, c('-'='white'). Default is NA, which will produce automated colours.
border_colour	Character: single value, the colour of borders around base positions. Default is NA, no assigned border colour.
pos_vec	Integer: a vector of base positions to plot, subsets alignment. Default is NULL, which will plot all bases.
show_bases	Logical: whether the values of bases should be plotted. Default is TRUE.
base_size	Numeric: the text size used for nucleotide bases. Default is 3.
show_legend	Logical: whether a legend should be plotted. Default is FALSE.

Examples

library(genomalicious)

# Create a link to raw external datasets in genomalicious
genomaliciousExtData <- paste0(find.package('genomalicious'), '/extdata')

# Path to the demo FASTA file
fasta <- paste0(genomaliciousExtData, '/data_COI_dna.fasta')

# Multi sequence alignmnet of demo COI data.
aln <- align_many_genes_dna(fasta, gene.names='COI')

# Plot base positions from 598 to 627
align_plot_dna(as.matrix(aln$COI$align), pos_vec=598:627)

# Custom colours, no text, and borders
align_plot_dna(
   as.matrix(aln$COI$align),
   nuc_colours=c(`A`='#ce0073',`T`='#e46adf',`G`='#59A3FF',`C`='#08c7e0'),
   border_colour='grey20',
   pos_vec=598:627,
   show_bases=FALSE
)

j-a-thia/genomalicious documentation built on Oct. 19, 2024, 7:51 p.m.