Intro

This is an R package to perform pairwise alignments of strings and plot them in a minimal style that is suitable for strings/sequences of any length. It is compatible with ggplot2 and DNA/AA sequence objects from Biostrings.

Installation

R version 4.4 and above

ggseqalign can be installed from its original source on GitHub (requires devtools).

install.packages("devtools")
devtools::install_git("https://github.com/simeross/ggseqalign.git")

Until the next major version of Bioconductor (expected October 2024), ggseqalign can be installed from the Devel version of Bioconductor.

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::valid()              # checks for out of date packages
BiocManager::install("ggseqalign")

See the BiocManager vignette for instructions on using multiple versions of Bioconductor.

earlier R versions

If you use any R version older than 4.4.0, install version 0.1.0 of this package.

install.packages("devtools")
devtools::install_git("https://github.com/simeross/ggseqalign@e1a2e99ee7d079d2e4331bc101382cfebe125fa8")

Bioconductor

This will be updated for installation instructions from Bioconductor if the submission is successful.

Quick start

All you need is this package and some strings to align and you are ready to go.

library(ggseqalign)

query_strings <- (c("boo", "fibububuzz", "bozz", "baofuzz"))
subject_string <- "boofizz"

alignment <- alignment_table(query_strings, subject_string)

plot_sequence_alignment(alignment)

To align DNA or AA sequences from a fasta file, read them in with Biostrings

library(ggseqalign)
library(Biostrings)

query_sequences <- Biostrings::readDNAStringSet("my_multi_sequence_fasta.fa")
subject_sequence <- Biostrings::readDNAStringSet("my_reference_fasta.fa")

alignment <- alignment_table(query_sequences, subject_sequence)

pl <- plot_sequence_alignment(alignment)
pl

To style the plot generated above to your own taste, use ggplot2, for example:

library(ggplot2)
 
pl +
 ylab("Sequence variants") +
 xlab("Length in bp") +
 scale_color_viridis_d() +
 theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
    axis.title = element_text())

Bug reports

If you come across bugs, please submit an issue

License

Artistic License 2.0.

Credit

The research and data generation that was a major motivation for me to finally create this package has received funding from the Norwegian Financial Mechanism 2014-2021, project DivGene: UMO-2019/34/H/NZ9/00559