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<img src="inst/hexlogo/hexlogo.png" alt="ggseqalign hex sticker" width="400"/> ## 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`. I am currently working on a Bioconductor submission for this package, but it should be usable in its current state. ## 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("") ``` 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install.packages("BiocManager") BiocManager::install(version = "devel") BiocManager::valid() # checks for out of date packages BiocManager::install("ggseqalign") ``` See the [BiocManager]( vignette for instructions on using multiple versions of Bioconductor.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("") ``` ### 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) ``` <img src="inst/figs/rm_ex1.png" alt="output of the code above" width="400"/> 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 ``` <img src="inst/figs/rm_ex2.png" alt="output of the code above" width="400"/> 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()) ``` <img src="inst/figs/rm_ex3.png" alt="output of the code above" width="400"/> ### 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](