https://github.com/simeross/ggseqalign
R package to plot pairwise alignments of strings, specifically DNA/AA sequences.
https://github.com/simeross/ggseqalign
alignment bioinformatics ggplot2-enhancements minimalistic r visualization
Last synced: 4 months ago
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R package to plot pairwise alignments of strings, specifically DNA/AA sequences.
- Host: GitHub
- URL: https://github.com/simeross/ggseqalign
- Owner: simeross
- Created: 2024-05-21T17:28:42.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-03-03T14:31:38.000Z (over 1 year ago)
- Last Synced: 2025-10-20T14:41:50.215Z (8 months ago)
- Topics: alignment, bioinformatics, ggplot2-enhancements, minimalistic, r, visualization
- Language: R
- Homepage:
- Size: 956 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
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README
## 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
### Bioconductor
I recommend installing `ggseqalign` from Bioconductor.
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggseqalign")
```
### GitHub (R version 4.4.0 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")
```
### 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")
```
## 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](https://github.com/simeross/ggseqalign/issues)
### 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](https://eeagrants.org/archive/2014-2021/projects/PL-Basic%20Research-0012)