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ggmsa R Package

repository·devel·Indexed 42 days ago

https://github.com/yulab-smu/ggmsa

An R package for the visual exploration, visualization, and annotation of multiple sequence alignments (MSA) for protein, DNA, and RNA sequences. It provides functions like ggmsa(), geom_seqlogo(), and geom_msaBar() to create publication-quality MSA plots.

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What's inside ggmsa

  1. Overview of ggmsa

    devel
    ggmsa is an R package designed for the visualization and annotation of multiple sequence alignments (protein, DNA, or RNA). It provides a simple and powerful interface to create publication-quality MSA plots.

  2. Install ggmsa

    devel

    You can install the released version of ggmsa via Bioconductor or the development version via GitHub using devtools.

    Via Bioconductor (Recommended)

    if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggmsa")

    Via GitHub (Development Version)

    if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")
    if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("ggmsa")

  3. Quick Example of ggmsa usage

    devel

    To create a publication-quality multiple sequence alignment (MSA) visualization, use the ggmsa() function. You can extend the plot using additional layers like geom_seqlogo() and geom_msaBar().

    In this example, we visualize a specific region of a protein sequence file.

    library(ggmsa)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(protein_sequences, start = 221, end = 280, char_width = 0.5, seq_name = TRUE) + 
  geom_seqlogo() + 
  geom_msaBar()