helixvis: Visualize alpha-helical peptide sequences

License: GPL v3 CRAN version Downloads

JOSS DOI Zenodo DOI

Purpose

Built by the lab of Regina Stevens-Truss, PhD (Professor & Chair, Department of Chemistry, Kalamazoo College), helixvis can be used to create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences. Specifically, this package allows the user to programmatically generate helical wheels and wenxiang diagrams to provide a bird’s eye, top-down view of alpha-helical oligopeptides. Although other tools exist to complete this task, they generally provide a graphical user interface for manual input of peptide sequences, without allowing for programmatic creation and customization of visualizations. Programmatic generation of helical wheels in open source R provides multiple benefits, including:

  • quick and easy incorporation of wheels into Rmarkdown documents
  • rapid generation of many peptides (e.g. all the elements of a peptide database) without manual steps
  • programmatic customization of visualizations using ggplot2
  • reproducibility: practically zero manual steps required for design and creation of helical wheels and wenxiang diagrams

Installation

helixvis is available on CRAN. The development version is available on GitHub. The following R code can be used to install and load helixvis.

# install from CRAN
install.packages("helixvis")

# install development version from GitHub repository
devtools::install_github("rrrlw/helixvis", build_vignettes = TRUE)

# load for use
library("helixvis")

Usage

The following code demonstrates the use of helixvis to using sample data included in the package (development version only).

# load helixvis
library("helixvis")

# load sample dataset
data("sequence")

# visualize helical wheel from first peptide in sample data
draw_wheel(sequence$Seq[1])

# save to workspace
ggplot2::ggsave(paste(sequence$Name[1], ".png", sep = ""),
                width = 6, height = 6)

# visualize wenxiang diagram from second peptide in sample data
draw_wenxiang(sequence$Seq[2])

# save to workspace
ggplot2::ggsave(paste(sequence$Name[2], ".png", sep = ""),
                width = 6, height = 6)

Contributions

Please report any bugs, suggestions, etc. on the issues page of the helixvis GitHub repository. Contributions (bug fixes, new features, etc.) are welcome via pull requests (generally from forked repositories).