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
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")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)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).
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