helixvis: Visualize alpha-helical peptide sequences in R
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
# 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$Seq) # save to workspace ggplot2::ggsave(paste(sequence$Name, ".png", sep = ""), width = 6, height = 6) # visualize wenxiang diagram from second peptide in sample data draw_wenxiang(sequence$Seq) # save to workspace ggplot2::ggsave(paste(sequence$Name, ".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).