Visualize Alpha-Helical Peptide Sequences

Create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences. Specifically, allows the user to programmatically generate helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of alpha-helical oligopeptides. See Wadhwa RR, et al. (2018) for more information.


helixvis has the following advantages over most web servers that draw helical wheels and/or wenxiang diagrams:

  • helixvis handles both types of diagrams. Most web servers draw either helical wheels or wenxiang diagrams; having a single tool that can draw both saves time.

  • helixvis handles multiple sequences. Most web servers take a single input sequence, and require the user to download each sequence's corresponding visualization individually. The ability to generate a visualization for an entire database of sequences with a single line of code makes helixvis a useful tool.

  • helixvis is installed locally. An internet connection is not required to use helixvis.

  • helixvis is open-source. With an active, public GitHub repository (https://github.com/rrrlw/helixvis), the code for helixvis is available to all users. Contributions, issue reports, and bug fixes are encouraged!

How do I use helixvis?

The helixvis package has two primary workhorse functions:

  • draw_wheel

  • draw_wenxiang

How do I get helixvis?

You can download helixvis by using the following R code:

install.packages("devtools")
devtools::install_github("rrrlw/helixvis")

We hope that helixvis will soon be available on CRAN.

Upcoming features

The following features are being planned for a minor release (or many minor releases):

  • Customizable image sizes (instead of only the default 600x600 pixels)

  • Customizable color choices for individual residues

  • Faster runtime for draw_* functions

The following features are being planned for a major release:

  • Helical nets. Although an older form of visualization, helical nets still have utility. A draw_net function is the goal.

Contact

Please report any issues at https://github.com/rrrlw/helixvis/issues. Find more contact information in the DESCRIPTION file at the top level of the helixvis GitHub repository at https://github.com/rrrlw/helixvis.

News

Reference manual

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install.packages("helixvis")

1.0.1 by Raoul Wadhwa, 10 months ago


https://github.com/rrrlw/helixvis


Report a bug at https://github.com/rrrlw/helixvis/issues


Browse source code at https://github.com/cran/helixvis


Authors: Raoul Wadhwa [cre, aut] , Regina Stevens-Truss [aut] , Vigneshwar Subramanian [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports ggplot2, ggforce, rlang

Suggests knitr, rmarkdown, covr, testthat


See at CRAN