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helixvis: Visualize alpha-helical peptide sequences\n\n[![Travis Build Status](https://travis-ci.org/rrrlw/helixvis.svg?branch=master)](https://travis-ci.org/rrrlw/helixvis)\n[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/rrrlw/helixvis?branch=master\u0026svg=true)](https://ci.appveyor.com/project/rrrlw/helixvis)\n[![Coverage Status](https://img.shields.io/codecov/c/github/rrrlw/helixvis/master.svg)](https://codecov.io/github/rrrlw/helixvis?branch=master)\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![CRAN version](http://www.r-pkg.org/badges/version/helixvis)](https://CRAN.R-project.org/package=helixvis)\n[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/helixvis)](https://CRAN.R-project.org/package=helixvis)\n\n[![JOSS DOI](https://joss.theoj.org/papers/10.21105/joss.01008/status.svg)](https://doi.org/10.21105/joss.01008)\n[![Zenodo DOI](https://zenodo.org/badge/134013329.svg)](https://zenodo.org/badge/latestdoi/134013329)\n\n## Purpose\n\nBuilt by the lab of [Regina Stevens-Truss, PhD](https://reason.kzoo.edu/chem/faculty/regina/) (Professor \u0026 Chair, Department of Chemistry, Kalamazoo College), helixvis can be used to create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences.\nSpecifically, 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.\nAlthough 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.\nProgrammatic generation of helical wheels in open source R provides multiple benefits, including:\n\n* quick and easy incorporation of wheels into Rmarkdown documents\n* rapid generation of many peptides (e.g. all the elements of a peptide database) without manual steps\n* programmatic customization of visualizations using ggplot2\n* reproducibility: practically zero manual steps required for design and creation of helical wheels and wenxiang diagrams\n\n## Installation\n\nhelixvis is available on [CRAN](https://CRAN.R-project.org/package=helixvis).\nThe development version is available on [GitHub](https://github.com/rrrlw/helixvis).\nThe following R code can be used to install and load helixvis.\n\n```r\n# install from CRAN\ninstall.packages(\"helixvis\")\n\n# install development version from GitHub repository\ndevtools::install_github(\"rrrlw/helixvis\", build_vignettes = TRUE)\n\n# load for use\nlibrary(\"helixvis\")\n```\n\n## Usage\n\nThe following code demonstrates the use of helixvis to using sample data included in the package (development version only).\n\n\n```r\n# load helixvis\nlibrary(\"helixvis\")\n\n# load sample dataset\ndata(\"sequence\")\n\n# visualize helical wheel from first peptide in sample data\ndraw_wheel(sequence$Seq[1])\n\n# save to workspace\nggplot2::ggsave(paste(sequence$Name[1], \".png\", sep = \"\"),\n                width = 6, height = 6)\n\n# visualize wenxiang diagram from second peptide in sample data\ndraw_wenxiang(sequence$Seq[2])\n\n# save to workspace\nggplot2::ggsave(paste(sequence$Name[2], \".png\", sep = \"\"),\n                width = 6, height = 6)\n```\n\n## Contributions\n\nPlease report any bugs, suggestions, etc. on the [issues page](https://github.com/rrrlw/helixvis/issues) of the [helixvis GitHub repository](https://github.com/rrrlw/helixvis).\nContributions (bug fixes, new features, etc.) are welcome via pull requests (generally from forked repositories).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frrrlw%2Fhelixvis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frrrlw%2Fhelixvis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frrrlw%2Fhelixvis/lists"}