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https://github.com/rrrlw/helixvis

Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.
https://github.com/rrrlw/helixvis

biochemistry cran helical-wheels peptide-sequences r visualization wenxiang-diagrams

Last synced: about 9 hours ago
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Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.

Host: GitHub
URL: https://github.com/rrrlw/helixvis
Owner: rrrlw
License: gpl-3.0
Created: 2018-05-18T23:34:09.000Z (over 6 years ago)
Default Branch: master
Last Pushed: 2019-01-25T23:11:20.000Z (almost 6 years ago)
Last Synced: 2024-11-23T21:06:01.897Z (about 2 months ago)
Topics: biochemistry, cran, helical-wheels, peptide-sequences, r, visualization, wenxiang-diagrams
Language: R
Homepage: https://rrrlw.github.io/helixvis
Size: 1.02 MB
Stars: 2
Watchers: 3
Forks: 0
Open Issues: 1
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        # helixvis: Visualize alpha-helical peptide sequences

[![Travis Build Status](https://travis-ci.org/rrrlw/helixvis.svg?branch=master)](https://travis-ci.org/rrrlw/helixvis)

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[![Coverage Status](https://img.shields.io/codecov/c/github/rrrlw/helixvis/master.svg)](https://codecov.io/github/rrrlw/helixvis?branch=master)

[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

[![CRAN version](http://www.r-pkg.org/badges/version/helixvis)](https://CRAN.R-project.org/package=helixvis)

[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/helixvis)](https://CRAN.R-project.org/package=helixvis)

[![JOSS DOI](https://joss.theoj.org/papers/10.21105/joss.01008/status.svg)](https://doi.org/10.21105/joss.01008)

[![Zenodo DOI](https://zenodo.org/badge/134013329.svg)](https://zenodo.org/badge/latestdoi/134013329)

## Purpose

Built by the lab of [Regina Stevens-Truss, PhD](https://reason.kzoo.edu/chem/faculty/regina/) (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](https://CRAN.R-project.org/package=helixvis).

The development version is available on [GitHub](https://github.com/rrrlw/helixvis).

The following R code can be used to install and load helixvis.

```r

# 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).

```r

# 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](https://github.com/rrrlw/helixvis/issues) of the [helixvis GitHub repository](https://github.com/rrrlw/helixvis).

Contributions (bug fixes, new features, etc.) are welcome via pull requests (generally from forked repositories).