Visualizing alpha-helical peptides in R with helixvis
Visualizing alpha-helical peptides in R with helixvis - Published in JOSS (2018)
Science Score: 93.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
○Committers with academic emails
-
○Institutional organization owner
-
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.
Basic Info
- Host: GitHub
- Owner: rrrlw
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://rrrlw.github.io/helixvis
- Size: 1.02 MB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 2
- Releases: 3
Topics
Metadata Files
README.md
helixvis: Visualize alpha-helical peptide sequences
Purpose
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
Installation
helixvis is available on CRAN. The development version is available on GitHub. 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::installgithub("rrrlw/helixvis", buildvignettes = 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 of the helixvis GitHub repository. Contributions (bug fixes, new features, etc.) are welcome via pull requests (generally from forked repositories).
Owner
- Name: Raoul
- Login: rrrlw
- Kind: user
- Location: Cleveland, Ohio
- Repositories: 10
- Profile: https://github.com/rrrlw
Medicine, mathematics, programming.
JOSS Publication
Visualizing alpha-helical peptides in R with helixvis
Authors
Department of Chemistry, Kalamazoo College, Kalamazoo, MI 49006, USA, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
Department of Chemistry, Kalamazoo College, Kalamazoo, MI 49006, USA
Editor
Yo Yehudi
Tags
antimicrobial peptide alpha helix wenxiang diagram helical wheel visualizationGitHub Events
Total
Last Year
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Raoul Wadhwa | r****a@g****m | 136 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 2
- Average time to close issues: 3 days
- Average time to close pull requests: less than a minute
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 1.44
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rrrlw (6)
- tomsing1 (3)
Pull Request Authors
- rrrlw (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 228 last-month
- Total docker downloads: 17
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
cran.r-project.org: helixvis
Visualize Alpha-Helical Peptide Sequences
- Homepage: https://github.com/rrrlw/helixvis
- Documentation: http://cran.r-project.org/web/packages/helixvis/helixvis.pdf
- License: GPL-3
-
Latest release: 1.0.1
published over 7 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.10 depends
- ggforce >= 0.1.3 imports
- ggplot2 >= 3.0.0 imports
- rlang >= 0.2.2 imports
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests