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https://github.com/Appsilon/shiny.molstar
R Shiny wrapper for Mol* (/'molstar/) - A visualization toolkit of large-scale molecular data
https://github.com/Appsilon/shiny.molstar
Last synced: 3 months ago
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R Shiny wrapper for Mol* (/'molstar/) - A visualization toolkit of large-scale molecular data
- Host: GitHub
- URL: https://github.com/Appsilon/shiny.molstar
- Owner: Appsilon
- Created: 2023-02-14T11:04:00.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-07-31T13:07:33.000Z (3 months ago)
- Last Synced: 2024-07-31T16:25:44.148Z (3 months ago)
- Language: R
- Homepage: https://appsilon.github.io/shiny.molstar/
- Size: 13.9 MB
- Stars: 13
- Watchers: 15
- Forks: 1
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
- awesome-shiny-extensions - shiny.molstar - Shiny wrapper for Mol*, a visualization toolkit of large scale molecular data. (Visualization / Biological Data)
README
# shiny.molstar 
> _R Shiny wrapper for Mol* (/'molstar/) - A visualization toolkit of large-scale molecular data_
[](https://github.com/Appsilon/shiny.molstar/actions/workflows/ci.yml)
Based on [Mol*](https://molstar.org) (/'molstar/) and powered by [shiny.react](https://appsilon.github.io/shiny.react/)
We created a R Shiny wrapper based on [shiny.react](https://appsilon.github.io/shiny.react/) and [molstar-react](https://www.npmjs.com/package/molstar-react) _(node.js library)_ that gives all the powerful tools of Mol* open-source toolkit for visualization and analysis of large-scale molecular data.
This package exports three new components that can be used in a Shiny application.
* `Molstar` creates a Molstar visualization of a protein using an URL to a valid filetype supported by Molstar or a "Protein Data Bank" id _(pdbId)_. See more below for available databases to find a valid `pdbId`.
* `AlphaFoldMolstar` similar to the Molstar component, but uses the UniProt id in the AlphaFold database to display the protein.
* `AlphaFoldDetails` creates a component that retrieves details of an AlphaFold protein id _(title, download links and a Predict Aligned Error image)_
### How to find a valid id or url?
A valid `pdbId` can be found in public databases such as:
* [EMBL-EBI database](https://www.ebi.ac.uk/pdbe/entry/search/index/)
* [RSCB.org](https://www.rcsb.org/)
The `uniProtId` can be found in any of the AlphaFold databases:
* [AlphaFold.com](https://alphafold.com/)
## Getting started
To install the package, run:
```{R}
remotes::install_github("Appsilon/shiny.molstar")
```
Take a look at basic [example app](https://github.com/Appsilon/shiny.molstar/blob/main/inst/examples/Minimal.R) to start working with shiny.molstar.
To learn about the Mol* language, follow the [Viewer documentation](https://molstar.org/viewer-docs/).
## Examples
A good way to learn more is to look at the examples. Once you install the library, you can run them with `shiny.molstar::runExample` function.
```{R}
shiny.molstar::runExample("FullPage")
shiny.molstar::runExample("Minimal")
shiny.molstar::runExample("AlphaFold")
shiny.molstar::runExample("AlphaFoldDetails")
```
### Full page example
Creating a full page viewer on a sample molecule _(example also available at `inst/examples/FullPage.R`)_
```{R}
library(shiny)
library(shiny.molstar)
shinyApp(
ui = tagList(
tags$style(HTML("html, body { margin: 0; }")),
Molstar(
pdbId = "1LOL",
useInterface = TRUE,
showControls = TRUE,
showAxis = TRUE
)
),
server = function(input, output) {
}
)
```
### Using AlphaFold database and details
Running an example from the package _(located at `inst/examples/AlphaFoldDetails.R`)_.
You can click on the button on the bottom of the example to get the minimal code to reproduce the same Shiny application _(unstyled and without the footer)_.
```{R}
shiny.molstar::runExample("AlphaFoldDetails")
```
## Appsilon
Appsilon is a **Posit (formerly RStudio) Full Service Certified Partner**.
Learn more at [appsilon.com](https://appsilon.com).
Get in touch [[email protected]](mailto:[email protected])
Explore the [Rhinoverse](https://rhinoverse.dev) - a family of R packages built around [Rhino](https://appsilon.github.io/rhino/)!
