dms-view

Sarah Hilton*, John Huddleston*, Allison Black, Khrystyna North, Adam Dingens, Trevor Bedford, and Jesse Bloom. (* equal contribution)

dms-view is an interactive visualization tool for deep mutational scanning experiments. You can find the tool at dms-view.github.io.

This repo contains the JavaScript and D3 code to run the tool itself. For information on how to use the tool, please see the documentation.

Please raise issues with the tool at github.com/dms-view/dms-view.github.io/issues.

Organization

The code and data for the docs, the tool, and the paper are found in the following directories:

./assets/

This directory contains the code for the dms-view.github.io tool.

• ./assets/css/ contains the CSS stylesheet.
• ./assets/fonts/ contains the font file for the logoplots
• ./assets/images/ contains static images used in the docs and the tool.
• ./assets/js/ contains the JavaScript code to run the tool.

./data/

This directory contains the default data for the tool from Lee et al., 2019.

./docs/

This directory contains the code for the dms-view docs.

./_layouts/

This directory contains the templates for the docs.

./paper/

This directory contains the code for the dms-view paper.

Testing

As described above, dms-view uses a default dataset from Lee et al., 2019. Below are two descriptions of different combinations of dropdown menus and selected sites, as well as pictures of what the tool should look like.

View 1 (default view)

When dms-view.github.io is loaded, the default view of the data section should look as follows:

Load view 1 to explore this example.

View 2

The data section should look as follows when you change

• condition to "2009-age-65"
• mutation metric to "Natural Frequencies"
• selected sites 144, 159, 192, 193, 222, 224

Load view 2 to explore this example.

Other views

In the documentation, we use dms-view to recreate paper figures for two different studies. Please see dms-view.github.io/docs/casestudies to see these examples

Contribute to dms-view

We welcome contributions to the dms-view code and documentation. Consult our contributing guide for more details.

Have you used dms-view for your own analyses and think these would make a great case study for our documentation? Open a new issue on GitHub to let us know more.

Building the complete website locally

Build the complete dms-view website locally with Jekyll and Bundler.

# Install dependencies for Jekyll.
bundle install

# Build the site.
bundle exec jekyll serve

View the local website in your browser at http://localhost:4000/.

See the documentation for more details on deploying or developing dms-view locally.