Addition of a new SNP Distance Search function for the Cov2Tree #592
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Added snpModal.jsx, main component for rendering SNP Distance Search
Added two files, nodeMapper.js and extract.js, which are used in generating the output for the SNP distance search. nodeMapper makes a map of the entire tree in order to perform downwards traversal, and extract does the actualn traversal and calculation of SNP distance.
|
@DLiarakos is attempting to deploy a commit to the theosanderson's projects Team on Vercel. A member of the Team first needs to authorize it. |
for more information, see https://pre-commit.ci
|
The latest updates on your projects. Learn more about Vercel for Git ↗︎
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Created a modal popup which appears when clicking a button set to only appear for the Cov2Tree. Users can then input a name of a node somewhere on the tree and a SNP distance threshold. Upon hitting search and after around a minute of processing time, the modal will then display a table which contains the first 100 samples on the tree within the specified distance, as well as the distance itself and the sample's PANGO lineage and GenBank Accession Number. The table also includes a button to download the full list of samples in .tsv format. As for additions to the codebase, this is all accomplished through 2 standalone JS scripts (nodeMapper.js and extract.js) and a new component I designed myself (snpModal.jsx), with only a small change to the SearchPanel component, meaning the overall code base for Taxonium is changed very little.