Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add filtering to LinearApolloDisplay #450

Open
garrettjstevens opened this issue Sep 24, 2024 · 1 comment · May be fixed by #469
Open

Add filtering to LinearApolloDisplay #450

garrettjstevens opened this issue Sep 24, 2024 · 1 comment · May be fixed by #469

Comments

@garrettjstevens
Copy link
Contributor

garrettjstevens commented Sep 24, 2024

JBrowse has track filtering, and one way of accessing it is through the track menu. The UI for adding filters looks like this:
image

Apollo needs something similar, although because the Apollo track configuration is dynamically generated, we can perhaps do something different from jexl.

Types of filters users have requested:

  • Filter by feature type, but ontology-aware (e.g. show all genes and is_a related terms, such as protein_coding_gene and pseudogene)
  • Filter by specific feature type (e.g. only genes and not pseudogenes)
  • Filter by a custom feature attribute
@garrettjstevens
Copy link
Contributor Author

garrettjstevens commented Oct 16, 2024

This will be accessible by a track menu item, the same idea as the menu items added in #461. The onClick for that menu item will queue a dialog (similar to the menu items in packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/addMenuItems.ts). For now the dialog can be a strict feature type filter, with a drop-down to choose a feature type like the drop-down in packages/jbrowse-plugin-apollo/src/components/AddChildFeature.tsx.

The filtered types can be stored as a string array in the .props of packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts, and then featuresMinMax, featureLayouts, in that file can check the filtered types and skip the features if necessary.

@shashankbrgowda shashankbrgowda linked a pull request Oct 21, 2024 that will close this issue
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
Status: No status
Development

Successfully merging a pull request may close this issue.

1 participant