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Add filtering to LinearApolloDisplay #450

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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

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@garrettjstevens
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garrettjstevens commented Sep 24, 2024 •
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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
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garrettjstevens commented Oct 16, 2024 •
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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
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Add filtering to LinearApolloDisplay shashankbrgowda/Apollo3
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