Mark Keller

Use zarrita.js-style strided arrays everywhere

1

**User story** Currently we are not consistent/great about internal representations of large arrays for expression/matrix data (all features and selected features) **Preferred solution** **Possible alternatives**

Stratification of violin plot based on sample sets

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Fixes #1782 Fixes #1774 Fixes #1776 Fixes #1040 Closes #1383 TODO: - [x] dot plot - [x] dot plot stratified by sample set ([example](https://user-images.githubusercontent.com/39313061/167825246-138d8aeb-5366-43cf-bc41-45764f8a45f5.png)) - [ ] Normalized expression for...

**User story** Currently, this line https://github.com/vitessce/vitessce/blob/e9ded44248fa50118be3de4c7848d2fc937ef37c/packages/view-types/obs-sets-manager/src/ObsSetsManagerSubscriber.js#L102 causes an infinite loop in WebSocket-syncing settings. We need to figure out an alternative approach to prevent this. **Preferred solution** - We should check...

**User story** Currently, user-defined data (e.g., lassos to create new cell sets) are stored directly in the coordination space in the config as JSON. When the user selects multiple times,...

```[tasklist] ### Tasks - [ ] Ignore lower resolutions coordination type or https://github.com/vitessce/vitessce/issues/1483 (https://portal.hubmapconsortium.org/search?mapped_data_types[0]=NanoDESI&entity_type[0]=Dataset) - [x] Figure out solution for auto-initialization (https://github.com/vitessce/vitessce/pull/1758) - [ ] Automatic upgrade from spatial to...

Support h5ad via reference spec

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Fixes #483 Depends on https://github.com/manzt/zarrita.js/pull/153 #### Background Create a reference spec JSON for a local or remote H5AD file using kerchunk: ```python from kerchunk.hdf import SingleHdf5ToZarr import json h5_url =...

Document the expected units for spatial coordinates (e.g., obsSpots, obsPoints) and relationship to pixel units

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**User story** We use the DeckGL ScatterplotLayer to render spots. This means that `spatialSpotRadius` corresponds to `getRadius` with `radiusUnits: 'meters'` which is the same as `radiusUnits: 'common'` because we use...

Enable physical size-based spot sizing

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**Describe the bug** **To Reproduce** **Data sharing** **Expected behavior** **Screenshots** **Configuration** **Environment:** - Release or git hash: - Browser: - Browser version:

**User story** Enable usage of color scales from: - https://personal.sron.nl/~pault/#fig:scheme_bright - https://matplotlib.org/stable/users/explain/colors/colormaps.html#qualitative **Preferred solution** Add a coordination type such as `obsSetColormap` which will be used for any obsSets for which...

**User story** For the websocket support and for provenance tracking, we want to ignore initialization-related config changes, but there is currently no way to distinguish these from interaction-related config changes....