Add SpatialQuery notebook #107
Open
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
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Outdated suggestions cannot be applied.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.
@ShaokunAn This is largely adapted from https://github.com/ShaokunAn/Spatial-Query/blob/main/examples/SpatialQuery-example.ipynb
(Note: It requires a more recent version of
vitessceto be installed in workspaces for all of the features to work. I added a spatial-query installation command to the notebook (but not a Vitessce one as I know that is typically installed at the workspace environment level). It currently installs from GitHub, I am not sure if this should be switched to install SpatialQuery from PyPI).I am not sure if the
metadata.jsonis correct - we may also want to add more datasets to the list on line 14 - @ShaokunAn do you want to update that list? Currently it includes the one HuBMAP ID from the example notebook linked above.