Added tutorial of external velocity calculation and integration #735
Conversation
This file contains hidden or 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
… in snapshots - Added a helper method _get_column_type to determine simplified type descriptions for DataFrame columns. - Updated the _snapshot method to capture column types for 'obs' and 'var' in the snapshot dictionary, improving clarity in data structure comparisons. - Modified print section methods to display column descriptions alongside keys for better visibility in output.
…velocity function - Introduced the @monitor decorator to track function execution. - Updated variable handling to set 'use_for_dynamics' and 'use_for_transition' based on the presence of 'use_for_pca' in adata.var, ensuring consistent behavior.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.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.
This pull request introduces several improvements and new features to the tracking and reporting of data changes in the
dynamopackage, as well as minor updates to tutorials and submodules. The main focus is on enhancing the monitoring of function calls and improving the detail and clarity of change reports for AnnData objects. Additionally, new monitoring decorators are applied to core functions, and tutorial documentation is updated.Tracking and reporting enhancements:
_track.pymonitoring system to capture and display column data types inobsandvarinstead of just column names, providing more informative reports on data changes. This includes a new_get_column_typehelper and updates to_snapshotand_print_reportto show type information. (dynamo/tools/_track.py) [1] [2]unskeys to include a✚symbol for added keys, making additions more visually distinct. (dynamo/tools/_track.py)Monitoring and function instrumentation:
@monitordecorator to theextveloandpseudotime_velocityfunctions, enabling automatic tracking of changes to AnnData objects during their execution. (dynamo/tools/_extvelo.py,dynamo/tools/pseudotime_velocity.py) [1] [2]Functionality improvements:
pseudotime_velocityto automatically setuse_for_dynamicsanduse_for_transitioninadata.var, copying fromuse_for_pcaif present, or defaulting toTrueotherwise, ensuring downstream compatibility. (dynamo/tools/pseudotime_velocity.py)Documentation and tutorials:
202_extveloto the conventional index, and updated thenotebookssubmodule to the latest commit. (docs/tutorials/index_conventional.md,docs/tutorials/notebooks) [1] [2]