[REF,ENH] Modifies and adds normalization procedures #119
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
Pull Request Test Coverage Report for Build 354
💛 - Coveralls |
Codecov Report
@@ Coverage Diff @@
## master #119 +/- ##
==========================================
+ Coverage 84.26% 90.49% +6.23%
==========================================
Files 33 32 -1
Lines 2180 1989 -191
==========================================
- Hits 1837 1800 -37
+ Misses 343 189 -154
Continue to review full report at Codecov.
|
Doesn't currently do anything, but it's there! For eventually doing something
Don't normalize donor expression after ROI aggregation
Better (sort of) NaN handling in correct.normalize_expression
Because we were removing all the samples who hadn't been assigned a label prior to normalization when `exact=False` the samples that were being used were all NaN. Now, we only remove samples without labels if `exact=True` (default).
They aren't handled elegantly (should they be?)
Need to handle NaNs to avoid warnings
Fixes this by dropping samples not assigned to a region rather than setting the values to NaN.
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Outdated suggestions cannot be applied.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.
Adds new normalization functions and modifies when/where normalization occurs in primary workflow.
To Do:
get_expression_data()workflow