Figure 3 #29
Figure 3 #29
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Additional details and impacted files@@ Coverage Diff @@
## main #29 +/- ##
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+ Coverage 46.81% 77.79% +30.98%
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Files 6 11 +5
Lines 361 653 +292
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+ Hits 169 508 +339
+ Misses 192 145 -47
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Pull Request Overview
This PR implements a new figure generation module (Figure 3) that analyzes the correlation between component weights and cell counts in CC-PF2 decomposition. The PR also adds comprehensive testing infrastructure for automatic figure validation and makes several improvements to the codebase.
Key changes include:
- Implementation of Figure 3 showing rank-1 component weight vs. sample size analysis
- Addition of automated figure testing framework to validate all figure generation scripts
- Updates to CC-PF2 implementation to properly handle component weights and standardization
Reviewed Changes
Copilot reviewed 8 out of 11 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| pyproject.toml | Added tensorly-viz dependency for visualization support |
| cellcommunicationpf2/tests/test_figures.py | New automated testing framework for figure generation validation |
| cellcommunicationpf2/tests/test_ccpf2.py | Updated tests to handle new CC-PF2 output format with weights |
| cellcommunicationpf2/figures/figure3.py | New figure showing correlation between component weights and cell counts |
| cellcommunicationpf2/figures/figure2.py | Comprehensive stability analysis figure with FMS calculations |
| cellcommunicationpf2/figures/figure1.py | Enhanced factor visualization with improved plotting functions |
| cellcommunicationpf2/figures/commonFuncs/plotFactors.py | Improved factor plotting with better error handling and visualization |
| cellcommunicationpf2/cc_pf2.py | Enhanced CC-PF2 implementation with proper weight handling and standardization |
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@Nathaniel-github This looks fine to me! |
| @@ -84,3 +89,89 @@ def genFigure(): | |||
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| print(f"Figure {sys.argv[1]} is done after {time.time() - start} seconds.\n") | |||
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| def correct_conditions(X: anndata.AnnData): | |||
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These don't seem directly related to the figures, so perhaps they should go outside of the figures folder?
| assert fig is not None | ||
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| # Close the figure to clean up | ||
| plt.close(fig) |
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