Rl/add motility analysis notebook #18
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add units to table and reformat a few cells.
subset of metrics for bivariate distributions
- add documentation - move experimental parameters to ../data/experimental_parameters.json - remove superfluous plot
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keithchev
approved these changes
Jul 11, 2024
- rename notebook 2 based off Keith's suggestion from code review on #18 - surprising (to me at least) that switching upper case to lower case does not get flagged as a change so adding a `_` to make the switch to lower case for notebook 1 - also add placeholder doi link for pub
lanery
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Jul 31, 2024
* Create 2_Motility_Analysis_Pools.ipynb * Update 1_Compute-Summary-Motility-Metrics.ipynb add units to table and reformat a few cells. * Update 2_Motility_Analysis_Pools.ipynb subset of metrics for bivariate distributions * fix legend * fix legend * Create 3_Scale-to-Pools.ipynb * Create 4_PCA.ipynb * update notebook formatting * reduce subset of metrics * rename notebooks * update input directories for published dataset * refactor: substrate --> vessel * calculate angular change as a rolling average * Create S1_Quality-Control.ipynb * remove unused import * Update S1_Quality-Control.ipynb * change table style in docs * Update 1_Compute-Summary-Motility-Metrics.ipynb - add documentation - move experimental parameters to ../data/experimental_parameters.json - remove superfluous plot * motility metrics for cc124 instead of cc1373 * Create experimental_parameters.json * Create 2_Quality-Control.ipynb * Delete 2_Analyze-Motility-in-Pools.ipynb * Delete 3_Compare-Pools-vs-Wells.ipynb * Delete 4_Perform-PCA.ipynb * Delete S1_Quality-Control.ipynb * linting: remove unused imports * Rename notebooks - rename notebook 2 based off Keith's suggestion from code review on #18 - surprising (to me at least) that switching upper case to lower case does not get flagged as a change so adding a `_` to make the switch to lower case for notebook 1 - also add placeholder doi link for pub * finish notebook name changes (for now) * Update README.md * Update README.md * start using arcadia-pycolor * Update dev.yml * refactor: "substrate" --> "vessel_type" * minor change to plot layout add `plt.tight_layout()` which throws a `UserWarning` for some reason, so suppress that warning * add `annotate_statistical_significance` Add function for measuring and annotating results of a stats test to a plot. Includes a function for mapping P values to number of asterisks for the annotation. * Create 3_motility-analysis-in-pools.ipynb * add `inner_kws` arg to violinplot * Delete plotting_pools.py functions no longer used * Update 3_motility-analysis-in-pools.ipynb * Update 3_motility-analysis-in-pools.ipynb * Create 4_compare-motility-in-pools-vs-wells.ipynb Add notebook for comparing pools vs wells. Used for Figure 7 in the pub. * add plots to results * Update 3_motility-analysis-in-pools.ipynb * try to fix linting issue * LINTTTTTT * Update 3_motility-analysis-in-pools.ipynb Bit of clean up in light of Dave's feedback on the pub. Removed what would have been Fig 6 (redundant) and updated documentation to match other notebooks. * Update 3_motility-analysis-in-pools.ipynb Correct ylabel and take stabs at linting issue * move stats testing and annotations to separate module * Update 4_compare-motility-in-pools-vs-wells.ipynb Make use of functionality in `stats_testing` to clean up notebook * Update 3_motility-analysis-in-pools.ipynb Make use of functionality in `stats_testing` to clean up notebook * Update 3_motility-analysis-in-pools.ipynb caught linting issue before it caught me! * update plots for pub figures * Update 2_temporal-variation-in-motility-metrics.ipynb Remove axis grid lines. * Update 2_temporal-variation-in-motility-metrics.ipynb Remove superfluous catch warnings. * Update figure-4.svg remove grid lines * Improvements from code review on #21 Add more documentation to notebooks 3 and 4. Combine finding annotation coordinates for both orientations based on Keith's refactoring. Miscellaneous refactoring and cleanup of `stats_testing.py`. * remove unused warnings import
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This PR makes some headway towards finalizing the repo for release with the upcoming pub "A high-throughput imaging assay for phenotyping unicellular swimming", which is currently in review.
Main changes are
2_Quality-Control.ipynb(open to a better name for this) - notebook for regression analysis (used to generate Figure 4 in the pub)1_Compute-Summary-Motility-Metrics.ipynbPR checklist
Fixes #123, Resolves #456).