Add more notebooks and plots for pub #21
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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
- 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
functions no longer used
Add notebook for comparing pools vs wells. Used for Figure 7 in the pub.
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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.
Correct ylabel and take stabs at linting issue
Make use of functionality in `stats_testing` to clean up notebook
Make use of functionality in `stats_testing` to clean up notebook
caught linting issue before it caught me!
Remove axis grid lines.
Remove superfluous catch warnings.
remove grid lines
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Looks good! The annotation function is really nice (I actually assumed at first it was some built-in function in seaborn that I'd never seen!). It could be worth pulling that into a utility function in arcadia-pycolor at some point, though I could imagine it might be tricky to get it work robustly for many different data and plots types...
I'm not sure how weird "weird" is but if it's truly super messed up somehow you could 1) rebase again and squash the messed up commits or 2) squash-merge the PR (which collapses the entire PR into a single commit to |
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Re: stats annotations on plots To your point about getting it to work robustly, I fully agree and am kind of hesitant to dedicate any more time to it at the moment... |
Interesting. That's a bummer. Though I kinda get it - it seems like the kind of thing that's both finicky/annoying to maintain and is also such a niche that it'll never be super widely used. In any case, agree that it's not something that we should spend a ton of time on. |
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`.
This PR adds additional notebooks and plots to accompany the forthcoming pub. Now also makes use of
arcadia_pycolor!Major additions
notebooks/3_motility-analysis-in-pools.ipynbnotebooks/4_compare-motility-in-pools-vs-wells.ipynbutils.pyfor annotating statistical significance in plotsMinor additions/changes
substratetovessel_typeresults/plotting_pools.pyAside: commit history seems weird -- is that because of rebase?
PR checklist
condaenvironments.