New Feature: Forestplot for CoxPH model #838
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Hm checking into the failed docs build |
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How did you make the option to have this dashed vertical bar before? That seemed quite nice! |
Co-authored-by: Eljas Roellin <[email protected]>
Co-authored-by: Eljas Roellin <[email protected]>
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And at the end flexing this feature in the survival notebook would be great.. :) |
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sorry, misclicked! |
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Medcat no more a doc build dependency; asked about state of Python 3.12 CogStack/MedCAT#510 |
for more information, see https://pre-commit.ci
Co-authored-by: Lukas Heumos <[email protected]>
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One a sidenote, there should be a pull request template with checkmarks and some suggested subtitles for the first comment, which we should use for all pull requests ideally. |
ehrapy/plot/_survival_analysis.py
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| Args: | ||
| adata: :class:`~anndata.AnnData` object containing all observations in `.uns`. | ||
| uns_key: Key in `.uns` where the CoxPHFitter object is stored. |
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Change to a brief description of the result that is stored there; mention and reference the ehrapy function who writes the results into this field
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This should be updated or at least synced with the uns_key argument description, where there is also still the wrong description about the CoxPHFitter object
ehrapy/plot/_survival_analysis.py
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| Args: | ||
| adata: :class:`~anndata.AnnData` object containing all observations in `.uns`. | ||
| uns_key: Key in `.uns` where the CoxPHFitter object is stored. | ||
| labels: List of labels for each coefficient, default uses the index of the coxph.summary. |
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what is coxph.summary? (I know, but users should be able to understand what this is doing by just following our documentation)
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I think in the updates of the current review request, this is still as it looked when I made this comment? :)
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My bad, very sorry, i should first fix it in my editor and then sign of here.
Co-authored-by: Eljas Roellin <[email protected]>
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Quick question on the additional functionality with the secondary helper plots "below" the forestplot; are you planning to add them, or are they too unstable/time consuming to set up at this stage? (fine if this is the case of course, could also be a later enhancement!) |
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There is no table intended under the forest plot. i believe you mean #742 |
Ah yes, had mixed this up, thanks! |
… of adata and summary table
PR Checklist
Resolves #743
docsis updatedThis pull request introduces a new plotting function for Cox Proportional Hazards models and updates related documentation and tests. The most important changes include adding a new plotting function, updating imports, and adding new tests.
New Feature:
cox_ph_forestplotfunction to generate forest plots for Cox Proportional Hazards models inehrapy/plot/_survival_analysis.py.Documentation Updates:
docs/usage/usage.mdto includeplot.cox_ph_forestplotin the list of available plotting functions.Import Adjustments:
ehrapy/plot/__init__.pyto import the newcox_ph_forestplotfunction.ehrapy/plot/_survival_analysis.pyto include necessary modules for the new plotting function.Testing Enhancements:
tests/plot/test_survival_analysis.pyto validate thecox_ph_forestplotfunction.tests/_scripts/coxph_forestplot_create_expected.ipynbto generate expected output for the new plotting function.Additional Fixtures:
mimic_2intests/conftest.pyto provide test data for the new function.