Documentation examples #391
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# Conflicts: # pertpy/tools/_distances/_distances.py
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Oct 16, 2023
…o dev_metadata * 'dev_metadata' of https://github.com/theislab/pertpy: Documentation examples (#391) [pre-commit.ci] pre-commit autoupdate (#395) Speed up tests by subsampling (#398) Installation Apple Silicon (#393) Add new distances (#304) Fix cinema OT test (#392) [pre-commit.ci] pre-commit autoupdate (#390) wasserstein distance return type float (#386) fix naming of example data in doc examples (#387) Add test for test_distances.py Catches error as reported in Issue #385. Fix mypy warning for distances Type hint for `groups` reverted, Iterable is too general.
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PR Checklist
Description of changes
So far, most public methods in the Documentation did not have examples showing how to use the respective method. Here, we add examples for public methods for the docs to facilitate usage.
Technical details
The following methods do not have a working example yet:
pertpy.plot.coda.effects_umap- @Zethson, could you please add / finish the example there?pertpy.plot.dialogue.pairplot(requires the creation of a DialoguePlot object first, which does not match the usual convention for creating plots (I'll open an issue)set_fdrforpertpy.tools.Tasccoda: set_fdr is currently implemented in base_coda but needs to work differently for scCODA and tascCODA (currently it works only for scCODA; I'll open an issue)pertpy.plot.milo.nhood_graph(currently throws a StopIteration error; I'll open an issue)