Adding annotation of potential doublets to anndata obs #193
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…o_split_potential_doublets
ambarrio
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Oct 21, 2024
| @@ -433,4 +437,12 @@ def anndata_metrics(adata: AnnData) -> AnnotateAnndataStatistics: | |||
| if "doublet_size_threshold" in adata.uns: | |||
| metrics["doublet_size_threshold"] = adata.uns["doublet_size_threshold"] | |||
|
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| if "is_potential_doublet" in adata.obs: | |||
| metrics["fraction_potential_doublets"] = adata.obs[ | |||
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If there are no is_potential_doublet here, what will it happen when run mean?
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There will be a key error, that's why we check for it first.
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But when adata.obs["is_potential_doublet"] returns empty and we called mean() - what happens then?
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We only run the mean() function if "is_potential_doublet" exists as a column in adata.obs. Otherwise that part is not run and "fraction_potential_doublets" remains the default value which is 0 right now but following the discussion we're going to change it to None.
| metrics["fraction_potential_doublets"] = adata.obs[ | ||
| "is_potential_doublet" | ||
| ].mean() | ||
| metrics["n_edges_to_split_potential_doublets"] = adata.obs[ |
johandahlberg
approved these changes
Oct 22, 2024
Co-authored-by: Johan Dahlberg <johan.dahlberg@pixelgen.tech>
Co-authored-by: Johan Dahlberg <johan.dahlberg@pixelgen.tech>
Co-authored-by: Johan Dahlberg <johan.dahlberg@pixelgen.tech>
Co-authored-by: Johan Dahlberg <johan.dahlberg@pixelgen.tech>
…l_doublets to None
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During the graph step, we split some components that appear to be technical multiplets through community detection. However we set parameters in a relatively conservative way so to avoid breaking up cells into multiple components. In the annotation step we are adding a less conservative parametrization to mark "potential doublets".
What is added:
Fixes: EXE-2025
Type of change
How Has This Been Tested?
The unit tests.
PR checklist: