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Fix coloc docs #20

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Feb 6, 2024
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Fix coloc docs #20

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25314ab
Fix typos
aeisenbarth Feb 6, 2024
c9e9b91
Separate enumeration from paragraph to avoid it being inlined in the …
aeisenbarth Feb 6, 2024
95f3131
Add doc entry for colocalization, since not found with :imported-memb…
aeisenbarth Feb 6, 2024
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8 changes: 8 additions & 0 deletions docs/api.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,11 @@ metaspace_converter
:members:
:undoc-members:
:show-inheritance:

metaspace_converter.colocalization
----------------------------------

.. automodule:: metaspace_converter.colocalization
:members:
:undoc-members:
:show-inheritance:
11 changes: 6 additions & 5 deletions metaspace_converter/colocalization.py
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Expand Up @@ -18,11 +18,12 @@ def coloc_ml_preprocessing(
Preprocessing for colocalization analysis according to the colocML publication
(https://doi.org/10.1093/bioinformatics/btaa085).

In the publication the authors evaluated colocalization metrics and preprocessing approaches.
In the publication, the authors evaluated colocalization metrics and preprocessing approaches.
They found the best performance for
1) median filtering of ion images with a (3, 3) kernel size and
2) quantile thresholding ad 50%, meaning all pixels with intensities below the 50%
quantile set to 0.

1. median filtering of ion images with a (3, 3) kernel size and
2. quantile thresholding at 50%, meaning all pixels with intensities below the 50%
quantile set to 0.

This function performs the same preprocessing steps.
Recommended for call before running the ``colocalization`` function.
Expand Down Expand Up @@ -76,7 +77,7 @@ def colocalization(adata: AnnData, layer: Optional[str] = "coloc_ml_preprocessin
In combination with the ``colocML_preprocessing`` function, this metric performed best in the
colocML publication (https://doi.org/10.1093/bioinformatics/btaa085).

It is recommended to call the the ``coloc_ml_preprocessing`` function beforehand.
It is recommended to call the ``coloc_ml_preprocessing`` function beforehand.

Args:
adata: An AnnData object.
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