diff --git a/docs/api.rst b/docs/api.rst index 96da798..df54350 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -8,3 +8,11 @@ metaspace_converter :members: :undoc-members: :show-inheritance: + +metaspace_converter.colocalization +---------------------------------- + +.. automodule:: metaspace_converter.colocalization + :members: + :undoc-members: + :show-inheritance: diff --git a/metaspace_converter/colocalization.py b/metaspace_converter/colocalization.py index 8230390..01ff4cd 100644 --- a/metaspace_converter/colocalization.py +++ b/metaspace_converter/colocalization.py @@ -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. @@ -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.