.. _`CellCellColocation3D`:
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CellCellColocation3D Pipeline
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Calculate cell-cell colocation array by KL in 3D coordinate and then generate its MST.

Usage
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.. code-block:: python3

  python3 CellColocation.py 

================== ===========================================================
argument           description
================== ===========================================================  
-h, --help         show this help message and exit
-i                 in.h5ad
-o                 prefix
-b                 binsize (for each slice), default 50 (refer to 50um if 1 unit=1um).
-m                 min cell number for a cell type, default 100.                                  
-f                 sample fraction, default 0.8. The bootstrap fraction.
-l                 loop number, default 100. The number of iterations for bootstrap.
-s                 spatial key in obsm, default 'spatial'
-a                 annotation key in obs, default 'annotation'
================== ===========================================================  

Please set -b based on your coordinate system !!!

Note: -b must be an integer

Reference
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Wei, R., He, S., Bai, S. et al. Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnol 40, 1190–1199 (2022). https://doi.org/10.1038/s41587-022-01233-1