Optional normalization for generic_cell_clustering.ipynb

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis

https://ark-analysis.readthedocs.io/en/latest/

MIT License

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Optional normalization for generic_cell_clustering.ipynb #1027

Closed camisowers closed 1 year ago

camisowers commented 1 year ago

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What is the purpose of this PR? Closes #1000. Make the 99.9 percentile normalization in cell clustering optional.

How did you implement your changes Adds a normalize flag to train_cell_SOM and in the CellSOMCluster class which is defaulted to True. Changing this arg to False will not conduct 99.9 percentile normalization on the data before cell clustering.

Remaining issues N/A

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