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UMAP and HDBSCAN for cytoflow #350

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I added UMAP to CytoFlow. This Pull Request contains three major adaptations:

  • BulkConditionOp
    • Allows adding multiple conditions to an experiment at once. Source is either a pandas.Dataframe or an csv File. Added conditions can be combined into one column. This operation is intended to be used when manual gating ground truth is available.
  • BaseDimensionalityReductionOp
    • Represents the (abstract) base class for dimensionality reduction now used by PCAOp and UMAPOp. I optionally added the possibility to rescale data before fitted and transformed with an dimensionality reduction algorithm. (Should be beneficial for both PCA and UMAP)
  • UMAPOp
    • The Operation using the umap python package. Implementation is very similar to that of PCAOp.

I added a couple of unittests for the adaptations. As well as added an example of using UMAP to the Machine Learning Notebook. I did not managed to build the docs, so this is still missing.

@CaRniFeXeR CaRniFeXeR changed the title UMAP for cytoflow UMAP and HDBSCAN for cytoflow Apr 27, 2023
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