8000 UMAP and HDBSCAN for cytoflow by CaRniFeXeR · Pull Request #350 · cytoflow/cytoflow · GitHub
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UMAP and HDBSCAN for cytoflow #350

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UMAP and HDBSCAN for cytoflow #350

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CaRniFeXeR
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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 and others added 23 commits April 6, 2023 16:42
@CaRniFeXeR
adds external_label operation
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ads vscode settings folder to .gitignore
d0c56f5
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renames external label op to bulk condition op
d5a8dda
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adds bulk condition combine logic
0f6d848
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adds documentation to bulk condition code files
bf6cb1b
@CaRniFeXeR
adds bulk condition to basic cytometry jupyter notebook
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@CaRniFeXeR
adds bulk conditions op unittest to check if no combined columns in c…
e7d4e29 
…reated if no combine_order is specified
@CaRniFeXeR
removes accidently created empty source file
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adds umap operation; refactors dimensionality reduction operations
eece772
@CaRniFeXeR
adds standardscaler for rescaling to base dimensionality reduction op…
c767f94 
…, adds tests for umap
@CaRniFeXeR
adds UMAP to machine learning notebook
b853641
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fixes exception handling bug in bulk condition op
e65bb8b
@CaRniFeXeR
adds hdbscan to requirements
e781082
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ensures bulk conditions created combined condition is of dtype category
e70873d
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adds subsample operation with tests
dea761b
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refactors channel scale initalization into one function
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refactors op default view init into one method
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adds umap2d view
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improves doc string in SubsampleOp
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removes problematic type reference from scaler
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adds 2D plot to umap op
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adds hdbscan clustering
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replaces pandas append with concat due to deprecation
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@CaRniFeXeR CaRniFeXeR changed the title UMAP for cytoflow UMAP and HDBSCAN for cytoflow Apr 27, 2023
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@bpteague is there any plan to include this PR?

@bpteague
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Hold your horses ... I've got some time this week and I"m working through issues and PRs. The goal is a new minor release next week.

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@CaRniFeXeR @bpteague
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