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FlowSOM#59

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mbuttner merged 11 commits into
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clustering-algorithms
Nov 7, 2023
Merged

FlowSOM#59
mbuttner merged 11 commits into
mainfrom
clustering-algorithms

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@burtonrj burtonrj commented Oct 14, 2023

I've introduced FlowSOM under the tools.clustering module. The FlowSOM implementation is as a a function flowsom_clustering and is similar to scanpy functions. Dependency on consensusclustering a package I've put together to implement consensus cluster in Python. Other things to note:

  • flowsom_clustering returns an annotated dataframe with the labels introduced under a new key (which the user can specify)
  • flowsom_clustering can optionally return the SOM and ConsensusClustering objects for inspection (see tutorial for an example)
  • FlowSOM tutorial added as a jupyter notebook - please review for a general overview of usage
  • Minor refactors to plotting functions to allow for Axes object to be passed - fixed minor bugs and missing docs

@burtonrj
Added a read_and_merge method - for clustering we often apply cluster…
e97afac 
…ing to multiple samples (after batch correction) and it would be helpful to have a utility function to read multiple FCS files, generage a sample ID column, and merge - implemented in accordance with the pytometry examples
@burtonrj
Implemented basic functionality for flowsom - viz functions and tests…
4d7a413 
… required
@burtonrj
Added docstrings
50e5462
@burtonrj
Added testing to cover flow_clustering function
ae1f1ab
@burtonrj
FlowSOM tutorial added and refactors to FlowSOM complete
4b93465 
* FlowSOM clustering moved to tools
* FlowSOM tutorial added to docs
* Some minor refactors to FlowSOM to allow modification of consensus clustering params
* Some minor refactors to plotting
@burtonrj burtonrj requested a review from mbuttner October 14, 2023 18:14
@burtonrj burtonrj linked an issue Oct 14, 2023 that may be closed by this pull request
Implement FlowSOM type of clustering #46
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mbuttner
mbuttner requested changes Oct 25, 2023
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Looks pretty good overall! I commented on a few occasions that need to be changed. Also, consider to run pre-commit to get past the code checks. Thanks!

Comment thread pytometry/tools/clustering/_flowsom.py Outdated
Comment thread pytometry/tools/clustering/_flowsom.py Outdated
Comment thread pytometry/read_write/_readfcs.py Outdated
Comment thread docs/tutorials/flowsom.ipynb Outdated
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burtonrj commented Oct 30, 2023

An issue I've noticed with the pre-commit config. Flake8 fails because I've used TypedDict in _flowsom.py and TypedDict is not supported pre python 3.8, however according to the pyproject.toml file pytometry only supports Python 3.9 or greater anyway.

I've updated the pre-commit yaml to ignore TYP001, let me know if this is okay.

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mbuttner commented Oct 30, 2023

An issue I've noticed with the pre-commit config. Flake8 fails because I've used TypedDict in _flowsom.py and TypedDict is not supported pre python 3.8, however according to the pyproject.toml file pytometry only supports Python 3.9 or greater anyway.

I've updated the pre-commit yaml to ignore TYP001, let me know if this is okay.

Sounds good to me.

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github-actions Bot commented Oct 31, 2023 •
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🚀 Deployed on https://6549fe01f1e20777540b1dcb--pytometry.netlify.app

@github-actions github-actions Bot temporarily deployed to pull request October 31, 2023 19:18 Inactive
@burtonrj burtonrj requested a review from mbuttner October 31, 2023 19:53
mbuttner
mbuttner approved these changes Nov 7, 2023
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Looks all good to me!

mbuttner
mbuttner requested changes Nov 7, 2023
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One minor thing - please execute the 03_flowsom notebook to display the plots (see netlify page).

Comment thread docs/examples/03_flowsom.ipynb
@github-actions github-actions Bot temporarily deployed to pull request November 7, 2023 09:06 Inactive
mbuttner
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All very good.

@mbuttner mbuttner merged commit a1e59b2 into main Nov 7, 2023
@mbuttner mbuttner deleted the clustering-algorithms branch November 7, 2023 16:47
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Implement FlowSOM type of clustering

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@burtonrj @mbuttner