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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Kmeans notebook minor fixes #966

Closed camisowers closed 1 year ago

camisowers commented 1 year ago

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What is the purpose of this PR?

Closes #963 and closes #964.

How did you implement your changes

Passed the cell_type_colarg into the appropriate functions, renamed the arg in create_neighborhood_matrix from cluster_name_col --> cell_type_col for consistency. Edited visualize.draw_heatmap to save images without cropping, and heatmaps are saved by default now.

Previously, the output files were saved with the same name each time the notebook was run, unless you manually changed them to indicate counts vs freq or a different cell column. Now, the results are saved to a subfolder within the neighborhood_analysis directory, indicated by the parameters specified by the user (i.e. cell_meta_cluster_radius50_counts) The produced cell table updated with kmeans clusters now saves in this new subfolder, rather than segmentation/cell_table.

Remaining issues NA

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