angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Deprecate use of cluster, metacluster, and mc_name outside of remapping #950

Closed alex-l-kong closed 1 year ago

alex-l-kong commented 1 year ago

What is the purpose of this PR?

Closes #846. It's much easier for the user to read pixel_som_cluster as opposed to cluster, pixel_meta_cluster as opposed to metacluster, and pixel_meta_cluster_rename as opposed to mc_name. We had used these as a result of standards Zak used, but these names should be reverted outside of the remapping process.

How did you implement your changes

Any function outside of metacluster_remap_gui needs to use the new standard of column naming. When the mapping is saved after a click event of New metacluster happens, the columns get renamed prior to the save.

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alex-l-kong commented 1 year ago

The example dataset version will be changed to main just before merging in.

camisowers commented 1 year ago

Same, adding the cluster_type arg is easy to follow.