Kmeans notebook cleanup

camisowers commented 1 year ago

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What is the purpose of this PR?

Closes #876.

How did you implement your changes

Added more clear descriptions of what is actually being shown by the generated heat maps. Also fixed a few pandas warning messages that were clogging up the notebook outputs.

The visualizations were all updated as well to reflect the example dataset with a cropped fov1.

Remaining issues If anyone has specific additions they want added into the kmeans notebook, let me know!

[ ] Possibly add more visualizations specifically for if someone used neighbor frequencies as their input.
[x] The kmeans notebook always regenerates the neighborhood matrix. It might be helpful to be able to simply read in a previously generated matrix, like how we have in the mixing score notebook.

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cliu72 commented 1 year ago

I think it looks great! Just some minor suggestions for wording, but open to other suggestions. I think being able to read in an existing neighborhood matrix is a good idea.

angelolab / ark-analysis

Kmeans notebook cleanup #946