Functional markers

[smith6jt-cop]

Is your feature request related to a problem? Please describe.
As it stands, the pipeline creates a boolean indication of functional markers for each cell to be used in the now removed pairwise enrichment notebook.

Describe the solution you'd like
Remove the portion of the ReadMe that refers to the notebook that isn't there anymore. Specify how the functional marker data can be incorporated into the analysis.

Describe alternatives you've considered
The SpaceCat repo could be used in this capacity with modifications of ark-analysis or parts of SpaceCat.

[camisowers]

Hi @smith6jt-cop, thanks for catching this outdated readme section! We'll open a PR to fix this soon.

Currently, the neighborhood analysis notebook allows users to examine functional marker expression within kmeans neighborhoods in images, but directing users to SpaceCat for further analysis is a great idea.

[smith6jt-cop]

Thanks for your reply. I don't see where the neighborhood analysis notebook you referenced allows for this. The last instructions for functional markers is another outdated section of code in 4_Post_Clustering.ipynb:

`# Save the thresholds as a csv file. Used in the Pairwise Spatial Enrichment Notebook

threshold_df = pd.DataFrame({'marker': [x[0] for x in threshold_list],
'threshold': [x[1] for x in threshold_list]})

threshold_df.to_csv(os.path.join(post_cluster_dir, 'marker_thresholds.csv'), index=False)
`

After generating columns of True or False for each marker, it is unclear what the next step is. Would you please clarify?

[camisowers]

Oh I see what you mean. The neighborhood analysis only looks at average marker expression not considering the binary functional positivity.

Currently there is no next step within ark itself, now that that pairwise spatial enrichment notebook has been removed. We are working on getting a new version up and running! In the mean time, we will work to ensure compatibility with SpaceCat for users to employ that as the next part of analysis.