baryshnikova-lab/safepy

SAFE on map wo/ edges

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cscheeder commented

I would like to reproduce the SAFE analysis on a map wo/ edges as shown in your recent preprint https://www.biorxiv.org/content/10.1101/2022.12.22.521593v1. Yet this seems to not be straight forward and I was wondering whether I can somewhere find an exmaple/tutorial on this?

Thanks and best regards,
Christian

abarysh commented

Hi Christian,
The commit 842e442 provides the functionality to load scatter plots and treat them as "networks". Example 3 (in the examples/ folder) shows how to use this functionality to annotate a UMAP plot with a single attribute. Using and combining multiple attributes (like in the case of Gene Ontology) should work the same as with regular networks. Let me know if you need any additional help in your specific case.
A.

cscheeder commented

Thanks a lot for adding the example. best, christian