Extend monkeybread neighbourhood to include n>1 cells

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

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Extend monkeybread neighbourhood to include n>1 cells #905

Open timtreis opened 3 weeks ago

timtreis commented 3 weeks ago

Just discussed with @maiiashulman. Would be great to extend the monkeybread nhood niche def method to include a "distance" parameter. Default is 1 = closest touching cell, could extend to > 1 with weights.

LLehner commented 2 weeks ago

@timtreis Where exactly would this be applied (and why)? Before calculating the niches you need to calculate the spatial neighborhood graph, where you already decide on how many neighbors you want to include. Also why is it restricted to this one approach when essentially all methods we implemented make use of the neighborhood?