Local microenvironment specificity

[JessicaChevallier]

Hello,

I'm currently using NICHES to analyze Visium ST data. Ideally, I want to run NICHES on clusters of spots. Does the "local microenvironment" talked about in the Bioinformatics paper refer to the microenvironment within a spot or a few spots away? Is there a specific parameter in RunNICHES that limits the spatial distance accounted for?

Thank you!
Jessica

[jcyang34]

By default it would be a few spots away (i.e., the interactions between the center spot and the nearby spots). There are two options to account for the spatial distance, the default is parameter k that indicates the k nearest neighboring spots for interactions on the spatial graph. Alternatively you can use rad.set to specify a radius value to include all the spots within this radius for computing the interactions