scverse
neigh_correct when computing spatial graph
Hi,
what does the parameter mean when build spatial neighborhood graph (https://squidpy.readthedocs.io/en/stable/_modules/squidpy/gr/_build.html#spatial_neighbors)?
And, here is the sturcture of 10x visium chip:
when I set the following
n_rings=2 and n_neighs=6, I expect there should be more neighbours when n_rings=2 than n_rings=1, but I have set n_neighs=6, are the neighbours still the same between n_rings=1 and n_rings=2 ?
sq.gr.spatial_neighbors(adata, n_rings=2, coord_type="grid", n_neighs=6)
In visium, one spot and it's 6 neighbours have the same euclidean distance. In this case, what will happens if I set n_neighs=3 or n_neighs=10 ? Is it mandatory to set n_neighs=6 for 10x visium ?
hi @wangjiawen2013 that's parameter is used when building visium neighbor graph, when there is some sway. This is because the actual coordinates of the spots might have some errors, and without that correction sometime the hexagonal graph structure is not preserved. I would suggest you to take a look with and without with your own data.
