HoloNet.tools.default_w_visium#
- HoloNet.tools.default_w_visium(adata, min_cell_distance=100, cover_distance=255, obsm_spatial_slot='spatial')#
Calculate a recommended value for the distance parameter in the edge weighting function.
- Parameters
- adata
AnnData Annotated data matrix.
- min_cell_distance
int(default:100) The min distance between spots is 100 micrometers in 10x Visium technology.
- cover_distance
int(default:255) Ligands cover a region with 255 micrometers diameter at a fixed concentration by default. The diameter of sender spot is 55 micrometers, and the ligands spread 100 micrometers.
- obsm_spatial_slot
str(default:'spatial') The slot name storing the spatial position information of each spot
- adata
- Return type
- Returns
: A integer for a recommended value for the distance parameter in the edge weighting function.