getAdj_auto: Calculate adjacency matrix by automatically choosing radius

In DR.SC: Joint Dimension Reduction and Spatial Clustering

Calculate adjacency matrix by automatically choosing radius

Description

an efficient function to find the radius by bi-section method , then find neighbors based on the matrix of position, which ensures that each spot has approximately lower.med~upper.med neighbors in the sense of median.

Usage

getAdj_auto(pos, lower.med=4, upper.med=6, radius.upper= NULL)

Arguments

pos	a n-by-2 matrix of position.
lower.med	an integer, the lower bound of median number of neighbors among all spots.
upper.med	an integer, the upper bound of median number of neighbors among all spots.
radius.upper	a real, the upper bound of radius, default as NULL. If radius.upper= NULL, the upper bound is automatically determined by algorithm.

Value

A sparse adjacency matrix containing the neighbourhood.

See Also

getAdj, getAdj_manual.

DR.SC documentation built on May 29, 2024, 2:12 a.m.