SNNConstruction: Building Unweighted Shared Nearest Neighbor Graph

In XuegongLab/HGC: A fast hierarchical graph-based clustering method

Description

This function builds a Shared Nearest Neighbor (SNN) graph in the input feature space using Euclidean distance metric.

Usage

SNN.Construction(mat, k, threshold)

Arguments

mat	the input data saved as a numerical matrix. The columns are the features and the rows are the samples.
k	the number of nearest neighbor number to build the original KNN.
threshold	the threshold parameter for the Jaccard index. The edges in KNN whose Jaccard indices are lower than it will be removed in building the SNN.

Details

The function builds an SNN which saved as a sparse matrix.

Value

An n by n binary dgCMatrix object C, where n is the number of input samples. The matrix C is the adjacency matrix of the built SNN graph. C[i,j] = 1 means that there is an edge between sample i and sample j.

Examples

data(Pollen)
Pollen.PCs <- Pollen[["PCs"]]
G <- SNN.Construction(Pollen.PCs)

XuegongLab/HGC documentation built on Dec. 18, 2021, 7:23 p.m.