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Compute Shared Nearest Neighbors (SNN) Graph

Source: R/hc_snn.R
hc_snn.Rd

hc_snn() computes a Shared Nearest Neighbors (SNN) graph from the distance matrix stored in the AnnDatR object.

Usage

hc_snn(
  AnnDatR,
  neighbors = 20,
  prune = 1/15,
  similarity = "euclidean",
  verbose = TRUE
)

Arguments

AnnDatR

An AnnDatR object containing the data with distance matrix results.

neighbors

Number of nearest neighbors to consider (default is 20).

prune

Pruning threshold for the SNN graph (default is 1/15).

similarity

Distance metric to use for nearest neighbor search (default is "euclidean"). Other options include "cosine", "manhattan", and "hamming".

verbose

Logical indicating whether to print progress messages (default is TRUE).

Value

SNN graph stored within the AnnDatR object.

Examples

# Compute SNN graph on an AnnDatR object after distance calculation
adata_res <- hc_pca(example_adata, components = 40)
adata_res <- hc_distance(adata_res, components = 20)
adata_res <- hc_snn(adata_res, neighbors = 15)
#> Building SNN based on a provided distance matrix
#> Computing SNN
adata_res$uns$neighbors$snn
#> A Graph object containing 981 cells