metasnf (version 2.1.2)

clust_fns_list: Build a clustering algorithms list

Description

This function can be used to specify custom clustering algorithms to apply to the final similarity matrices produced by each run of the batch_snf function.

Usage

clust_fns_list(clust_fns = NULL, use_default_clust_fns = FALSE)

Value

A list of clustering algorithm functions that can be passed into the batch_snf and generate_settings_list functions.

Arguments

clust_fns

A list of named clustering functions

use_default_clust_fns

If TRUE, prepend the base clustering algorithms (spectral_eigen and spectral_rot, which apply spectral clustering and use the eigen-gap and rotation cost heuristics respectively for determining the number of clusters in the graph) to clust_fns.

Examples

# Using just the base clustering algorithms --------------------------------
# This will just contain spectral_eigen and spectral_rot
cfl <- clust_fns_list(use_default_clust_fns = TRUE)

# Adding algorithms provided by the package --------------------------------
# This will contain the base clustering algorithms (spectral_eigen,
#  spectral_rot) as well as two pre-defined spectral clustering functions
#  that force the number of clusters to be two or five
cfl <- clust_fns_list(
     clust_fns = list(
        "two_cluster_spectral" = spectral_two,
        "five_cluster_spectral" = spectral_five
    )
)

# Adding your own algorithms -----------------------------------------------
# This will contain the base and user-provided clustering algorithms
my_clustering_algorithm <- function(similarity_matrix) {
    # your code that converts similarity matrix to clusters here...
}

# Suppress the base algorithms----------------------------------------------
# This will contain only user-provided clustering algorithms
cfl <- clust_fns_list(
    clust_fns = list(
        "two_cluster_spectral" = spectral_two,
        "five_cluster_spectral" = spectral_five
    )
)