metasnf (version 2.1.2)

get_matrix_order: Return the hierarchical clustering order of a matrix

Description

Return the hierarchical clustering order of a matrix

Usage

get_matrix_order(matrix, dist_method = "euclidean", hclust_method = "complete")

Value

A numeric vector of the ordering derived by the specified hierarchical clustering method applied to the provided matrix.

Arguments

matrix

Matrix to cluster.

dist_method

Distance method to use when calculating sorting order to of the matrix. Argument is directly passed into stats::dist. Options include "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski".

hclust_method

Agglomerative method to use when calculating sorting order by stats::hclust. Options include "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", or "centroid".

Examples

# \donttest{
dl <- data_list(
    list(subc_v, "subcortical_volume", "neuroimaging", "continuous"),
    list(income, "household_income", "demographics", "continuous"),
    list(pubertal, "pubertal_status", "demographics", "continuous"),
    list(anxiety, "anxiety", "behaviour", "ordinal"),
    list(depress, "depressed", "behaviour", "ordinal"),
    uid = "unique_id"
)

sc <- snf_config(
    dl = dl,
    n_solutions = 20,
    min_k = 20,
    max_k = 50
)

sol_df <- batch_snf(dl, sc)

ext_sol_df <- extend_solutions(
    sol_df,
    dl = dl,
    min_pval = 1e-10 # p-values below 1e-10 will be thresholded to 1e-10
)

# Calculate pairwise similarities between cluster solutions
sol_aris <- calc_aris(sol_df)

# Extract hierarchical clustering order of the cluster solutions
meta_cluster_order <- get_matrix_order(sol_aris)
# }