subsample_pairwise_aris: Calculate pairwise adjusted Rand indices across subsamples of...

In metasnf: Meta Clustering with Similarity Network Fusion

Calculate pairwise adjusted Rand indices across subsamples of data

Description

Given a list of subsampled solutions data frames from 'batch_snf_subsamples(), this function calculates the adjusted Rand indices across all the subsamples of each solution. ARI calculation between two subsamples only factors in observations that were present in both subsamples.

Usage

subsample_pairwise_aris(subsample_solutions, verbose = FALSE)

Arguments

subsample_solutions	A list of solutions data frames from subsamples of the data. This object is generated by the function batch_snf_subsamples().
verbose	If TRUE, output progress to console.

Value

A two-item list: "raw_aris", a list of inter-subsample pairwise ARI matrices (one for each full cluster solution) and "ari_summary", a data frame containing the mean and SD of the inter-subsample ARIs for each original cluster solution.

Examples

# my_dl <- data_list(
#     list(subc_v, "subcortical_volume", "neuroimaging", "continuous"),
#     list(income, "household_income", "demographics", "continuous"),
#     list(pubertal, "pubertal_status", "demographics", "continuous"),
#     uid = "unique_id"
# )
# 
# sc <- snf_config(my_dl, n_solutions = 5, max_k = 40)
# 
# my_dl_subsamples <- subsample_dl(
#     my_dl,
#     n_subsamples = 20,
#     subsample_fraction = 0.85
# )
# 
# batch_subsample_results <- batch_snf_subsamples(
#     my_dl_subsamples,
#     sc,
#     verbose = TRUE
# )
# 
# pairwise_aris <- subsample_pairwise_aris(
#     batch_subsample_results
#     verbose = TRUE
# )
#
# # Visualize ARIs 
# ComplexHeatmap::Heatmap(
#     pairwise_aris[[1]],
#     heatmap_legend_param = list(
#         color_bar = "continuous",
#         title = "Inter-Subsample\nARI",
#         at = c(0, 0.5, 1)
#     ),
#     show_column_names = FALSE,
#     show_row_names = FALSE
# )

metasnf documentation built on April 3, 2025, 5:40 p.m.