global_hierarchical_clusterer: Create a dude to perform hierarchical clustering in a global...

In mappeR: Construct and Visualize TDA Mapper Graphs

Create a dude to perform hierarchical clustering in a global context using the hclust package.

Description

Create a dude to perform hierarchical clustering in a global context using the hclust package.

Usage

global_hierarchical_clusterer(method, dists)

Arguments

method	A string to pass to hclust to tell it what kind of clustering to do.
dists	The global distance matrix on which to run clustering to determine a global cutting height.

Details

This clusterer determines cutting heights for dendrograms by cutting them all according to the best cutting height when the data is clustered together. "Best" here means cutting the dendrogram just above the merge point with the longest unbroken gap until the next merge points.

Value

A function that inputs a list of distance matrices and returns a list containing one vector per matrix, whose element names are data point names and whose values are cluster labels (relative to each matrix).

Examples

data = data.frame(x = sapply(1:100, function(x) cos(x)), y = sapply(1:100, function(x) sin(x)))
projx = data$x

dists = dist(data)

num_bins = 10
percent_overlap = 25

cover = create_width_balanced_cover(min(projx), max(projx), num_bins, percent_overlap)

create_1D_mapper_object(data, dists, projx, cover, global_hierarchical_clusterer("mcquitty", dists))

mappeR documentation built on June 9, 2025, 5:08 p.m.