kNNCoords: Add KNN-topology-based embedding coordinates to the map

In EmbedSOM: Fast Embedding Guided by Self-Organizing Map

Add KNN-topology-based embedding coordinates to the map

Description

Internally, this does not use FNN::get.knn() anymore.

Usage

kNNCoords(
  k = 4,
  dim = NULL,
  dist.method = NULL,
  distFn = function(x) x,
  layoutFn = igraph::layout_with_kk
)

Arguments

k	Size of the neighborhoods (default 4)
dim	Dimension of the result (passed to layoutFn)
dist.method	The method to compute distances, passed to stats::dist() as parameter method
distFn	Custom transformation function of the distance matrix
layoutFn	iGraph-compatible graph layouting function (default igraph::layout_with_kk)

Value

a function that transforms the map, usable as coordsFn parameter

EmbedSOM documentation built on April 4, 2025, 5:15 a.m.