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 uses FNN::get.knn() to compute the k-neighborhoods. That function only supports Euclidean metric, therefore kNNCoords throws a warning whenever a different metric is used.

Usage

kNNCoords(
  k = 4,
  dim = 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)
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 July 5, 2022, 5:14 p.m.