EmbedSOM (version 2.2)

kNNCoords: 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
)

Value

a function that transforms the map, usable as coordsFn parameter

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)