GraphCoords: Add Kamada-Kawai-generated embedding coordinates to the map

In EmbedSOM: Fast Embedding Guided by Self-Organizing Map

Add Kamada-Kawai-generated embedding coordinates to the map

Description

This uses a complete graph on the map codebook, which brings overcrowding problems. It is therefore useful to transform the distances for avoiding that (e.g. by exponentiating them slightly using distFn function).

Usage

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

Arguments

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.