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).

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 July 5, 2022, 5:14 p.m.