EmbedSOM (version 2.2)

GraphCoords: 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
)

Value

a function that transforms the map, usable as coordsFn parameter

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)