som_model: Process the output from SOM to display the map and data

In mulgar: Functions for Pre-Processing Data for Multivariate Data Visualisation using Tours

Process the output from SOM to display the map and data

Description

This function generates a grid of points to match the nodes from the self-organising map (SOM), and jitters points from the data so they can be seen relative to the grid. This allows the clustering of points by SOM to be inspected.

Usage

som_model(x_som, j_val = 0.5)

Arguments

x_som	object returned by kohonen::som
j_val	amount of jitter, should range from 0-1, default 0.3

Value

• data this object contains

  • original variables from the data

  • map1, map2 location of observations in 2D som map, jittered

  • distance distances between observations and the closest node

  • id row id of data

• net this object contains

  • values of the nodes in the high-d space

  • map1, map2 nodes of the som net

  • distance distances between observations and the closest node

  • id row id of net

• edges from, to specifying row ids of net to connect with lines

• edges_s x, xend, y, yend for segments to draw lines to form 2D map

Examples

require(kohonen)
data(clusters)
c_grid <- kohonen::somgrid(xdim = 5, ydim = 5,
  topo = 'rectangular')
c_som <- kohonen::som(as.matrix(clusters[,1:5]), grid = c_grid)
c_data_net <- som_model(c_som)
require(ggplot2)
ggplot() +
  geom_segment(data=c_data_net$edges_s,
    aes(x=x, xend=xend, y=y, yend=yend)) +
  geom_point(data=c_data_net$data, aes(x=map1, y=map2),
    colour="orange", size=2, alpha=0.5)

mulgar documentation built on April 12, 2025, 1:23 a.m.