mulgar (version 1.0.5)

som_model: 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)

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

Arguments

x_som

object returned by kohonen::som

j_val

amount of jitter, should range from 0-1, default 0.3

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)