R package Kohonen - how to draw hexagons instead of circles, as in the Matlab SOM toolkit?

Question

Is it possible to build a SOM map (Kohonen package) with hexagons as elementary shapes instead of circles? Now different phrases (quantity, changes, etc.) are displayed in the form of circles with white surroundings.

The goal is to create SOM visual effects similar to the Matlab SOM Toolbox.

This discussion suggests that building a hexagon would be impossible.

Answer 1

, @NBremer. , u- R "kohonen". :

R SOM

Answer 2

, , . , ,

, kohonen. : http://nbremer.blogspot.nl/2013/07/on-creation-of-extended-self-organizing.html

, : <<Heatmap matrix variable>> - , . [1,1] node (1- , 1- ), [1,2] node , [2,1] node .. , Heatmap,

library(RColorBrewer) #to use brewer.pal
library(fields) #to use designer.colors

#Function to create the polygon for each hexagon
Hexagon <- function (x, y, unitcell = 1, col = col) {
  polygon(c(x, x, x + unitcell/2, x + unitcell, x + unitcell, 
            x + unitcell/2), c(y + unitcell * 0.125, y + unitcell * 
                               0.875, y + unitcell * 1.125, y + unitcell * 0.875, 
                               y + unitcell * 0.125, y - unitcell * 0.125), 
          col = col, border=NA)
}#function

#Start with a matrix that would be the numerical representation of you heatmap
#Here [1,1] will become the lower left node (1st row, 1st column), 
#[1,2] will become the node to the right
#[2,1] will be the first node to the left in the second row
#So visually you work your way from bottom left to top right
x <- as.vector(<<Heatmap matrix variable>>)

#Number of rows and columns of your SOM
SOM_Rows <- dim(<<Heatmap matrix variable>>)[1]
SOM_Columns <- dim(<<Heatmap matrix variable>>)[2]

#To make room for the legend
par(mar = c(0.4, 2, 2, 7))

#Initiate the plot window but do show any axes or points on the plot
plot(0, 0, type = "n", axes = FALSE, xlim=c(0, SOM_Columns), 
     ylim=c(0, SOM_Rows), xlab="", ylab= "", asp=1)

#Create the color palette 
#I use designer.colors to interpolate 50 colors between 
#the maxmimum number of allowed values in Brewer 
ColRamp <- rev(designer.colors(n=50, col=brewer.pal(9, "Spectral")))

#Make a vector with length(ColRamp) number of bins between the minimum and 
#maximum value of x. 
#Next match each point from x with one of the colors in ColorRamp
ColorCode <- rep("#FFFFFF", length(x)) #default is all white
Bins <- seq(min(x, na.rm=T), max(x, na.rm=T), length=length(ColRamp))
for (i in 1:length(x))
    if (!is.na(x[i])) ColorCode[i] <- ColRamp[which.min(abs(Bins-x[i]))] 

#Actual plotting of hexagonal polygons on map
offset <- 0.5 #offset for the hexagons when moving up a row
for (row in 1:SOM_Rows) {
  for (column in 0:(SOM_Columns - 1)) 
     Hexagon(column + offset, row - 1, col = ColorCode[row + SOM_Rows * column])
  offset <- ifelse(offset, 0, 0.5)
}

#Add legend to the right if you want to
image.plot(legend.only=TRUE, col=ColRamp, zlim=c(min(x, na.rm=T), max(x, na.rm=T)))

Answer 3

Voronoi, ().

• $grid$pts kohonen,
• $codes

lattice:

require ("kohonen")
require ("latticeExtra")
require ("deldir")
som.wines <- som (scale (wines), grid = somgrid(5, 5, "hexagonal"))

df <- as.data.frame (cbind (som.wines$grid$pts, som.wines$codes))
levelplot (alcohol ~ x * y, data = df, panel = panel.voronoi, aspect = "iso)

:

( , , , 2010 ).