Easy SOM

Authors

[Editor] Hu Zheng;

[Contributors]

Note

Hiplot website

This page is the tutorial for source code version of the Hiplot Easy SOM plugin. You can also use the Hiplot website to achieve no code ploting. For more information please see the following link:

https://hiplot.cn/basic/easy-som?lang=en

Establish the SOM model and conduct the visulization.

Setup

  • System Requirements: Cross-platform (Linux/MacOS/Windows)

  • Programming language: R

  • Dependent packages: kohonen

# Install packages
if (!requireNamespace("kohonen", quietly = TRUE)) {
  install.packages("kohonen")
}

# Load packages
library(kohonen)

Data Preparation

# Load data
data <- read.delim("files/Hiplot/050-easy-som-data.txt", header = T)

# convert data structure
target <- data[,1]
target <- factor(target, levels = unique(target))
data <- data[,-1]
data <- as.data.frame(data)
for (i in 1:ncol(data)) {
  data[,i] <- as.numeric(data[,i])
}
data <- as.matrix(data)
set.seed(7)
kohmap <- xyf(scale(data), target, grid = somgrid(xdim=6, ydim=4, topo="hexagonal"), rlen=100)

color_key <- c("#A50026","#D73027","#F46D43","#FDAE61","#FEE090","#FFFFBF","#E0F3F8",
               "#ABD9E9","#74ADD1","#4575B4","#313695")
colors <- function (n, alpha, rev = FALSE) {
  colorRampPalette(color_key)(n)
}

# View data
head(data)
     alcohol malic.acid  ash ash.alkalinity magnesium tot..phenols flavonoids
[1,]   12.86       1.35 2.32           18.0       122         1.51       1.25
[2,]   12.88       2.99 2.40           20.0       104         1.30       1.22
[3,]   12.81       2.31 2.40           24.0        98         1.15       1.09
[4,]   12.70       3.55 2.36           21.5       106         1.70       1.20
[5,]   12.51       1.24 2.25           17.5        85         2.00       0.58
[6,]   12.60       2.46 2.20           18.5        94         1.62       0.66
     non.flav..phenols proanth col..int. col..hue OD.ratio proline
[1,]              0.21    0.94      4.10     0.76     1.29     630
[2,]              0.24    0.83      5.40     0.74     1.42     530
[3,]              0.27    0.83      5.70     0.66     1.36     560
[4,]              0.17    0.84      5.00     0.78     1.29     600
[5,]              0.60    1.25      5.45     0.75     1.51     650
[6,]              0.63    0.94      7.10     0.73     1.58     695

Visualization

# Easy SOM
p <- function () {
  par(mfrow = c(3,2))
  xyfpredictions <- classmat2classvec(getCodes(kohmap, 2))
  plot(kohmap, type="counts", col = as.integer(target),
       palette.name = colors,
       pchs = as.integer(target), 
       main = "Counts plot", shape = "straight", border = NA)
  
  som.hc <- cutree(hclust(object.distances(kohmap, "codes")), 3)
  add.cluster.boundaries(kohmap, som.hc)

  plot(kohmap, type="mapping",
       labels = as.integer(target), col = colors(3)[as.integer(target)],
       palette.name = colors,
       shape = "straight",
       main = "Mapping plot")

  ## add background colors to units according to their predicted class labels
  xyfpredictions <- classmat2classvec(getCodes(kohmap, 2))
  bgcols <- colors(3)
  plot(kohmap, type="mapping", col = as.integer(target),
       pchs = as.integer(target), bgcol = bgcols[as.integer(xyfpredictions)],
       main = "Another mapping plot", shape = "straight", border = NA)
  
  similarities <- plot(kohmap, type="quality", shape = "straight",
                       palette.name = colors)
  
  plot(kohmap, type="codes", shape = "straight", 
       main = c("Codes X", "Codes Y"), palette.name = colors)
}

p()
FigureΒ 1: Easy SOM