Labelling Points on a Plot (R Language)

Question

I am using the R programming language and learning about kohonen package by following this tutorial. The kohonen R package allows the user to run Kohonen Networks (also called SOM - Self Organizing Maps), a type of unsupervised machine learning algorithm used in data visualization.

I ran the following code and produced the below plots:

#load libraries
library(kohonen) #fitting SOMs
library(RColorBrewer) #colors, using predefined palettes

#process data
iris_complete <-iris[complete.cases(iris),] #only complete cases... the iris dataset floats around in the sky with diamonds.
iris_unique <- unique(iris_complete) # Remove duplicates
iris.sc = scale(iris_unique[, 1:4])

#run the SOM
iris.grid = somgrid(xdim = 10, ydim=10, topo="hexagonal", toroidal = TRUE)
set.seed(33) #for reproducability
iris.som <- som(iris.sc, grid=iris.grid, rlen=700, alpha=c(0.05,0.01), keep.data = TRUE)

#make plots (3 different plots)
plot(iris.som, type="count")

plot(iris.som, type="dist.neighbours", 
     palette.name=grey.colors, shape = "straight")

var <- 1 #define the variable to plot
plot(iris.som, 
     type = "property", 
     property = getCodes(iris.som)[,var], 
     main=colnames(getCodes(iris.som))[var], 
     palette.name=terrain.colors)

From here, I am trying to modify these plots so that they are more recognizable. I am trying to add a "label" (a number from 1-100) to each circle so that is easier to identify each circle:

I am not sure if there is a straightforward way to place a number on each corresponding circle. Looking at the som() function in the kohonen package (https://www.rdocumentation.org/packages/kohonen/versions/2.0.19/topics/som), it seems it is possible to determine which observation belongs to which circle:

#determine which circle each observation belongs to
a = iris.som$unit.classif

#pull the original data
b = iris.som$data

#combine both of them into one frame
c = rbind(a,b)

But I am not sure if it is possible to "superimpose" these numbers on to the corresponding circles. Does anyone know if this can be done?

Update:

I tried the following code:

iris_unique$ID <- seq_along(iris_unique[,1]) 
plot(iris.som, type="mapping", bg = rgb(colour4), shape = "straight", 
     border = "grey", labels = iris_unique[,6])

or:

library(plotly)

plot1 = plot(iris.som, type="mapping", bg = rgb(colour4), shape = "straight", 
             border = "grey", labels = iris_unique[,6])

plotly_plot = ggplotly(plot1)

But I don't think that this is correct.

user_14812170 · Answer

You can find the coordinates of the center of each circle or hexagon in iris.som$grid$pts. One way to put the labels on the coordinates is to assign a name to each circle by using dimnames(), and then assign the names as the labels on the corresponding circle's coordinates by using text().

iris.som$grid$pts
#          x         y
#  [1,]  1.5 0.8660254
#  [2,]  2.5 0.8660254
#  [3,]  3.5 0.8660254
#  [4,]  4.5 0.8660254
#  [5,]  5.5 0.8660254
#  up to [100,] 10.0 8.6602540

# Assign a name for each coordinate. For example, "1", "2", "3", etc

dimnames(iris.som$grid$pts) = list(as.character(1:100), c("x","y"))  

#iris.som$grid$pts
#       x         y
#1    1.5 0.8660254
#2    2.5 0.8660254
#3    3.5 0.8660254
#4    4.5 0.8660254
#5    5.5 0.8660254

# Put the names on the plot 
text(iris.som$grid$pts, dimnames(iris.som$grid$pts[[1]]))

# Do the same steps for other plots
plot(iris.som, type="dist.neighbours", 
     palette.name=grey.colors, shape = "straight")
text(iris.som$grid$pts, dimnames(iris.som$grid$pts[[1]]))

Note that if you use RStudio, you may need to adjust the width of your plotting pane to display all the labels properly.

Labelling Points on a Plot (R Language)

1 Answers