A basic vignette on grids in SOMbrero

26 janvier, 2024

Source: vignettes/b-doc-grids.Rmd

Definition and purpose of a myGrid class object

Objects of class myGrid are made to display the SOM grid.

Basic functions on a myGrid class object

In this section, we will consider only the four basic functions that can be applied on a myGrid class object:

  • initGrid,
  • print.myGrid
  • summary.myGrid
  • plot.myGrid

The initGrid function

The initGrid function initializes a new myGrid object. It has 3 arguments:

  • dimension, which is a vector of two integers. The first one is the x dimension (number of neurons/units on the x axis) and the second one is the y dimension. The default dimensions are x=5 and y=5,

  • topo, which is the chosen topology. The value of this argument must be one of square or hexagonal. The__default value__ is square.

  • dist.type, which is the distance type to compute the distance between two neurons of the grid. The default value is euclidean and the coordinates of the neurons on the grid are chosen so as the minimum Euclidean distance between two neurons is exactly 1. hexagonal topoology is only compatible with the Euclidean distance.

The following R code initializes a new myGrid object of square topology, x dimension 5 and y dimension 6, and distance type maximum.

first_grid <- initGrid(dimension = c(5,6), topo = "square", dist.type = "maximum")

The print.myGrid function

The myGrid object print function prints the main features of the chosen object in the console. The only argument is the object to be printed.

Considering the previously initialized grid, the print command is:

print(first_grid)
## 
##       Self-Organizing Map structure
## 
##         Features   :
##            topology     :  square 
##            x dimension  :  5 
##            y dimension  :  6 
##            distance type:  maximum

The summary.myGrid function

The myGrid object summary function is quite simple. It only prints the class of the object and then calls the print function previously described. The only argument is the object to be summarized.

summary(first_grid)
## 
## Summary
## 
##       Class            :  myGrid 
## 
##       Self-Organizing Map structure
## 
##         Features   :
##            topology     :  square 
##            x dimension  :  5 
##            y dimension  :  6 
##            distance type:  maximum

The plot.myGrid function

The myGrid object plot function draws the squared area corresponding to the object, in a new graphical window. It has 3 parameters:

  • the object to be plotted,

  • show.names, boolean, indicating if the names of the neurons should be displayed on the graph (default to TRUE)

  • names, a vector, giving the names of the neurons if show.names = TRUE, default to the number of the neuron.

plot(first_grid)

plot(first_grid) + ggplot2::scale_fill_manual(values = rep("white", 30))

my_palette <- colorRampPalette(c("white", "pink", "purple"))(30)
plot(first_grid, show.names = FALSE) + 
  ggplot2::scale_fill_manual(values = my_palette)

Hexagonal grids can be displayed similarly:

second_grid <- initGrid(dimension = c(4, 5), topo = "hexagonal")
plot(second_grid, names = paste0("N", 1:20)) + 
  ggplot2::ggtitle("Hexagonal SOM grid")

Session information

This vignette has been compiled with the following environment:

## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Europe/Paris
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] SOMbrero_1.4-2 markdown_1.7   igraph_1.4.3  
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.6           utf8_1.2.3           generics_0.1.3      
##  [4] xml2_1.3.4           lattice_0.22-5       stringi_1.7.12      
##  [7] digest_0.6.31        magrittr_2.0.3       evaluate_0.21       
## [10] grid_4.3.2           fastmap_1.1.1        rprojroot_2.0.3     
## [13] jsonlite_1.8.4       backports_1.4.1      ggwordcloud_0.6.1   
## [16] purrr_1.0.1          fansi_1.0.4          scales_1.2.1        
## [19] textshaping_0.3.6    jquerylib_0.1.4      cli_3.6.1           
## [22] rlang_1.1.1          scatterplot3d_0.3-41 munsell_0.5.0       
## [25] withr_2.5.0          cachem_1.0.8         yaml_2.3.7          
## [28] tools_4.3.2          deldir_1.0-6         checkmate_2.0.0     
## [31] memoise_2.0.1        dplyr_1.1.2          colorspace_2.1-0    
## [34] interp_1.0-33        ggplot2_3.4.2        vctrs_0.6.2         
## [37] R6_2.5.1             png_0.1-8            lifecycle_1.0.3     
## [40] stringr_1.5.0        fs_1.6.2             ragg_1.2.5          
## [43] pkgconfig_2.0.3      desc_1.4.2           hexbin_1.28.2       
## [46] pkgdown_2.0.7        bslib_0.4.2          pillar_1.9.0        
## [49] gtable_0.3.3         data.table_1.14.8    glue_1.6.2          
## [52] Rcpp_1.0.10          systemfonts_1.0.4    highr_0.10          
## [55] xfun_0.39            tibble_3.2.1         tidyselect_1.2.0    
## [58] rstudioapi_0.14      knitr_1.42           farver_2.1.1        
## [61] htmltools_0.5.5      labeling_0.4.2       metR_0.14.1         
## [64] rmarkdown_2.21       compiler_4.3.2       gridtext_0.1.5