vignettes/b-doc-grids.Rmd
b-doc-grids.Rmd
myGrid
class object
Objects of class myGrid
are made to display the SOM grid.
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
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
.
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
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
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")
This vignette has been computed with the following environment:
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## 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
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] SOMbrero_1.4-1 markdown_1.1 igraph_1.2.10
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.1.1 xfun_0.24 bslib_0.3.1
## [4] purrr_0.3.4 lattice_0.20-45 colorspace_2.0-2
## [7] vctrs_0.3.8 generics_0.1.0 htmltools_0.5.2
## [10] yaml_2.2.1 utf8_1.2.2 rlang_0.4.11
## [13] hexbin_1.28.2 pkgdown_2.0.1 jquerylib_0.1.4
## [16] pillar_1.6.2 glue_1.4.2 DBI_1.1.1
## [19] lifecycle_1.0.0 metR_0.11.0 stringr_1.4.0
## [22] munsell_0.5.0 gtable_0.3.0 ragg_1.2.1
## [25] memoise_2.0.1 evaluate_0.14 labeling_0.4.2
## [28] ggwordcloud_0.5.0 knitr_1.33 fastmap_1.1.0
## [31] fansi_0.5.0 highr_0.9 Rcpp_1.0.7
## [34] backports_1.2.1 checkmate_2.0.0 scales_1.1.1
## [37] cachem_1.0.6 desc_1.4.0 scatterplot3d_0.3-41
## [40] jsonlite_1.7.2 farver_2.1.0 deldir_1.0-6
## [43] systemfonts_1.0.3 fs_1.5.0 interp_1.0-33
## [46] textshaping_0.3.6 ggplot2_3.3.5 png_0.1-7
## [49] digest_0.6.27 stringi_1.6.2 dplyr_1.0.7
## [52] grid_4.1.2 rprojroot_2.0.2 tools_4.1.2
## [55] magrittr_2.0.1 sass_0.4.0 tibble_3.1.3
## [58] crayon_1.4.1 pkgconfig_2.0.3 ellipsis_0.3.2
## [61] data.table_1.14.0 lubridate_1.7.10 assertthat_0.2.1
## [64] rmarkdown_2.10 R6_2.5.1 compiler_4.1.2