aweSOMreorder {aweSOM}R Documentation

Reorder variables for SOM plot

Description

Reorders a set of variables for prettier display on SOM plots. Variables that have similar variations along the cell plots while be ordered close together. Reordering is computed from the first component of a kernel PCA performed on the matrix of displayed values (with the variables as rows, and the cells as columns).

Usage

aweSOMreorder(
  som,
  data = NULL,
  variables = NULL,
  scales = c("contrast", "range", "same"),
  values = c("mean", "median", "prototypes")
)

Arguments

som

kohonen object, a SOM created by the kohonen::som function.

data

data.frame containing the variables to plot. This is typically not the training data, but rather the unscaled original data, as it is easier to read the results in the original units, and this allows to plot extra variables not used in training. If not provided, the training data is used.

variables

character vector containing the names of the variables to plot. If not provided, all columns of data will be selected. All variables must be numeric.

scales

character, controls the scaling of the variables on the plot. The default "constrast" maximizes the displayed contrast by scaling the displayed heights of each variable from minimum to maximum of the displayed value. Alternatively, "range" uses the minimum and maximum of the observations for each variable, and "same" displays all variables on the same scale, using the global minimum and maximum of the data.

values

character, the type of value to be displayed. The default "mean" uses the observation means (from data) for each cell. Alternatively, "median" uses the observation medians for each cell, and "prototypes" uses the SOM's prototypes values.

Value

Returns a character vector containing the reordered variables names.

Examples

## Build training data
dat <- iris[, c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")]
### Scale training data
dat <- scale(dat)
## Train SOM
### Initialization (PCA grid)
init <- somInit(dat, 4, 4)
ok.som <- kohonen::som(dat, grid = kohonen::somgrid(4, 4, 'hexagonal'),
                       rlen = 100, alpha = c(0.05, 0.01),
                       radius = c(2.65,-2.65), init = init,
                       dist.fcts = 'sumofsquares')
## Reorder variables
ordered.vars <- aweSOMreorder(ok.som)
## Plot with reordered variables
aweSOMplot(som = ok.som, type = 'Circular', data = iris,
           variables= ordered.vars)

[Package aweSOM version 1.2 Index]