aweSOMreorder {aweSOM}  R Documentation 
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).
aweSOMreorder( som, data = NULL, variables = NULL, scales = c("contrast", "range", "same"), values = c("mean", "median", "prototypes") )
som 

data 

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. 
Returns a character vector containing the reordered variables names.
## 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)