plot.somRes: Plot a `somRes` class object

Description

Produce graphics to help interpreting a somRes object.

Usage

# S3 method for somRes
plot(
  x,
  what = c("obs", "prototypes", "energy", "add"),
  type = switch(what, obs = "hitmap", prototypes = "color", add = "pie", energy =
    "energy"),
  variable = NULL,
  my.palette = NULL,
  is.scaled = if (x$parameters$type == "numeric") TRUE else FALSE,
  show.names = TRUE,
  names = if (what != "energy") switch(type, graph = 1:prod(x$parameters$the.grid$dim),
    1:prod(x$parameters$the.grid$dim)) else NULL,
  proportional = TRUE,
  pie.graph = FALSE,
  pie.variable = NULL,
  s.radius = 1,
  view = if (x$parameters$type == "korresp") "r" else NULL,
  ...
)

Arguments

x: A somRes class object.
what: What you want to plot. Either the observations (obs, default case), the evolution of energy (energy), the prototypes (prototypes) or an additional variable (add).
type: Further argument indicating which type of chart you want to have. Choices depend on the value of what (what="energy" has no type argument). Default values are "hitmap" for obs, "color" for prototypes and "pie" for add. See section ``Details'' below for further details.
variable: Either the variable to be used for what="add" or the index of the variable of the data set to consider. For type="boxplot", the default value is the sequence from 1 to the minimum between 5 and the number of columns of the data set. In all other cases, default value is 1. See somRes.plotting for further details.
my.palette: A vector of colors. If omitted, predefined palettes are used, depending on the plot case. This argument is used for the following combinations: all "color" types and "prototypes"/"poly.dist".
is.scaled: A boolean indicating whether values should be scaled prior to plotting or not. Default value is TRUE when type="numeric" and FALSE in the other cases.
show.names: Boolean used to indicate whether each neuron should have a title or not, if relevant. Default to TRUE. It is feasible on the following cases: all "color", "lines", "meanline", "barplot", "boxplot", "names" types, "add"/"pie", "prototypes"/"umatrix", "prototypes"/"poly.dist" and "add"/"words".
names: The names to be printed for each neuron if show.names=TRUE. Default to a number which identifies the neuron.
proportional: Boolean used when what="add" and type="pie". It indicates if the pies should be proportional to the number of observations in the class. Default value is TRUE.
pie.graph: Boolean used when what="add" and type="graph". It indicates if the vertices should be pies or not.
pie.variable: The variable needed to plot the pies when what="add", type="graph" and argument pie.graph=TRUE.
s.radius: The size of the pies to be plotted (maximum size when proportional=TRUE) for what="add", type="graph" and pie.graph=TRUE. The default value is 0.9.
view: Used only when the algorithm's type is "korresp". It indicates whether rows ("r") or columns ("c") must be drawn.
...: Further arguments to be passed to the underlined plot function (which can be plot, barplot, pie... depending on type; see somRes.plotting for further details).

Author

Élise Maigné <elise.maigne@inrae.fr>
Madalina Olteanu olteanu@ceremade.dauphine.fr
Nathalie Vialaneix nathalie.vialaneix@inrae.fr

Details

See somRes.plotting for further details and more examples.

Examples

Run this code

# run the SOM algorithm on the numerical data of 'iris' data set
iris.som <- trainSOM(x.data = iris[, 1:4], nb.save = 2)
# plots
# on energy
plot(iris.som, what = "energy") 
# on observations
plot(iris.som, what = "obs", type = "lines")
# on prototypes
plot(iris.som, what = "prototypes", type = "3d", variable = "Sepal.Length")
# on an additional variable: the flower species
plot(iris.som, what = "add", type = "pie", variable = iris$Species)