simplexplot: Simplex visualization

In archetypes: Archetypal Analysis

Description

The stochastic nature of the alpha coefficients implies that they exist on a standard (K-1)-simplex with the K archetypes Z as the corners, and the coefficients as the coordinate with respect to these corners. A standard simplex can be projected to two dimensions via a skew orthogonal projection, where all the vertices of the simplex are shown on a circle connected by edges. The individual alpha coefficients can be then projected into this circle.

Usage

simplexplot(object, radius = 10, order = NULL, labels_cex = 1,
  labels = NULL, show_labels = TRUE, points_col = "#00000044",
  points_pch = 19, points_cex = 1, projection = simplex_projection,
  show_points = TRUE, show_circle = TRUE, circle_col = "lightgray",
  show_edges = TRUE, edges_col = "lightgray", show_direction = FALSE,
  direction_length = 1, directions_col = points_col, ...)

Arguments

object	An archetypes object
radius	Radius of the projection
order	Order of the archetypes
labels_cex	Label expansion
labels	Labels
show_labels	Show labels
points_col	Color of the points
points_pch	Plot character of the points
points_cex	Character expansion of the points
projection	Projection function; see archmap_projections
show_points	Show the points
show_circle	Show the circle
circle_col	Color of the circle
show_edges	Show the edges
edges_col	Color of the edges
direction_length	Expansion of the direction pointers
directions_col	Color of the direction pointers
show_direction	Show direction pointers
...	Additional arguments; currently ignored

Value

Invisible list of all computed components needed for the simplex visualization.

References

See Section 6 in "Probabilistic Archetypal Analysis" by Seth and Eugster (2014), http://arxiv.org/abs/1312.7604.

Examples

### This example reproduces parts of the Figure 7 shown in
  ### "Probabilistic Archetypal Analysis" by Seth and Eugster (2014)

  data("toy", package = "archetypes")

  suppressWarnings(RNGversion("3.5.0"))
  set.seed(1234); a3 <- archetypes(toy, k = 3)
  set.seed(1237); a4 <- archetypes(toy, k = 4)
  set.seed(1238); a5 <- archetypes(toy, k = 5)

  simplexplot(a3)
  simplexplot(a3, show_direction = TRUE, show_points = FALSE)
  simplexplot(a4, projection = tspsimplex_projection)
  simplexplot(a5, show_direction = TRUE, show_points = FALSE,
    direction_length = 2, directions_col = "black")

Example output

Loading required package: modeltools
Loading required package: stats4
Loading required package: nnls

archetypes documentation built on May 2, 2019, 9:18 a.m.