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Plot methods for ljmds objects

Source: R/plot.R
plot.ljmds.Rd

Reproduces the diagnostic figures used in Satoh (2026):

  • "trajectory": cluster centroid trajectories on the modified MDS configuration.

  • "dendrogram": Ward dendrogram on H with k coloured boxes.

  • "cmd": time-collapsed MDS map of H, points coloured by class.

  • "means": class-mean smoothed occurrence curves.

  • "panels": all keywords overlaid on a single panel; per class, individual smoothed occurrence curves are drawn as thin semi-transparent lines and the class mean as a thick opaque line of the same colour.

Usage

# S3 method for class 'ljmds'
plot(
  x,
  type = c("trajectory", "dendrogram", "cmd", "means", "panels"),
  class.col = grDevices::palette.colors(8, "Classic Tableau"),
  ...
)

# S3 method for class 'ljmds.sel'
plot(x, pal = grDevices::hcl.colors(64, "YlGnBu", rev = TRUE), ...)

Arguments

x

An object returned by ljmds.pipeline().

type

One of "trajectory", "dendrogram", "cmd", "means", "panels".

class.col

Optional colour palette for the classes. Defaults to the current R palette (grDevices::palette.colors(8, "Classic Tableau")); recycled if k exceeds its length.

...

Further arguments passed to underlying plot calls.

pal

Diverging or sequential palette used for the heatmap cells of plot.ljmds.sel(). Default is a reversed YlGnBu sequential palette so that high silhouette values appear darker.

Details

All five figure types are drawn without a main title so the caller can place a caption externally (e.g. in a LaTeX figure environment).

See also

ljmds.pipeline() which produces the object, ljmds.select() for (h, k) selection, ljmds.animate() for the dynamic counterpart.