Plot a distance matrix as a 2D projection

Reduces a distance matrix to two dimensions using Classical MDS, Isotonic MDS, or t-SNE, and returns a ggplot2 scatter plot in which proximity reflects similarity. Points can optionally be highlighted or split into facet panels by group.

Usage

plot_dist(
  d,
  method = c("cmds", "isomds", "tsne"),
  highlight = NULL,
  gp = NULL,
  point.alpha = 0.8
)

Arguments

d

A distance matrix of class dist. Labels must be set (i.e. labels(d) must not be NULL). Duplicate labels are not permitted.

method

Character string specifying the dimensionality-reduction method. One of:

"cmds"

Classical (metric) Multidimensional Scaling via cmdscale. This is the default.

"isomds"

Non-metric (isotonic) MDS via isoMDS. Automatically falls back to "cmds" with a message when n < 3.

"tsne"

t-distributed Stochastic Neighbour Embedding via Rtsne. Perplexity is set automatically to min(30, floor((n - 1) / 3)).

highlight

Optional character vector of labels to highlight in the plot. Matching identifiers are plotted in red; all others in black. NULL (default) disables highlighting. Every value must be present in labels(d).

gp

Optional named character vector mapping labels to group names (names(gp) = labels, values = group names). When supplied, the plot is split into one facet panel per group via facet_wrap. The set of names must match labels(d) exactly. NULL (default) produces a single panel.

point.alpha

Alpha transparency value for points.

Value

A ggplot object. The plot can be further customised with standard ggplot2 additions before printing or saving.

See also

cmdscale, isoMDS, Rtsne, ggplot

Examples

# Basic usage with the built-in eurodist dataset
plot_dist(eurodist)


# Non-metric MDS with two highlighted cities
plot_dist(eurodist, method = "isomds",
          highlight = c("Madrid", "Rome"))


# Classical MDS split by a user-defined grouping
regions <-
  c(Athens = "South",  Barcelona = "South", Brussels = "North",
    Calais = "North",  Cherbourg = "North", Cologne = "North",
    Copenhagen = "North", Geneva = "South", Gibraltar = "South",
    Hamburg = "North", `Hook of Holland` = "North", Lisbon = "South",
    Lyons = "South",  Madrid = "South",  Marseilles = "South",
    Milan = "South",  Munich = "North",  Paris = "North",
    Rome = "South",   Stockholm = "North", Vienna = "North")

plot_dist(eurodist, method = "cmds", gp = regions,
          highlight = c("Madrid", "Cherbourg", "Rome", "Brussels"))