dist_cohesion_plot {pald}

Distance Cohesion Plot

Description

Provides a plot of cohesion against distance, with the threshold indicated by a horizontal line.

Usage

dist_cohesion_plot(
  d,
  mutual = FALSE,
  xlim_max = NULL,
  cex = 1,
  colors = NULL,
  weak_gray = FALSE
)

Arguments

d

A matrix of pairwise distances or a dist object.

mutual

Set to TRUE to consider mutual cohesion (i.e., symmetrized using the minimum); the default is FALSE.

xlim_max

If desired, set the maximum value of distance which is displayed on the x-axis.

cex

Factor by which points should be scaled relative to the default.

colors

A vector of color names, if none is given a default is provided.

weak_gray

Set to TRUE to display the plot with all weak ties plotted in gray; the default is FALSE.

Details

The plot of cohesion against distance provides a visualization for the manner in which distance is transformed. The threshold distinguishing strong and weak ties is indicated by a horizontal line. When there are separated regions with different density, one can often observe vertical bands of color, see example below and Berenhaut, Moore, and Melvin (2022). For each distance pair in d, the corresponding value of cohesion is computed. If the pair is within a single cluster, the point is colored (with the same color provided by the pald and plot_community_graphs functions). Weak ties appear below the threshold.

Note that cohesion is not symmetric, and so all n^2 points are plotted. A gray point above the threshold corresponds to a pair in which the value of cohesion is greater than the threshold in only one direction. If one only wants to observe mutual cohesion (i.e., cohesion made symmetric via the minimum), set mutual = TRUE.

Value

A plot of cohesion against distance with threshold indicated by a horizontal line.

Examples

D <- dist(exdata2)
dist_cohesion_plot(D)
dist_cohesion_plot(D, mutual = TRUE)
C <- cohesion_matrix(D)
threshold <- strong_threshold(C) #the horizontal line
dist_cohesion_plot(D, mutual = TRUE, weak_gray = TRUE)