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Temporal Network Prism (3D Glass Box)

Source: R/plot-temporal.R
plot_temporal.Rd

Plots a network at different time points as vertical planes inside a 3D oblique-projection box, with time running from left to right. Each network plane extends into the depth of the box, and all planes share one node layout. At least two time points are required.

Usage

plot_temporal(
  x,
  time = NULL,
  slices = NULL,
  cumulative = FALSE,
  labels = NULL,
  layout = "spring",
  node_size = 2.5,
  node_color = "steelblue",
  color_by = c("layer", "node"),
  node_shape = 21,
  node_border = "gray30",
  edge_color = "#E41A1C",
  edge_width = 1.5,
  edge_alpha = 0.35,
  plane_color = "gray92",
  plane_alpha = 0.2,
  plane_border = "gray60",
  plane_lty = 2,
  box = TRUE,
  box_color = "gray40",
  connections = FALSE,
  connection_color = "gray50",
  connection_alpha = 0.15,
  minimum = 0,
  show_labels = FALSE,
  label_size = 0.4,
  title = NULL,
  angle = c(1, 0.7),
  seed = 42,
  ...
)

Arguments

x

An edge list data frame with columns from, to, optionally weight, and a time column; a cograph_network whose stored edge data contain the time column; or a list of network objects.

time

Character. Name of the time column. Required for data frame input. It also labels the time axis.

slices

Integer or NULL. Number of equal-width bins of the numeric time column. Empty bins are kept as empty planes. Default NULL uses the unique time values.

cumulative

Logical. If TRUE, each plane contains all edges up to its time point. Default FALSE.

labels

Character vector of layer labels, one per plane. The default NULL uses the time values, or "T1", "T2", ... for list input.

layout

Character or matrix. A character value computes one Fruchterman-Reingold layout from the summed network. A two-column matrix supplies shared coordinates, one row per node. Default "spring".

node_size

Numeric. Point size (cex). Default 2.5.

node_color

Character or vector. Node fill color. A single color applies to every node. An unnamed vector is recycled across layers and colors each plane as a whole, unless color_by = "node". A named vector is matched to node names and gives each node the same color on every plane. A named vector that lacks a node raises an error of class cograph_node_color_incomplete. Default "steelblue".

color_by

One of "layer" (default) or "node". It sets whether an unnamed node_color vector is recycled over layers or over nodes. A named node_color always colors by node.

node_shape

Integer. Point shape (pch). Default 21 (filled circle).

node_border

Character. Node border color. Default "gray30".

edge_color

Character or vector. Edge color (single or per-layer). Default "#E41A1C".

edge_width

Numeric. Maximum added edge width. An edge has width 0.3 + edge_width * abs(w) / max(abs(w)). Default 1.5.

edge_alpha

Numeric. Edge transparency (0-1). Default 0.35.

plane_color

Character or vector. Plane fill color (single or per-layer). Default "gray92".

plane_alpha

Numeric. Plane fill transparency (0-1). Default 0.2.

plane_border

Character. Plane border color. Default "gray60".

plane_lty

Integer. Plane border line type. Default 2 (dashed).

box

Logical. Whether the 3D bounding box is plotted. Default TRUE.

box_color

Character. Box edge color. Default "gray40".

connections

Logical. Whether lines connect each node to itself on the next plane. Default FALSE.

connection_color

Character. Color of the connecting lines. Default "gray50".

connection_alpha

Numeric. Transparency of the connecting lines. Default 0.15.

minimum

Numeric. Only edges with weight greater than minimum are plotted. Default 0.

show_labels

Logical. Show node labels. Default FALSE.

label_size

Numeric. Label text size. Default 0.4.

title

Character or NULL. Plot title. Default NULL.

angle

Numeric vector of length 2: c(dz_x, dz_y) controlling the oblique projection shear. Default c(1.0, 0.7).

seed

Integer or NULL. Random seed for the shared layout. The caller's random number state is restored on exit. NULL sets no seed. Default 42.

...

Currently unused.

Value

Invisibly, a list of weight matrices, one per plane, with one row and one column per node.

See also

plot_network_evolution, plot_mlna

Examples

set.seed(1)
edges <- data.frame(
  from = sample(LETTERS[1:5], 30, replace = TRUE),
  to   = sample(LETTERS[1:5], 30, replace = TRUE),
  week = sample(1:3, 30, replace = TRUE))
cograph::plot_temporal(edges, time = "week")