plot_trajectories: Plot Individual Trajectories

In cograph: Analysis and Visualization of Complex Networks

Plot Individual Trajectories

Description

Creates an alluvial-style diagram where each individual's trajectory is shown as a separate line. This is an alias for plot_transitions() with track_individuals = TRUE.

Usage

plot_trajectories(
  x,
  from_title = NULL,
  title = NULL,
  from_colors = NULL,
  flow_color_by = "first",
  node_width = 0.08,
  node_border = NA,
  node_spacing = 0.02,
  label_size = 3.5,
  label_position = c("beside", "inside", "above", "below", "outside"),
  mid_label_position = NULL,
  label_halo = TRUE,
  label_color = "black",
  label_fontface = "plain",
  label_nudge = 0.02,
  title_size = 5,
  title_color = "black",
  title_fontface = "bold",
  curve_strength = 0.6,
  line_alpha = 0.3,
  line_width = 0.5,
  jitter_amount = 0.8,
  show_totals = FALSE,
  total_size = 4,
  total_color = "white",
  total_fontface = "bold",
  show_values = FALSE,
  value_position = c("center", "origin", "destination"),
  value_size = 3,
  value_color = "black",
  value_halo = NULL,
  value_fontface = "bold",
  value_nudge = 0.03,
  value_min = 0,
  value_digits = 2,
  column_gap = 1,
  proportional_nodes = TRUE,
  node_label_format = NULL,
  bundle_size = NULL,
  bundle_legend = TRUE,
  bundle_legend_size = 3,
  bundle_legend_color = "grey50",
  bundle_legend_fontface = "italic",
  bundle_legend_position = c("bottom", "top")
)

Arguments

x	Input data in one of several formats: A transition matrix (rows = from, cols = to, values = counts) Two vectors: pass before as x and after as second argument (contingency table computed automatically, like chi-square) A 2-column data frame (raw observations; table computed automatically) A data frame with columns: from, to, count A list of matrices for multi-step transitions
from_title	Title for the left column. Default "From". For multi-step, use a vector of titles (e.g., c("T1", "T2", "T3", "T4")).
title	Optional plot title. Applied via ggplot2::labs(title = title).
from_colors	Colors for left-side nodes. Default uses palette.
flow_color_by	Color flows by "source", "destination", or NULL (use flow_fill). Default NULL.
node_width	Width of node rectangles (0-1 scale). Default 0.08.
node_border	Border color for nodes. Default NA (no border).
node_spacing	Vertical spacing between nodes (0-1 scale). Default 0.02.
label_size	Size of node labels. Default 3.5.
label_position	Position of node labels: "beside" (default), "inside", "above", "below", "outside". Applied to first and last columns. See mid_label_position for middle columns.
mid_label_position	Position of labels for intermediate (middle) columns. Same options as label_position. Default NULL uses label_position value.
label_halo	Logical: add white halo around labels for readability? Default TRUE.
label_color	Color of state name labels. Default "black".
label_fontface	Font face of state name labels ("plain", "bold", "italic", "bold.italic"). Default "plain".
label_nudge	Distance between node edge and label (in plot units). Default 0.02. Increase for more spacing.
title_size	Size of column titles. Default 5.
title_color	Color of column title text. Default "black".
title_fontface	Font face of column titles. Default "bold".
curve_strength	Controls bezier curve shape (0-1). Default 0.6.
line_alpha	Alpha for individual tracking lines. Default 0.3.
line_width	Width of individual tracking lines. Default 0.5.
jitter_amount	Vertical jitter for individual lines (0-1). Default 0.8.
show_totals	Logical: show total counts on nodes? Default FALSE.
total_size	Size of total labels. Default 4.
total_color	Color of total labels. Default "white".
total_fontface	Font face of total labels. Default "bold".
show_values	Logical: show transition counts on flows? Default FALSE.
value_position	Position of flow values: "center", "origin", "destination", "outside_origin", "outside_destination". Default "center".
value_size	Size of value labels on flows. Default 3.
value_color	Color of value labels. Default "black".
value_halo	Logical: add halo around flow value labels? Default NULL (inherits from label_halo).
value_fontface	Font face of flow value labels. Default "bold".
value_nudge	Distance of value labels from node edge when using "origin" or "destination" positions. Default 0.03.
value_min	Minimum count to show a flow value label. Default 0 (show all). Use to hide small flows (e.g., value_min = 100).
value_digits	Number of decimal places for flow value labels and node totals. Default 2.
column_gap	Horizontal spread of columns (0-1). Default 1 uses full width. Use smaller values (e.g., 0.6) to bring columns closer together.
proportional_nodes	Logical: size nodes proportionally to counts? Default TRUE.
node_label_format	Format string for node labels with {state} and {count} placeholders. Default NULL (plain state name). Example: "{state} (n={count})".
bundle_size	Controls line bundling for large datasets. Default NULL (no bundling). Integer >= 2: each drawn line represents that many cases. Numeric in (0,1): reduce to this fraction of original lines (e.g., 0.15 keeps about 15 percent of lines).
bundle_legend	Logical or character: show annotation when bundling is active? Default TRUE shows "Each line ~ N cases" below the plot. Pass a string to use custom text (with {n} placeholder for count).
bundle_legend_size	Size of the bundle legend text. Default 3.
bundle_legend_color	Color of the bundle legend text. Default "grey50".
bundle_legend_fontface	Font face of the bundle legend text. Default "italic".
bundle_legend_position	Position of the bundle legend: "bottom" (default) or "top".

Value

A ggplot2 object.

See Also

plot_transitions, plot_alluvial

Examples

## Not run: 
# Track individual trajectories across time points
df <- data.frame(
  Baseline = c("Light", "Light", "Intense", "Resource"),
  Week4 = c("Light", "Intense", "Intense", "Light"),
  Week8 = c("Resource", "Intense", "Light", "Light")
)
plot_trajectories(df, flow_color_by = "first")

## End(Not run)

cograph documentation built on April 1, 2026, 1:07 a.m.