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Plot the trajectory confluence matrix (finals vs intermediates)

Source: R/plot_trajectory_confluence_matrix.R
plot_trajectory_confluence_matrix.Rd

A heatmap of how each intermediate (absorbed) trajectory's papers spread across the final trajectories. By default rows are the final trajectories tr::cNgN and columns are the intermediate trajectories trN (swap with orientation); the fill is the coupling strength (shared documents) and each intermediate's dominant-final cell is outlined. Which intermediates appear is decided by the same pruning the other flow plots use (plot_trajectory_lines_2d(), plot_trajectory_confluence()), so the column set is consistent across views.

Usage

plot_trajectory_confluence_matrix(
  flow,
  conf = NULL,
  fill = c("n_shared", "prop_of_group", "prop_of_traj"),
  orientation = c("finals-cols", "finals-rows"),
  order_by = c("terminal", "reach", "size", "alpha", "cluster"),
  min_n = 5,
  min_prop = 0.05,
  min_total_size = 0,
  min_duration_years = 0,
  min_target_n = 0,
  mark_terminal = TRUE,
  show_values = FALSE,
  label_size = 2.5,
  axis_text_size = NULL,
  axis_title_size = NULL,
  legend_position = "right",
  legend_text_size = NULL,
  bg = "white",
  title = "Trajectory matrix"
)

Arguments

flow

A sniff_trajectory_braid() object.

conf

An optional precomputed sniff_trajectory_confluence() object for flow; NULL (default) computes it.

fill

"n_shared" (default, log-scaled), "prop_of_group", or "prop_of_traj".

orientation

"finals-cols" (default): final trajectories tr::cNgN on the rows (y-axis), intermediate trajectories trN on the columns (x-axis) – the "finals (rows) x intermediates (cols)" matrix. "finals-rows" is the transpose (finals on the columns, intermediates on the rows).

order_by

How the intermediate trajectories are ordered along their axis: "terminal" (default, grouped by dominant final then reach), "reach" (total shared documents), "size" (trajectory size at handoff), "alpha" (alphabetical), or "cluster" (seriation that reorders both axes by hierarchical clustering – intermediates by their destination profile and finals by their source profile – so alike rows and columns form blocks).

min_n, min_prop, min_total_size, min_duration_years

Thresholds selecting which intermediate trajectories are shown, passed to the same prune as plot_trajectory_lines_2d(): an intermediate is kept only if it transfers >= min_n papers and >= min_prop of its cohort, has total size >= min_total_size and lifespan >= min_duration_years.

min_target_n

Minimum shared documents a cell must have to be drawn (default 0, all cells); raise it to hide the long tail of small overlaps. Cells with zero shared documents are never drawn. Final trajectories are always kept on their axis, even when the thresholds leave them with no cell.

mark_terminal

Outline each intermediate's dominant-final cell (default TRUE).

show_values

Print the value inside each cell (default FALSE). The text colour auto-contrasts (dark on light cells, light on dark) for legibility.

label_size

Font size of the in-cell values (default 2.5).

axis_text_size

Font size of the axis (trajectory id) tick labels; NULL (default) keeps the theme default.

axis_title_size

Font size of the axis titles ("Final Trajectory" / "Intermediate Trajectory"); NULL (default) keeps the theme default.

legend_position

Where to put the colourbar: "right" (default), "left", "top", "bottom", "none", or a c(x, y) coordinate inside the panel (each in 0..1). "top"/"bottom" draw the colourbar horizontally.

legend_text_size

Font size of the legend text; NULL (default) keeps the theme default.

bg

Panel/plot background colour (default "white"). A darker background (e.g. "grey20") raises contrast against the bright cells; the grid lines and the terminal outline auto-adapt to its luminance.

title

Plot title (default "Trajectory matrix"); NULL removes it.

Value

A ggplot object.

See also

sniff_trajectory_braid(), plot_trajectory_lines_2d(), plot_trajectory_confluence()

Other visualization: plot_groups_influence_matrix(), plot_groups_influence_network(), plot_groups_lineage_2d(), plot_groups_lineage_3d(), plot_groups_map(), plot_groups_map_animation(), plot_groups_map_interactive(), plot_groups_per_year(), plot_trajectory_confluence(), plot_trajectory_confluence_interactive(), plot_trajectory_dag(), plot_trajectory_dag_interactive(), plot_trajectory_dispersion(), plot_trajectory_dynamics(), plot_trajectory_dynamics_interactive(), plot_trajectory_formation(), plot_trajectory_lines_2d(), plot_trajectory_lines_3d()

Examples

if (FALSE) { # \dontrun{
flow <- sniff_trajectory_braid(docs_per_group)
plot_trajectory_confluence_matrix(flow, min_n = 20, show_values = TRUE)
plot_trajectory_confluence_matrix(flow, order_by = "cluster", bg = "grey20")
} # }