Plot the quasi-potential landscape (Stage 2 output)

Shows U(x) = -log p(x) along the state-transition axis. Point-estimate critical-point classifications and barrier heights are omitted by default; they require explicit diagnostic opt-in until uncertainty is available. The returned scientific caption describes the selected component, plotted encodings, missing observations, and exploratory claim boundary separately from the graphic.

Usage

plot_potential(std, colour_by = NULL, show_critical_points = FALSE)

Arguments

std

StateTransitionData with metadata()$stage2 present

colour_by

character column name in colData(std) to colour the rug of sample positions, or NULL (default NULL)

show_critical_points

logical; explicitly opt in to point-estimate well/barrier classifications and barrier-height segments. Defaults to FALSE because current output does not estimate critical-point uncertainty; opt-in output is exploratory diagnostic information only.

Value

a ggplot object

Examples

if (FALSE) { # \dontrun{
# Requires Stage 2 to have been run
plot_potential(std_with_stage2)
} # }