plot.shift_magnitude_counts: Plot One Shift Count Or Frequency Comparison

In bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits

Plot One Shift Count Or Frequency Comparison

Description

Summarize inferred rate increases and decreases for one set of search outputs. The default paired frequency plot mirrors the count/frequency comparison used for Berv et al. (2026) Supplementary Figure 5.

Usage

## S3 method for class 'shift_magnitude_counts'
plot(
  x,
  statistic = c("frequency", "count"),
  colors = c(increase = "#377eb8", decrease = "#e41a1c"),
  point_cex = 1.15,
  line_col = grDevices::adjustcolor("grey35", alpha.f = 0.35),
  boxplot = TRUE,
  paired_lines = TRUE,
  paired_test = TRUE,
  reference_line = NULL,
  ylim = NULL,
  ylab = NULL,
  main = NULL,
  mar = c(4.5, 4.2, 2.4, 0.8),
  oma = c(0, 0, 0, 0),
  ...
)

Arguments

x	A shift_magnitude_counts object.
statistic	Plot "frequency" or raw "count" values.
colors	Named colors for "increase" and "decrease".
point_cex	Point size for run-level observations.
line_col	Color for paired run-level segments.
boxplot	Logical; overlay compact boxplots.
paired_lines	Logical; draw paired decrease-to-increase segments for each run.
paired_test	Logical; annotate the plot with a paired Wilcoxon test when at least two runs are available.
reference_line	Optional horizontal reference line. Defaults to 0.5 for frequencies and no line for counts.
ylim	Optional common y-axis limits.
ylab, main	Plot labels.
mar, oma	Graphical margins passed to graphics::par().
...	Additional graphical parameters passed to graphics::plot().

Value

Invisibly returns a list with the count data, paired tests, and plot settings.

Examples

transitions <- data.frame(
  rate_change = c("root", "increase", "increase", "decrease", "decrease"),
  rate_delta = c(NA, 3, 4, -1, -2)
)
counts <- shift_magnitude_counts(list(run1 = transitions, run2 = transitions))
plot(counts)

bifrost documentation built on Nov. 5, 2026, 9:07 a.m.