plot.net_sequence_comparison: Plot Method for net_sequence_comparison

In Nestimate: Network Estimation, Bootstrap, and Higher-Order Analysis

Plot Method for net_sequence_comparison

Description

Visualizes pattern-level standardized residuals across groups. Two styles are available:

"pyramid"

Back-to-back bars of pattern proportions, shaded by each side's standardized residual. Requires exactly 2 groups.

"heatmap"

One tile per (pattern, group) cell, colored by standardized residual. Works for any number of groups.

Residuals are read directly from the resid_<group> columns in $patterns, which are always populated regardless of the inference method chosen in sequence_compare.

Usage

## S3 method for class 'net_sequence_comparison'
plot(
  x,
  top_n = 10L,
  style = c("pyramid", "heatmap"),
  sort = c("statistic", "frequency"),
  alpha = 0.05,
  show_residuals = FALSE,
  ...
)

Arguments

x	A net_sequence_comparison object.
top_n	Integer. Show top N patterns. Default: 10.
style	Character. "pyramid" (default) or "heatmap".
sort	Character. "statistic" (default) ranks patterns by test statistic or residual magnitude. "frequency" ranks by total occurrence count across all groups.
alpha	Numeric. Significance threshold for p-value display in the pyramid. Default: 0.05.
show_residuals	Logical. If TRUE, print the standardized residual value inside each pyramid bar. Default: FALSE. Ignored for the heatmap (which always shows residuals).
...	Additional arguments (ignored).

Value

A ggplot object, invisibly.

Examples

seqs <- data.frame(
  V1 = sample(LETTERS[1:4], 60, TRUE),
  V2 = sample(LETTERS[1:4], 60, TRUE),
  V3 = sample(LETTERS[1:4], 60, TRUE),
  V4 = sample(LETTERS[1:4], 60, TRUE)
)
grp <- rep(c("X", "Y"), 30)
net <- build_network(seqs, method = "relative")
res <- sequence_compare(net, group = grp, sub = 2:3, test = "chisq")

Nestimate documentation built on April 20, 2026, 5:06 p.m.