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("auto", "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. "auto" (default) draws the back-to-back pyramid for exactly 2 groups and the heatmap for any other number; "pyramid" and "heatmap" force a specific style.
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: patterns with p_value < alpha are starred and drawn in bold dark text, the rest stay plain grey. 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 July 11, 2026, 1:09 a.m.