sequence_plot: Sequence Plot (heatmap, index, or distribution)

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

Sequence Plot (heatmap, index, or distribution)

Description

Single entry point for three categorical-sequence visualisations.

• type = "heatmap" (default): dense carpet, rows reordered by sort / dendrogram (single panel).

• type = "index": same data layout, but rows separated by thin gaps (no dendrogram). Supports grouping via group or a net_clustering, plus a ncol x nrow facet grid.

• type = "distribution": dispatches to distribution_plot.

Usage

sequence_plot(
  x,
  type = c("heatmap", "index", "distribution"),
  sort = c("lcs", "frequency", "start", "end", "hamming", "osa", "lv", "dl", "qgram",
    "cosine", "jaccard", "jw"),
  tree = NULL,
  group = NULL,
  scale = c("proportion", "count"),
  geom = c("area", "bar"),
  na = TRUE,
  row_gap = 0,
  dendrogram_width = 1.2,
  k = NULL,
  k_color = "white",
  k_line_width = 2.5,
  state_colors = NULL,
  na_color = "grey90",
  cell_border = NA,
  frame = FALSE,
  width = NULL,
  height = NULL,
  main = NULL,
  show_n = TRUE,
  time_label = "Time",
  xlab = NULL,
  y_label = NULL,
  ylab = NULL,
  tick = NULL,
  ncol = NULL,
  nrow = NULL,
  legend = NULL,
  legend_size = NULL,
  legend_title = NULL,
  legend_ncol = NULL,
  legend_border = NA,
  legend_bty = "n"
)

Arguments

x	Wide-format sequence data (data.frame or matrix) or a net_clustering. One row per sequence, one column per time point.
type	One of "heatmap" (default), "index", or "distribution".
sort	Row-ordering strategy for heatmap / within-panel for index. One of "lcs" (default), "frequency", "start", "end", or any build_clusters distance ("hamming", "osa", "lv", "dl", "qgram", "cosine", "jaccard", "jw").
tree	Optional hclust/dendrogram/agnes object to supply row ordering (heatmap only; overrides sort).
group	Optional grouping vector (length nrow(x)) producing one facet per group. Index/distribution only. Ignored for heatmap.
scale, geom, na	Passed to distribution_plot when type = "distribution".
row_gap	Fraction of row height used as vertical gap between sequences in index plots. 0 (default) = dense like heatmap. Try 0.15 for visible separators at low row counts.
dendrogram_width	Width ratio of the dendrogram panel (heatmap).
k	Optional integer. When supplied in type = "heatmap", cuts the dendrogram into k clusters and draws thin horizontal separators between them in the carpet. Ignored when there is no dendrogram (e.g. sort = "start") or for other types.
k_color	Colour for the cluster separator lines. Default "white".
k_line_width	Line width for the cluster separators. Default 2.5.
state_colors	Vector of colours, one per state.
na_color	Colour for NA cells.
cell_border	Cell border colour. NA = off.
frame	If TRUE (default), draw a box around each panel. If FALSE, no box - axis ticks and labels still appear.
width, height	Optional device dimensions in inches. When supplied, opens a new graphics device via grDevices::dev.new(). In knitr chunks use the fig.width / fig.height chunk options instead.
main	Plot title.
show_n	Append "(n = N)" to the title.
time_label, xlab	X-axis label. xlab is an alias.
y_label, ylab	Y-axis label (distribution only). ylab alias.
tick	Show every Nth x-axis label. NULL = auto.
ncol, nrow	Facet grid dimensions (index + distribution).
legend	Legend position: "bottom", "right", or "none". Default varies by type.
legend_size	Legend text size. NULL (default) auto-scales from the device width so the legend looks proportional at 5 in vs 12 in figures (clamped to [0.65, 1.2]).
legend_title	Optional legend title.
legend_ncol	Number of legend columns.
legend_border	Swatch border colour.
legend_bty	"n" or "o".

Value

Invisibly, a list describing the plot (shape depends on type).

See Also

distribution_plot, build_clusters

Examples

sequence_plot(trajectories)
sequence_plot(trajectories, type = "index")
sequence_plot(trajectories, type = "distribution")

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