Plot Sequence Motif Summaries — plot_sequence

Draws a dependency-free base-R bar chart of structural motif measurements.

Usage

plot_sequence_motifs(
  x,
  metric = c("sequence_prevalence", "n_occurrences", "n_sequences", "occurrence_share"),
  top_n = 20L,
  motif_lengths = NULL,
  ties = c("include", "first"),
  horizontal = TRUE
)

Arguments

x: A motif extraction, summary, or filtered-motif object.
metric: Structural metric to plot: "sequence_prevalence", "n_occurrences", "n_sequences", or "occurrence_share".
top_n: Positive whole number giving the requested number of motifs.
motif_lengths: Optional vector of positive whole-number motif lengths to retain.
ties: Top-n boundary policy. "include" retains all motifs tied on the selected metric; "first" retains exactly top_n after deterministic secondary sorting.
horizontal: Logical value indicating whether bars should be horizontal.

Value

Invisibly returns the exact motif table used for plotting, including plot_rank, plot_value, plot_label, and bar_midpoint.

Details

The plot is descriptive. It does not perform inferential testing or assign substantive meaning to motif frequency or prevalence. Empty inputs produce an informative blank plot and return an empty table.

Examples

sequences <- data.frame(
  id = c(rep("s1", 5L), rep("s2", 4L)),
  position = c(1:5, 1:4),
  state = c("A", "B", "A", "B", "C", "A", "B", "C", "B")
)

extracted <- extract_sequence_ngrams(
  sequences,
  sequence_id_col = "id",
  order_col = "position",
  state_col = "state"
)

plot_sequence_motifs(
  extracted,
  metric = "sequence_prevalence",
  top_n = 10
)