Plot state distributions over aligned positions — plot_sequence_state_distribution • gp3sequences

Plot state distributions over aligned positions

Usage

plot_sequence_state_distribution(
  data,
  sequence_id_col = "sequence_id",
  order_col = "sequence_order",
  state_col = "state",
  proportion = TRUE,
  state_levels = NULL,
  palette = "Dark 3",
  ...
)

Arguments

data: Long-format sequence data or a prepared result.
sequence_id_col, order_col, state_col: Core sequence columns.
proportion: Plot position-wise proportions rather than counts.
state_levels: Optional state ordering.
palette: Base HCL palette.
...: Additional arguments passed to graphics::matplot().

Value

A position-by-state matrix, invisibly.

Examples

data <- data.frame(sequence_id = rep(c("a", "b"), each = 4L),
                   sequence_order = rep(1:4, 2L),
                   state = c("A", "B", "C", "D", "A", "C", "C", "D"))
plot_sequence_state_distribution(data)