% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sequence-visualisations-extended.R
\name{plot_sequence_state_distribution}
\alias{plot_sequence_state_distribution}
\title{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{
\item{data}{Long-format sequence data or a prepared result.}

\item{sequence_id_col, order_col, state_col}{Core sequence columns.}

\item{proportion}{Plot position-wise proportions rather than counts.}

\item{state_levels}{Optional state ordering.}

\item{palette}{Base HCL palette.}

\item{...}{Additional arguments passed to \code{\link[graphics:matplot]{graphics::matplot()}}.}
}
\value{
A position-by-state matrix, invisibly.
}
\description{
Plot state distributions over aligned positions
}
\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)
}
