% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotLRrank.R
\name{plotLRrank}
\alias{plotLRrank}
\alias{plotLRrank.blisa}
\alias{plotLRrank.data.frame}
\title{Dot plot ranking LR pairs by number of significant hotspot bins}
\usage{
plotLRrank(x, ...)

\method{plotLRrank}{blisa}(x, top = 30, pt_size = 4, flip = FALSE, ...)

\method{plotLRrank}{data.frame}(x, top = 30, pt_size = 4, flip = FALSE, ...)
}
\arguments{
\item{x}{A \code{blisa} object or a data frame of LR results. The data frame
must contain columns \code{sig_numbers} and \code{annotation}.}

\item{...}{Additional arguments passed to the relevant method.}

\item{top}{Integer or \code{NULL}. Number of top LR pairs (by
\code{sig_numbers}) to display. Default \code{30}.}

\item{pt_size}{Numeric. Point size passed to \code{geom_point}. Default 4.}

\item{flip}{Logical. When \code{TRUE}, LR pairs are placed on the x-axis
and the hotspot count on the y-axis (vertical orientation). Default
\code{FALSE} (LR pairs on y-axis, horizontal orientation).}
}
\value{
A \code{ggplot} object.
}
\description{
Generic function for ranking LR pairs. Dispatches on the class of \code{x}:
\itemize{
\item \code{plotLRrank.blisa} accepts a \code{blisa} object and uses its
\code{LR_results} slot directly.
\item \code{plotLRrank.data.frame} accepts the \code{LR_results} data
frame directly.
}
}
\section{Methods (by class)}{
\itemize{
\item \code{plotLRrank(blisa)}: Method for a \code{blisa} object. Extracts
\code{LR_results} and delegates to \code{plotLRrank.data.frame}.

\item \code{plotLRrank(data.frame)}: Method for a data frame of LR results (e.g. the
\code{LR_results} slot of a \code{blisa} object).

}}
