% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotCCILR.R
\name{plotCCILR}
\alias{plotCCILR}
\alias{plotCCILR.blisa}
\alias{plotCCILR.default}
\title{Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair}
\usage{
plotCCILR(x, ...)

\method{plotCCILR}{blisa}(x, index = 1, ligand = NULL, receptor = NULL, ...)

\method{plotCCILR}{default}(x, lr_pair, ...)
}
\arguments{
\item{x}{A \code{blisa} object or a CCI scores data frame (the
\code{CCI_scores} slot of a \code{blisa} object).}

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

\item{index}{Integer. Row index into \code{LR_results} selecting the
ligand-receptor pair to visualise. Ignored when both \code{ligand} and
\code{receptor} are supplied. Default \code{1} (top-ranked pair).}

\item{ligand}{Character. Ligand gene symbol. When both \code{ligand} and
\code{receptor} are provided the matching LR pair is located automatically
and \code{index} is ignored. Must be supplied together with
\code{receptor}.}

\item{receptor}{Character. Receptor gene symbol. Must be supplied together
with \code{ligand}.}

\item{lr_pair}{Character. Column name in the CCI scores data frame
corresponding to the ligand-receptor pair to visualise
(e.g. \code{"CXCL12_CXCR4"}).}
}
\value{
A \code{Heatmap} object.
}
\description{
Generic function. Reshapes the CCI data frame into a receiver-by-sender
cell-type matrix for one selected LR pair and draws a clustered heatmap.
}
\section{Methods (by class)}{
\itemize{
\item \code{plotCCILR(blisa)}: Method for a \code{blisa} object. The LR pair is
selected by \code{index} (default 1, the top-ranked pair) unless both
\code{ligand} and \code{receptor} are supplied, in which case the matching
row is located automatically and \code{index} is ignored. Stops with an
informative error if \code{CCI_scores} is \code{NULL} or the selected LR
pair has no significant hotspots.

\item \code{plotCCILR(default)}: Method for a CCI scores data frame (e.g. the
\code{CCI_scores} slot of a \code{blisa} object). The LR pair is selected
by column name via \code{lr_pair}.

}}
\seealso{
\code{\link{plotCCI}} for an overview heatmap across all LR pairs;
\code{\link{plotCCIsummary}} for an aggregated sender-by-receiver heatmap.
}
