% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/CCA_wrappers.r
\name{compareClusterCalls}
\alias{compareClusterCalls}
\title{Compare two cluster sets matched to CCA}
\usage{
compareClusterCalls(cl, ref.cl, cl.anno, plot.title = NA,
  plot.silent = TRUE, heat.colors = colorRampPalette(c("grey99",
  "orange", "red"))(100), row.cl.num = min(length(unique(cl)),
  length(unique(ref.cl))))
}
\arguments{
\item{cl}{a matrix (rows=genes x columns=samples) of gene expression data
(e.g., scRNA-seq)}

\item{by.rows}{By rows (TRUE; default) or by columns}
}
\value{
a reordered matrix
}
\description{
This function takes cluster calls defined in two different data sets and then
determines to what extent these cluster calls match up with cluster calls from CCA.
}