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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/CCA_wrappers.r
\title{Compare two cluster sets matched to CCA}
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)),
\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}
a reordered matrix
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.
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