--- a
+++ b/man/compAgree.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compAgree.R
+\name{compAgree}
+\alias{compAgree}
+\title{Comparison of agreement between two subtypes}
+\usage{
+compAgree(
+  moic.res = NULL,
+  subt2comp = NULL,
+  doPlot = TRUE,
+  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
+    "#023E8A", "#9D4EDD"),
+  box.width = 0.1,
+  fig.name = NULL,
+  fig.path = getwd(),
+  width = 6,
+  height = 5
+)
+}
+\arguments{
+\item{moic.res}{An object returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms.}
+
+\item{subt2comp}{A data.frame of subtypes that need to compare with current subtype with rownames for samples and columns for other subtypes.}
+
+\item{doPlot}{A logic value to indicate if generating alluvial diagram to show the agreement of different subtypes; TRUE by default.}
+
+\item{clust.col}{A string vector storing colors for each cluster.}
+
+\item{box.width}{A numeric valur to indicate the width for box in alluvial diagram.}
+
+\item{fig.name}{A string value to indicate the name of the figure.}
+
+\item{fig.path}{A string value to indicate the output path for storing the figure.}
+
+\item{width}{A numeric value to indicate the width of alluvial diagram.}
+
+\item{height}{A numeric value to indicate the height of alluvial diagram.}
+}
+\value{
+A figure of agreement (.pdf) if \code{doPlot = TRUE} and a data.frame storing four agreement measurements, including Rand Index (RI), Adjusted Mutual Information (AMI), Jaccard Index (JI), and Fowlkes-Mallows (FM).
+}
+\description{
+Compute the Rand Index, Jaccard Index, Fowlkes-Mallows, and Normalized Mutual Information for agreement of two partitions, and generate alluvial diagrams for visualization.
+}
+\examples{
+# There is no example and please refer to vignette.
+}