% 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.

}